sbml-svn — SVN commit notification list for the SBML project.

[sbml-svn] SF.net SVN: sbml:[26322] trunk/specifications

[<luc...@us...>]

Revision: 26322
          http://sourceforge.net/p/sbml/code/26322
Author:   luciansmith
Date:     2022-07-13 17:10:40 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Added Paths:
-----------
    trunk/specifications/README.txt

Removed Paths:
-------------
    trunk/specifications/RelaxNG/
    trunk/specifications/sbml-level-1/
    trunk/specifications/sbml-level-2/
    trunk/specifications/sbml-level-3/

Added: trunk/specifications/README.txt
===================================================================
--- trunk/specifications/README.txt	                        (rev 0)
+++ trunk/specifications/README.txt	2022-07-13 17:10:40 UTC (rev 26322)
@@ -0,0 +1,12 @@
+All of the sources for the SBML specifications have been moved to github in the following repository:
+
+https://github.com/sbmlteam/sbml-specifications
+
+In addition, the 'project' files needed to compile the TeX documents have also been moved to github:
+
+https://github.com/sbmlteam/specifications-tex
+https://github.com/sbmlteam/specifications-bib
+
+Please update any links you may have to point at the new locations.
+
+Previous versions of these files may still be obtained here (by checking out a previous revision of the code), and are also available at github, where the history of the specs was migrated along with the source.

[sbml-svn] SF.net SVN: sbml:[26321] trunk/sbmlvalidator

[<luc...@us...>]

Revision: 26321
          http://sourceforge.net/p/sbml/code/26321
Author:   luciansmith
Date:     2022-07-13 17:06:03 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Modified Paths:
--------------
    trunk/sbmlvalidator/README.txt

Removed Paths:
-------------
    trunk/sbmlvalidator/LICENSE.html
    trunk/sbmlvalidator/LICENSE.txt
    trunk/sbmlvalidator/build.xml
    trunk/sbmlvalidator/validator/
    trunk/sbmlvalidator/validator_servlet/
    trunk/sbmlvalidator/validator_ui/
    trunk/sbmlvalidator/validator_ws/
    trunk/sbmlvalidator/validator_wsClient/

Deleted: trunk/sbmlvalidator/LICENSE.html
===================================================================
--- trunk/sbmlvalidator/LICENSE.html	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/LICENSE.html	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,201 +0,0 @@
-<!-- 
- This file uses only basic HTML formatting because it is also
- included by machine-generated documentation files.  Do not add
- more HTML formatting because it may break the documentation-
- generation system code in ./docs/src/ .
--->
-
-The majority of libSBML is copyrighted as follows:
-
-<ul>
-
-<li> Copyright &copy; 2013-2016 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK<br>
-    3. University of Heidelberg, Heidelberg, Germany<br>
-
-<li> Copyright &copy; 2009-2013 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK<br>
-
-<li> Copyright &copy; 2006-2008 by the California Institute of Technology,
-    Pasadena, CA, USA 
-
-<li> Copyright &copy; 2002-2005 jointly by the following organizations: <br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. Japan Science and Technology Agency, Japan
-</ul>
-
-<p>
-Portions of the source code comprising libSBML were copyrighted and
-contributed by third parties, and placed under the same LGPL 2.1
-license as the rest of libSBML. The following are their copyright
-statements:
-
-<ul>
-
-<li> Copyright &copy; 2004-2008 by European Media Laboratories
-Research gGmbH, Heidelberg, Germany (for the "SBML Layout" code
-and associated examples.)
-
-</ul>
-    
-<p>
-LibSBML is free software; you can redistribute it and/or modify 
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation; either version 2.1 of
-the License, or any later version.
-
-<p>
-This software is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
-MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software
-and documentation provided hereunder is on an "as is" basis, and
-the copyright holders have no obligations to provide maintenance,
-support, updates, enhancements or modifications.  In no event
-shall the copyright holders be liable to any party for direct,
-indirect, special, incidental or consequential damages, including
-lost profits, arising out of the use of this software and its
-documentation, even if the copyright holders have been advised of
-the possibility of such damage.  See the GNU Lesser General Public
-License for more details.
-
-<p>
-You should have received a copy of the GNU Lesser General Public
-License along with this library in the file named "COPYING.txt"
-included with the software distribution.  A copy is also
-available online at the Internet address
-  <a href="http://sbml.org/software/libsbml/COPYING.html">
-    http://sbml.org/software/libsbml/COPYING.html</a> for your
-convenience.  You may also write to obtain a copy from the Free
-Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-MA 02110-1301, USA.
-
-
-<h2>Third-party software incorporated into both the libSBML
-binary and source-code distributions</h2>
-
-LibSBML incorporates an open-source compression library written by
-a third party.  The following is information about the copyright
-and distribution terms of this library:
-
-<ul>
-  <li> <em>MiniZip1.01e</em>, copyright &copy; 1998-2005
-    Gilles Vollant, released under terms compatible with the LGPL.
-    Please see the file src/sbml/compress/00README.txt for more
-    information about MiniZip 1.01e and its license terms.</li>
-
-</ul>
-
-
-<h2>Additional third-party software incorporated only into
-the libSBML source code distribution</h2>
-
-<p>
-Additional software is used to produce the documentation of
-libSBML.  The binary distributions of libSBML do not include this
-software; they are only present in the source code distribution
-and the libSBML documentation archives.
-
-<ul>
-  <li> <em>Argparse 1.2.1</em>, copyright &copy; 2006-2009 Steven J. Bethard
-  (ste...@gm...) and distributed under the Python Software
-  Foundation License version 2.  Code downloaded from
-  <a href="http://code.google.com/p/argparse">http://code.google.com/p/argparse</a>
-  on 2012-02-10.</li>
-
-  <li> <em>Google Code Prettify</em>, distributed under the terms
-    of the Apache License Version 2.0, January 2004.  Code
-    downloaded from <a href="http://code.google.com/p/google-code-prettify/">
-    http://code.google.com/p/google-code-prettify</a> on 2013-10-16.</li>
-
-  <li> <em>PrettyTable</em>, copyright &copy; 2009-2013 Luke Maurits,
-  distributed under the following BSD-derivative license:
-
-<blockquote>
-    Copyright (c) 2009-2013 Luke Maurits (lu...@ma...)
-    All rights reserved.<br>
-    With contributions from:<br>
-    <ul>
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> Chris Clark
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> Christoph Robbert
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> Klein Stephane
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> "maartendb"
-    </ul>
-    Redistribution and use in source and binary forms, with or
-    without modification, are permitted provided that the
-    following conditions are met:
-    <ul>
-    <li> Redistributions of source code must retain the above
-      copyright notice, this list of conditions and the
-      following disclaimer. 
-
-    <li> Redistributions in binary form must reproduce the above
-      copyright notice, this list of conditions and the
-      following disclaimer in the documentation and/or other
-      materials provided with the distribution.
-
-    <li> The name of the author may not be used to endorse or
-      promote products derived from this software without
-      specific prior written permission.
-    </ul>
-    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
-    CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
-    INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-    CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-    NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-    OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-</blockquote>
-
-  <li> <em>ExcludeDoclet</em>, copyright &copy; 2004 by Sun
-Microsystems, Inc., and distributed under the following
-open-source terms:
-
-<blockquote>
-   Copyright 2004 Sun Microsystems, Inc. All Rights Reserved.
-   <p>
-   Redistribution and use in source and binary forms, with or
-   without modification, are permitted provided that the
-   following conditions are met:
-   <ul>
-   <li> Redistribution of source code must retain the above
-   copyright notice, this list of conditions and the following
-   disclaimer.
-
-   <li> Redistribution in binary form must reproduce the above
-   copyright notice, this list of conditions and the following
-   disclaimer in the documentation and/or other materials provided
-   with the distribution. Neither the name of Sun Microsystems,
-   Inc. nor the names of contributors may be used to endorse or
-   promote products derived from this software without specific
-   prior written permission.
-   </ul>
-
-   This software is provided "AS IS," without a warranty of any
-   kind. ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND
-   WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY,
-   FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE
-   HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN") AND ITS
-   LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY
-   LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS
-   SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
-   LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR
-   FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR
-   PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY
-   OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE
-   THIS SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY
-   OF SUCH DAMAGES.<br>
-   <p>
-   You acknowledge that this software is not designed, licensed
-   or intended for use in the design, construction, operation or
-   maintenance of any nuclear facility.
-</blockquote>
-
-</ul>

Deleted: trunk/sbmlvalidator/LICENSE.txt
===================================================================
--- trunk/sbmlvalidator/LICENSE.txt	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/LICENSE.txt	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,167 +0,0 @@
-           Licensing and Distribution Terms for libSBML
-
-The majority of libSBML is copyrighted as follows:
-
-* Copyright (C) 2013-2016 jointly by the following organizations:
-  1. California Institute of Technology, Pasadena, CA, USA
-  2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-  3. University of Heidelberg, Heidelberg, Germany
-
-* Copyright (C) 2009-2013 jointly by the following organizations: 
-  1. California Institute of Technology, Pasadena, CA, USA
-  2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- 
-* Copyright (C) 2006-2008 by the California Institute of Technology,
-    Pasadena, CA, USA 
- 
-* Copyright (C) 2002-2005 jointly by the following organizations: 
-  1. California Institute of Technology, Pasadena, CA, USA
-  2. Japan Science and Technology Agency, Japan
-
-Portions of the source code comprising libSBML were copyrighted
-and contributed by third parties, and placed under the same LGPL
-2.1 license as the rest of libSBML. The following are their
-copyright statements:
-
-* Copyright (C) 2004-2008 by European Media Laboratories Research
-  gGmbH, Heidelberg, Germany.  (For the "SBML Layout" code.)
-
-LibSBML is free software; you can redistribute it and/or modify 
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation; either version 2.1 of
-the License, or any later version.
-
-This software is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
-MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software
-and documentation provided hereunder is on an "as is" basis, and
-the copyright holders have no obligations to provide maintenance,
-support, updates, enhancements or modifications.  In no event
-shall the copyright holders be liable to any party for direct,
-indirect, special, incidental or consequential damages, including
-lost profits, arising out of the use of this software and its
-documentation, even if the copyright holders have been advised of
-the possibility of such damage.  See the GNU Lesser General Public
-License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this library in the file named "COPYING.txt"
-included with the software distribution.  A copy is also
-available online at the Internet address
-http://sbml.org/software/libsbml/COPYING.html for your
-convenience.  You may also write to obtain a copy from the Free
-Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-MA 02110-1301,  USA.
-
-
-     Third-party software incorporated into both the libSBML
-               binary and source-code distributions
-
-LibSBML incorporates an open-source compression library written by
-a third party.  The following is information about the copyright
-and distribution terms of this library:
-
-* MiniZip 1.01e, copyright (C) 1998-2005 Gilles Vollant, released 
-  under terms compatible with the LGPL.  Please see the file
-  src/sbml/compress/00README.txt for more information about
-  MiniZip 1.01e and its license terms.
-
-
-        Additional third-party software incorporated only
-            into the libSBML source code distribution
-
-Additional software is used to produce the documentation of
-libSBML.  The binary distributions of libSBML do not include this
-software; they are only present in the source code distribution
-and the libSBML documentation archives.
-
-* Argparse 1.2.1, copyright (C) 2006-2009 Steven J. Bethard
-  <ste...@gm...> and distributed under the Python Software
-  Foundation License version 2.  Code downloaded from 
-  http://code.google.com/p/argparse/ on 2012-02-10.
-
-* Google Code Prettify, distributed under the terms of the
-  Apache License Version 2.0, January 2004.  Code downloaded from 
-  http://code.google.com/p/google-code-prettify/ on 2013-10-16.
-
-* PrettyTable, copyright (C) 2009-2013 Luke Maurits, distributed
-  under the following BSD-derivative license:
-
-    Copyright (c) 2009-2013 Luke Maurits <lu...@ma...>
-    All rights reserved.
-    With contributions from:
-     * Chris Clark
-     * Christoph Robbert
-     * Klein Stephane
-     * "maartendb"
-    
-    Redistribution and use in source and binary forms, with or
-    without modification, are permitted provided that the
-    following conditions are met:
-
-    * Redistributions of source code must retain the above
-      copyright notice, this list of conditions and the
-      following disclaimer. 
-
-    * Redistributions in binary form must reproduce the above
-      copyright notice, this list of conditions and the
-      following disclaimer in the documentation and/or other
-      materials provided with the distribution.
-
-    * The name of the author may not be used to endorse or
-      promote products derived from this software without
-      specific prior written permission.
-
-    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
-    CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
-    INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-    CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-    NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-    OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-* ExcludeDoclet, copyright (C) 2004 by Sun Microsystems, Inc., and
-  distributed under the following open-source terms:
-
-   Copyright 2004 Sun Microsystems, Inc. All Rights Reserved.
-
-   Redistribution and use in source and binary forms, with or
-   without modification, are permitted provided that the
-   following conditions are met:
-
-    - Redistribution of source code must retain the above
-   copyright notice, this list of conditions and the following
-   disclaimer.
-
-   - Redistribution in binary form must reproduce the above
-   copyright notice, this list of conditions and the following
-   disclaimer in the documentation and/or other materials provided
-   with the distribution. Neither the name of Sun Microsystems,
-   Inc. nor the names of contributors may be used to endorse or
-   promote products derived from this software without specific
-   prior written permission.
-
-   This software is provided "AS IS," without a warranty of any
-   kind. ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND
-   WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY,
-   FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE
-   HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN") AND ITS
-   LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY
-   LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS
-   SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
-   LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR
-   FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR
-   PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY
-   OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE
-   THIS SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY
-   OF SUCH DAMAGES.
-
-   You acknowledge that this software is not designed, licensed
-   or intended for use in the design, construction, operation or
-   maintenance of any nuclear facility.

Modified: trunk/sbmlvalidator/README.txt
===================================================================
--- trunk/sbmlvalidator/README.txt	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/README.txt	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,99 +1,7 @@
+The SBML Validator code has been moved to github in the following repository:
 
-                        Online SBML Validator
+https://github.com/sbmlteam/sbmlvalidator
 
-	    Frank Bergmann, Ben Bornstein, Sarah Keating, 
-                   Akiya Jouraku and Michael Hucka
+Please update any links you may have to point at the new locations.
 
-    Mailing lists and online web forums for discussing SBML are at
-                        http://sbml.org/Forums
-
-        To contact the core developers directly, send email to
-                        sbm...@ca...
-
-   ,---------------------------------------------------------------.
-  | Table of contents                                               |
-  | 1. Introduction                                                 |
-  | 2. Installation                                                 |
-  | 3. Licensing and distribution                                   |
-  | 4. Acknowledgments                                              |
-   `---------------------------------------------------------------'
-
-
-1. Introduction
-======================================================================
-
-This is the source code to the Online SBML Validator running at
-http://sbml.org/Facilities/Validator .  This facility allows users to
-upload SBML files and have them tested for adherence to the syntax and
-other rules defined by the SBML specifications.  The validation is
-actually performed by libSBML (http://sbml.org/Software/libSBML) for
-core SBML and accepted SBML Level 3 packages, and by a RELAX NG
-validation engine for unofficial, draft SBML Level 3 package
-definitions.  The code you see here is the system that permits files
-to be uploaded to the server and processed to produce a report of the
-results.
-
-
-2. Installation
-======================================================================
-
-Information forthcoming ....
-
-
-
-3. LICENSING AND DISTRIBUTION
-======================================================================
-
-Copyright (C) 2011-2016 jointly by the following organizations:
-    1. California Institute of Technology, Pasadena, CA, USA
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
-    3. University of Heidelberg, Heidelberg, Germany
-
-Copyright (C) 2009-2011 jointly by the following organizations:
-    1. California Institute of Technology, Pasadena, CA, USA
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
-
-Copyright (C) 2006-2008 by the California Institute of Technology,
-    Pasadena, CA, USA
-
-Copyright (C) 2002-2005 jointly by the following organizations:
-    1. California Institute of Technology, Pasadena, CA, USA
-    2. Japan Science and Technology Agency, Japan
-
-This library is free software; you can redistribute it and/or modify
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation.  A copy of the license
-agreement is provided in the file named "LICENSE.txt" included with
-this software distribution and also available online as
-http://sbml.org/software/libsbml/license.html
-
-
-4. ACKNOWLEDGMENTS
-======================================================================
-
-This system has undergone many revisions.  It was originally written
-by Ben Borenstein, and later (around 2014-2016) overhauled
-significantly by Frank Bergmann.
-
-This and other projects of the SBML Team have been supported by the
-following organizations: the National Institutes of Health (USA) under
-grants R01 GM070923 and R01 GM077671; the International Joint Research
-Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the
-Japanese Ministry of Agriculture; the Japanese Ministry of Education,
-Culture, Sports, Science and Technology; the BBSRC e-Science
-Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the
-Army Research Office's Institute for Collaborative Biotechnologies
-(USA); the Air Force Office of Scientific Research (USA); the
-California Institute of Technology (USA); the University of
-Hertfordshire (UK); the Molecular Sciences Institute (USA); the
-Systems Biology Institute (Japan); and Keio University (Japan).
-
-
------------------------------------------------
-File author: M. Hucka, F. Bergmann
------------------------------------------------
-
-# The following is for [X]Emacs users.  Please leave in place.
-# Local Variables:
-# fill-column: 70
-# End:
+Previous versions of these files may still be obtained here (by checking out a previous revision of the code), and are also available at github, where the history of the code was migrated along with the source.

Deleted: trunk/sbmlvalidator/build.xml
===================================================================
--- trunk/sbmlvalidator/build.xml	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/build.xml	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<project basedir="." default="default" name="validator">
-    <property environment="env"/>
-    <property name="validator.location" value="validator"/>
-    <property name="validator_ui.location" value="validator_ui"/>
-    <property name="validator_servlet.location" value="validator_servlet"/>
-    <property name="validator_ws.location" value="validator_ws"/>
-    <property name="validator_wsClient.location" value="validator_wsClient"/>
-    <target name="clean">
-        <ant antfile="build.xml" dir="${validator.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_ui.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_servlet.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_ws.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_wsClient.location}" inheritAll="false" target="clean"/>
-    </target>
-    <target depends="clean" name="cleanall"/>
-    <target name="build">
-        <ant antfile="build.xml" dir="${validator.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_ui.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_servlet.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_ws.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_wsClient.location}" inheritAll="false" target="build"/>
-    </target>
-	<target name="default">
-        <ant antfile="build.xml" dir="${validator.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_ui.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_servlet.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_ws.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_wsClient.location}" inheritAll="false" />
-    </target>
-</project>

[sbml-svn] SF.net SVN: sbml:[26320] trunk/SBMLToolbox

[<luc...@us...>]

Revision: 26320
          http://sourceforge.net/p/sbml/code/26320
Author:   luciansmith
Date:     2022-07-13 17:03:56 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Modified Paths:
--------------
    trunk/SBMLToolbox/README.txt

Removed Paths:
-------------
    trunk/SBMLToolbox/AUTHORS.txt
    trunk/SBMLToolbox/COPYING.html
    trunk/SBMLToolbox/COPYING.txt
    trunk/SBMLToolbox/FUNDING.txt
    trunk/SBMLToolbox/LICENSE.html
    trunk/SBMLToolbox/LICENSE.txt
    trunk/SBMLToolbox/NEWS.txt
    trunk/SBMLToolbox/VERSION.html
    trunk/SBMLToolbox/VERSION.txt
    trunk/SBMLToolbox/dev/
    trunk/SBMLToolbox/docs/
    trunk/SBMLToolbox/graphics/
    trunk/SBMLToolbox/src/
    trunk/SBMLToolbox/win32_installer/

Deleted: trunk/SBMLToolbox/AUTHORS.txt
===================================================================
--- trunk/SBMLToolbox/AUTHORS.txt	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/AUTHORS.txt	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,15 +0,0 @@
-	      SBMLToolbox has been primarily developed by
-
-			     Sarah Keating
-
-	    with contributions from (in alphabetical order)
-	Arsen Batagov, Ben Bornstein, Will Bryant, Bill Denney,
-     Andrew Finney, Thomas Grotkj\xE6r, Mike Hucka, Pieter Pareit, 
-                  Kieran Smallbone, Sumant Turlapati,
-		   and others in the SBML community.
-
-	For more information about SBML or SBMLToolbox, contact:
-
-			     The SBML Team
-			  http://www.sbml.org/
-		      mailto:sbm...@ca...

Deleted: trunk/SBMLToolbox/COPYING.html
===================================================================
--- trunk/SBMLToolbox/COPYING.html	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/COPYING.html	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,618 +0,0 @@
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Deleted: trunk/SBMLToolbox/COPYING.txt
===================================================================
--- trunk/SBMLToolbox/COPYING.txt	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/COPYING.txt	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,513 +0,0 @@
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Deleted: trunk/SBMLToolbox/FUNDING.txt
===================================================================
--- trunk/SBMLToolbox/FUNDING.txt	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/FUNDING.txt	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,11 +0,0 @@
-This and other projects of the SBML Team have been supported by the
-following organizations: the National Institutes of Health (USA) under
-grants R01 GM070923 and R01 GM077671; the International Joint Research
-Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese
-Ministry of Agriculture; the Japanese Ministry of Education, Culture,
-Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the
-DARPA IPTO Bio-Computation Program (USA); the Army Research Office's
-Institute for Collaborative Biotechnologies (USA); the Air Force Office of
-Scientific Research (USA); the California Institute of Technology (USA);
-the University of Hertfordshire (UK); the Molecular Sciences Institute
-(USA); the Systems Biology Institute (Japan); and Keio University (Japan).

Deleted: trunk/SBMLToolbox/LICENSE.html
===================================================================
--- trunk/SBMLToolbox/LICENSE.html	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/LICENSE.html	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,54 +0,0 @@
-<!-- 
- This file uses only basic HTML formatting because it is also
- included by machine-generated documentation files.  Do not add
- more HTML formatting because it may break the documentation-
- generation system.
--->
-
-Copyright &copy; 2009-2012 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK<br>
-<p>
-Copyright &copy; 2006-2008 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. University of Hertfordshire, Hatfield, UK<br>
-<p>
-Copyright &copy; 2003-2005 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. Japan Science and Technology Agency, Japan<br>
-    3. University of Hertfordshire, Hatfield, UK<br>
-
-<p>
-SBMLToolbox is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or any later version.
-
-<p>
-This software is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
-MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The
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-Lesser General Public License for more details.
-
-<p>
-You should have received a copy of the GNU Lesser General Public
-License along with this library in the file named "LICENSE.txt"
-included with the software distribution.  A copy is also
-available online at the Internet address
-http://sbml.org/Software/SBMLToolbox/LICENSE.html for your
-convenience.  You may also write to obtain a copy from the Free
-Softwar...
 
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[sbml-svn] SF.net SVN: sbml:[26319] trunk/project

[<luc...@us...>]

Revision: 26319
          http://sourceforge.net/p/sbml/code/26319
Author:   luciansmith
Date:     2022-07-13 17:00:19 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Added Paths:
-----------
    trunk/project/README.txt

Removed Paths:
-------------
    trunk/project/bib/
    trunk/project/sourceforge/
    trunk/project/tex/

Added: trunk/project/README.txt
===================================================================
--- trunk/project/README.txt	                        (rev 0)
+++ trunk/project/README.txt	2022-07-13 17:00:19 UTC (rev 26319)
@@ -0,0 +1,8 @@
+The 'project' files for SBML (which are used to build the various SBML specifications) have been moved to github, in the following two repositories:
+
+https://github.com/sbmlteam/specifications-tex
+https://github.com/sbmlteam/specifications-bib
+
+Please update any links you may have to point at the new locations.
+
+Previous versions of these files may still be obtained here (by checking out a previous revision of the code), and are also available at github, where the history of those directories was migrated along with the source.

[sbml-svn] SF.net SVN: sbml:[26318] trunk/libsbml

[<luc...@us...>]

Revision: 26318
          http://sourceforge.net/p/sbml/code/26318
Author:   luciansmith
Date:     2022-07-13 16:54:48 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and leave a note pointing people to the new source repository.

Modified Paths:
--------------
    trunk/libsbml/README.txt

Removed Paths:
-------------
    trunk/libsbml/AUTHORS.txt
    trunk/libsbml/CMakeLists.txt
    trunk/libsbml/COPYING.html
    trunk/libsbml/COPYING.txt
    trunk/libsbml/FUNDING.txt
    trunk/libsbml/LICENSE.html
    trunk/libsbml/LICENSE.txt
    trunk/libsbml/Makefile.in
    trunk/libsbml/NEWS.txt
    trunk/libsbml/OLD_NEWS.txt
    trunk/libsbml/README-code-from-svn.txt
    trunk/libsbml/VERSION.txt
    trunk/libsbml/VERSION_PACKAGES.ac
    trunk/libsbml/acinclude.m4
    trunk/libsbml/aclocal.m4
    trunk/libsbml/autogen.sh
    trunk/libsbml/cmake_uninstall.cmake.in
    trunk/libsbml/common.cmake
    trunk/libsbml/comp-package.cmake
    trunk/libsbml/config/
    trunk/libsbml/configure
    trunk/libsbml/configure.ac
    trunk/libsbml/dev/
    trunk/libsbml/docs/
    trunk/libsbml/examples/
    trunk/libsbml/fbc-package.cmake
    trunk/libsbml/groups-package.cmake
    trunk/libsbml/l3v2extendedmath-package.cmake
    trunk/libsbml/layout-package.cmake
    trunk/libsbml/libsbml.spec.in
    trunk/libsbml/libtoolize.sh
    trunk/libsbml/macosx/
    trunk/libsbml/multi-package.cmake
    trunk/libsbml/qual-package.cmake
    trunk/libsbml/render-package.cmake
    trunk/libsbml/src/

Deleted: trunk/libsbml/AUTHORS.txt
===================================================================
--- trunk/libsbml/AUTHORS.txt	2021-10-23 00:01:15 UTC (rev 26317)
+++ trunk/libsbml/AUTHORS.txt	2022-07-13 16:54:48 UTC (rev 26318)
@@ -1,16 +0,0 @@
-                 LibSBML 5 was primarily developed by
- 
-            Sarah Keating, Frank Bergmann, Ben Bornstein,
-            Akiya Jouraku, Lucian Smith, and Michael Hucka
-
-           with contributions from (in alphabetical order):
-     Gordon Ball, Bill Denney, Christoph Flamm, Akira Funahashi,
-     Ralph Gauges, Martin Ginkel, Alex Gutteridge, Stefan Hoops,
-    Totte Karlsson, Moriyoshi Koizumi, Ben Kovitz, Rainer Machne,
-          Nicolas Rodriguez, Fengkai Zhang and many others.
-                                     
-         For more information about SBML or libSBML, contact:
-
-                            The SBML Team
-                         http://www.sbml.org/
-                     mailto:sbm...@go...

Deleted: trunk/libsbml/CMakeLists.txt
===================================================================
--- trunk/libsbml/CMakeLists.txt	2021-10-23 00:01:15 UTC (rev 26317)
+++ trunk/libsbml/CMakeLists.txt	2022-07-13 16:54:48 UTC (rev 26318)
@@ -1,1543 +0,0 @@
-###############################################################################
-#
-# Description       : CMake build script for libSBML
-# Original author(s): Frank Bergmann <fbe...@ca...>
-# Organization      : California Institute of Technology
-#
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2013-2017 jointly by the following organizations:
-#     1. California Institute of Technology, Pasadena, CA, USA
-#     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#     3. University of Heidelberg, Heidelberg, Germany
-#
-# Copyright (C) 2009-2013 jointly by the following organizations:
-#     1. California Institute of Technology, Pasadena, CA, USA
-#     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-#     Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-#     1. California Institute of Technology, Pasadena, CA, USA
-#     2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation.  A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-#
-###############################################################################
-
-cmake_minimum_required(VERSION 2.6)
-project(libsbml)
-
-if(POLICY CMP0054)
-    cmake_policy(SET CMP0054 NEW)
-endif()
-
-if(POLICY CMP0058)
-    cmake_policy(SET CMP0058 OLD)
-endif()
-
-
-
-set(LIBSBML_ROOT_SOURCE_DIR "${CMAKE_SOURCE_DIR}" CACHE PATH
-    "Path to the libSBML root source directory")
-set(LIBSBML_ROOT_BINARY_DIR "${CMAKE_BINARY_DIR}" CACHE PATH
-    "Path to the libSBML root build directory")
-
-include (CMakeTestCCompiler)
-include (CheckCSourceCompiles)
-include (CheckCXXSourceCompiles)
-include (CheckStructHasMember)
-include (CheckLibraryExists)
-include (CheckFunctionExists)
-include (CheckCCompilerFlag)
-include (CheckCSourceRuns)
-include (CheckSymbolExists)
-include (CheckTypeSize)
-if (${CMAKE_VERSION} VERSION_GREATER 2.8.4)
-	include(GNUInstallDirs)
-else ()
-	set (CMAKE_INSTALL_DATADIR "share/libsbml/")
-	set (CMAKE_INSTALL_LIBDIR "lib")
-	set (CMAKE_INSTALL_INCLUDEDIR "include")
-	set (CMAKE_INSTALL_BINDIR "bin")
-	set (CMAKE_INSTALL_DATADIR "share")
-	set (CMAKE_INSTALL_FULL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")
-	set (CMAKE_INSTALL_FULL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")
-endif ()
-
-###############################################################################
-#
-# Parse VERSION.txt to determine the package version
-#
-
-set(LIBSBML_VERSION_MAJOR)
-set(LIBSBML_VERSION_MINOR)
-set(LIBSBML_VERSION_PATCH)
-set(LIBSBML_VERSION_RELEASE)
-set(LIBSBML_DOTTED_VERSION)
-
-if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt")
-
-    file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt" VersionString NEWLINE_CONSUME)
-    string(STRIP "${VersionString}" VersionString)
-    set(LIBSBML_DOTTED_VERSION ${VersionString})
-    string(REPLACE "." ";" VersionString "${VersionString}" )
-    string(REPLACE "-" ";" VersionString "${VersionString}" )
-    list(LENGTH VersionString versionLength)
-    list(GET VersionString 0 LIBSBML_VERSION_MAJOR )
-    list(GET VersionString 1 LIBSBML_VERSION_MINOR )
-    list(GET VersionString 2 LIBSBML_VERSION_PATCH )
-
-    if(${versionLength} GREATER 3)
-        list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
-    endif()
-
-endif()
-
-# version number needs to be calculated correctly
-MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_VERSION_MINOR} * 100 + ${LIBSBML_VERSION_PATCH}" )
-set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")
-set(PACKAGE_NAME "libSBML")
-
-set(PACKAGE_CONFIG_DIR "${CMAKE_INSTALL_LIBDIR}/cmake" CACHE PATH
-    "Path into which the cmake config files should be installed")
-
-
-# PACKAGE_VERSION gets overridden by using other packages, so setting
-# the PROJECT_VERSION, which will be used when exporting targets in
-# src/CMakeLists.txt
-set(PROJECT_VERSION ${PACKAGE_VERSION})
-
-if (WITH_DOXYGEN OR WITH_PYTHON)
-  # configure the version for documentation / bindings
-  configure_file(
-      ${CMAKE_CURRENT_SOURCE_DIR}/docs/src/common-text/libsbml-version.html.in
-      ${CMAKE_CURRENT_SOURCE_DIR}/docs/src/common-text/libsbml-version.html
-  )
-endif()
-
-# add make dist and make check target as they are already familiar for
-# everyone using the gnumake build
-add_custom_target(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
-add_custom_target(check COMMAND ${CMAKE_MAKE_PROGRAM} test)
-
-###############################################################################
-#
-# The next lines configure the parameters for packaging the binaries.
-# They can be invoked with "make package" or "nmake package" or by using
-# cpack -G zip|deb|rpm|dmg|nsis
-#
-
-include(InstallRequiredSystemLibraries)
-
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "An API library for reading/writing/manipulating SBML.")
-set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}")
-set(CPACK_PACKAGE_VENDOR "The libSBML Team")
-set(CPACK_PACKAGE_CONTACT "LibSBML Team <lib...@go...>")
-set(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.txt")
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/COPYING.txt")
-set(CPACK_PACKAGE_VERSION_MAJOR "${LIBSBML_VERSION_MAJOR}")
-set(CPACK_PACKAGE_VERSION_MINOR "${LIBSBML_VERSION_MINOR}")
-set(CPACK_PACKAGE_VERSION_PATCH "${LIBSBML_VERSION_PATCH}")
-set(CPACK_RPM_PACKAGE_LICENSE "LGPL")
-set(CPACK_RPM_PACKAGE_GROUP "Libraries/Development")
-set(CPACK_DEBIAN_PACKAGE_SECTION "Libraries")
-
-set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR};/.vs/;/.vscode/;/.svn/;/.libs/;/.deps/;/.bzr/;.*.o$;.*.lo$;.*.la$;${CPACK_SOURCE_IGNORE_FILES};/.DS_Store;/.svnignore;blib;libsbml-dist")
-
-if(UNIX)
-    set(CPACK_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
-    set(CPACK_SET_DESTDIR "ON")
-endif()
-
-if(CMAKE_SIZEOF_VOID_P EQUAL 4)
-    set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "i386")
-    set(CPACK_RPM_PACKAGE_ARCHITECTURE "i386")
-else()
-    set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
-    set(CPACK_RPM_PACKAGE_ARCHITECTURE "x86_64")
-endif()
-
-include(CPack)
-
-
-###############################################################################
-#
-# Here we have the main configuration options for libsbml.
-#
-
-# Build static / shared library
-# option(BUILD_SHARED_LIBS  "Build shared library. (Set to OFF to build static libraries.)" OFF)
-
-# Whether to compile examples
-option(WITH_EXAMPLES "Compile the libSBML example programs."  OFF)
-
-# Which language bindings should be built
-option(WITH_CSHARP   "Generate the C# language interface for libSBML."     OFF)
-option(WITH_JAVA     "Generate the Java language interface for libSBML."   OFF)
-option(WITH_PYTHON   "Generate the Python language interface for libSBML." OFF)
-option(WITH_PERL     "Generate the Perl language interface for libSBML."   OFF)
-option(WITH_PHP      "Generate the PHP language interface for libSBML."    OFF)
-option(WITH_RUBY     "Generate the Ruby language interface for libSBML"    OFF)
-option(WITH_R        "Generate the R language interface for libSBML"       OFF)
-option(WITH_OCTAVE   "Generate the Octave language interface for libSBML." OFF)
-option(WITH_MATLAB   "Generate the MATLAB language interface for libSBML." OFF)
-option(WITH_JAVASCRIPT   "Generate the experimental Node.js language interface for libSBML." OFF)
-
-if (WITH_JAVASCRIPT)
-
-  set(_PF86 "ProgramFiles(x86)")
-  find_program(NODE_GYP_EXECUTABLE
-        NAMES node-gyp node-gyp.cmd
-        PATHS
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-              "$ENV{ProgramFilesProgramFiles}/nodejs/"
-              "$ENV{ProgramW6432}/nodejs/"
-        DOC "The file name of the node-gyp executable."
-        )
-
-  find_program(NODEJS_EXECUTABLE
-        NAMES node nodeexe
-        PATHS
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-              "$ENV{ProgramFiles}/nodejs/"
-              "$ENV{ProgramW6432}/nodejs/"
-        DOC "The file name of the nodejs executable."
-        )
-  # check that we found node-gyp
-  if (NOT NODE_GYP_EXECUTABLE)
-        message(FATAL_ERROR
-"In oder to build the JavaScript language interface, libSBML needs the
-node-gyp executable. Please set the variable named NODE_GYP_EXECUTABLE.")
-  endif()
-
-  # ensure that the swig version is high enough for javascript
-  if (SWIG_VERSION AND NOT SWIG_VERSION VERSION_GREATER 3.0.1)
-        message(FATAL_ERROR
-"SWIG version 3.0.2 or greater is needed in order to build the JavaScript
-language interface for libSBML, but only version ${SWIG_VERSION} was found.")
-  endif()
-
-endif()
-
-# Add an option to compile with all warnings shown
-option(WITH_WALL     "Compile with -Wall, so that the compiler will display all warnings." OFF)
-mark_as_advanced(WITH_WALL)
-
-if(WITH_WALL)
-    if(MSVC OR USING_INTEL)
-        add_definitions(/W4)
-        string(REPLACE "/W3" "/W4" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
-        string(REPLACE "/W3" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-    else()
-        add_definitions(-Wall)
-    endif()
-endif()
-
-# Add an option to instruct libSBML to not include SBMLTypes.h and other files internally.
-option(LIBSBML_USE_STRICT_INCLUDES
-"Compile using 'strict includes' rules: libSBML header files won't
-use SBMLTypes.h, among others." OFF)
-if(LIBSBML_USE_STRICT_INCLUDES)
-  add_definitions(-DLIBSBML_USE_STRICT_INCLUDES)
-endif(LIBSBML_USE_STRICT_INCLUDES)
-mark_as_advanced(LIBSBML_USE_STRICT_INCLUDES)
-
-set(LIBSBML_BUILD_TYPE "native")
-if (CMAKE_SIZEOF_VOID_P EQUAL 4)
-  set(LIBSBML_BUILD_TYPE "32bit")
-else()
-  set(LIBSBML_BUILD_TYPE "64bit")
-endif()
-if (APPLE AND ENABLE_UNIVERSAL)
-  set(LIBSBML_BUILD_TYPE "universal")
-endif()
-
-# When allocation of memory fails or the libSBML C API is unable to open
-# a file, libSBML can exit the current process. By default this behavior
-# is disabled.
-#
-option (EXIT_ON_ERROR "Call exit(-1) in case of allocation or file error." OFF)
-mark_as_advanced(EXIT_ON_ERROR)
-
-# Use the version number in the shared library.
-#
-option (LIBSBML_SHARED_VERSION
-"Include version information into the compiled libSBML shared library." ON)
-mark_as_advanced(LIBSBML_SHARED_VERSION)
-
-# Enable the generation of unit tests. If enabled, all test runners
-# will be created and can be run with "make test" or ctest.
-# This won't work in Visual Studio 2003, so we disable this option there.
-#
-if(NOT ${CMAKE_GENERATOR} MATCHES "Visual Studio 6" AND NOT ${CMAKE_GENERATOR} MATCHES "Visual Studio 7")
-    option(WITH_CHECK
-"Compile the libSBML unit tests. (You can then run the tests with the
-command 'make test' or 'ctest'.)" OFF)
-endif()
-
-# Choose the xml parsing library to be used.
-option(WITH_EXPAT    "Use the Expat XML parser library."     OFF)
-option(WITH_LIBXML   "Use the libxml2 XML parser library."   ON )
-option(WITH_XERCES   "Use the Xerces XML parser library."    OFF)
-
-# Use C++ namespace.
-option(WITH_CPP_NAMESPACE "Use a C++ namespace for libSBML."   OFF)
-
-# Generate documentation.
-option(WITH_DOXYGEN  "Generate documentation for libSBML using Doxygen."  OFF )
-# marks as advanced, so as to hide documentation generation
-mark_as_advanced(WITH_DOXYGEN)
-
-# Re-generate the swig bindings? This really should be on by default
-# otherwise one might have the wrong wrapper code without support for
-# the libsbml packages one wants.
-option(WITH_SWIG     "Regenerate the programming language interface code
-(for Java, Python, etc.) using SWIG."  ON )
-
-# Set build type default.
-set(CMAKE_BUILD_TYPE "Release" CACHE STRING
-  "Choose the type of build to perform. The options are: None (CMAKE_CXX_FLAGS
-or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel.")
-if("${CMAKE_BUILD_TYPE}" STREQUAL "")
-  set(CMAKE_BUILD_TYPE "Release" CACHE STRING
-    "Choose the type of build to perform. The options are: None (CMAKE_CXX_FLAGS
-or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel." FORCE)
-endif()
-
-# Set the default dependency directory.
-set(LIBSBML_DEPENDENCY_DIR ${LIBSBML_ROOT_SOURCE_DIR}/dependencies/ CACHE PATH
-  "Directory containing libraries that libSBML depends upon.
-(Particularly important on Windows.)")
-if("${LIBSBML_DEPENDENCY_DIR}" STREQUAL "")
-  set(LIBSBML_DEPENDENCY_DIR ${LIBSBML_ROOT_SOURCE_DIR}/dependencies/ CACHE PATH
-    "Directory containing libraries that libSBML depends upon.
-(Particularly important on Windows.)" FORCE)
-endif()
-
-if (WITH_PYTHON)
-    # add option to enable Python API2 (with warnings)
-    option(PYTHON_USE_API2_WARNINGS   "Enable the new Python API2 with warnings."    OFF)
-endif (WITH_PYTHON)
-
-###############################################################################
-#
-# If WITH_SWIG is selected, we need to find swig
-#
-set(LIBSBML_USE_CPP_NAMESPACE OFF)
-if(WITH_CPP_NAMESPACE)
-    add_definitions(-DLIBSBML_USE_CPP_NAMESPACE=1)
-    set(LIBSBML_USE_CPP_NAMESPACE ON)
-endif()
-
-if(WITH_SWIG)
-    find_program(SWIG_EXECUTABLE
-        NAMES swig
-        PATHS
-              c:/swigwin-3.0.10
-              c:/swigwin-3.0.9
-              c:/swigwin-3.0.8
-              c:/swigwin-3.0.7
-              c:/swigwin-3.0.6
-              c:/swigwin-3.0.5
-              c:/swigwin-3.0.4
-              c:/swigwin-3.0.3
-              c:/swigwin-3.0.2
-              c:/swigwin-3.0.1
-              c:/swigwin-2.0.12
-              c:/swigwin-2.0.11
-              c:/swigwin-2.0.10
-              c:/swigwin-2.0.9
-              c:/swigwin-2.0.8
-              c:/swigwin-2.0.7
-              c:/swigwin-2.0.6
-              c:/swigwin-2.0.5
-              c:/swigwin-2.0.4
-              c:/swigwin-2.0.3
-              c:/swigwin-2.0.2
-              c:/swigwin-2.0.1
-              c:/swigwin-2.0.0
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-              "C:/Program Files (x86)/Swig"
-              "C:/Program Files/Swig"
-        DOC "The file name of the SWIG executable."
-        )
-    find_package(SWIG)
-    if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
-      message(WARNING
-"You are using SWIG version ${SWIG_VERSION}.  We strongly recommend
-using version 2.0.4 or greater. For libSBML JavaScript support, you
-will need version 3.0.1 at minimum.")
-    endif()
-    set(SWIG_EXTRA_ARGS -DLIBSBML_COMPILED_IN_SRC)
-    add_definitions(-DLIBSBML_COMPILED_IN_SRC)
-    set(SWIG_SWIGDOCDEFINES)
-endif(WITH_SWIG)
-
-
-###############################################################################
-#
-# Locate expat if needed
-#
-
-set(LIBSBML_XML_LIBRARY)
-set(LIBSBML_XML_LIBRARY_INCLUDE)
-set(LIBSBML_XML_LIBRARY_LIBS)
-
-if(WITH_EXPAT)
-  if (NOT LIBEXPAT_LIBRARY)
-    find_library(LIBEXPAT_LIBRARY
-        NAMES libexpat.lib expat
-        PATHS ${LIBSBML_DEPENDENCY_DIR}/lib
-              /usr/lib /usr/local/lib
-              /usr/lib/i386-linux-gnu
-        DOC "The file name of the Expat library."
-                )
-
-  endif()
-
-  if (NOT LIBEXPAT_INCLUDE_DIR)
-    find_path(LIBEXPAT_INCLUDE_DIR
-        NAMES expat.h
-        PATHS ${LIBSBML_DEPENDENCY_DIR}/include
-              /usr/include /usr/local/include
-              ${CMAKE_OSX_SYSROOT}/usr/include
-        DOC "The directory containing the Expat include files."
-              )
-  endif()
-
-    add_definitions( -DUSE_EXPAT )
-    list(APPEND SWIG_EXTRA_ARGS -DUSE_EXPAT)
-
-    set(LIBSBML_XML_LIBRARY "expat")
-    set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBEXPAT_INCLUDE_DIR})
-    set(LIBSBML_XML_LIBRARY_LIBS ${LIBEXPAT_LIBRARY})
-
-    if(NOT EXISTS "${LIBEXPAT_INCLUDE_DIR}/expat.h")
-        message(FATAL_ERROR
-"The include directory specified for Expat appears to be invalid.
-It should contain the file expat.h, but it does not.")
-    else()
-        if (LIBEXPAT_INCLUDE_DIR AND EXISTS "${LIBEXPAT_INCLUDE_DIR}/expat.h")
-            file(STRINGS "${LIBEXPAT_INCLUDE_DIR}/expat.h" expat_version_str
-                 REGEX "^#[\t ]*define[\t ]+XML_(MAJOR|MINOR|MICRO)_VERSION[\t ]+[0-9]+$")
-
-            unset(EXPAT_VERSION_STRING)
-            foreach(VPART MAJOR MINOR MICRO)
-                foreach(VLINE ${expat_version_str})
-                    if(VLINE MATCHES "^#[\t ]*define[\t ]+XML_${VPART}_VERSION[\t ]+([0-9]+)$")
-                        set(EXPAT_VERSION_PART "${CMAKE_MATCH_1}")
-                        if(EXPAT_VERSION_STRING)
-                            set(EXPAT_VERSION_STRING "${EXPAT_VERSION_STRING}.${EXPAT_VERSION_PART}")
-                        else()
-                            set(EXPAT_VERSION_STRING "${EXPAT_VERSION_PART}")
-                        endif()
-                    endif()
-                endforeach()
-            endforeach()
-
-            if (EXPAT_VERSION_STRING VERSION_LESS 1.95.9)
-                     message(FATAL_ERROR
-"Expat version ${EXPAT_VERSION_STRING} is not compatible with libSBML.
-Please use a version newer than 1.95.8 or an alternate XML parser.")
-            endif()
-        endif()
-    endif()
-endif(WITH_EXPAT)
-
-
-###############################################################################
-#
-# Locate Libxml2 if needed
-#
-set(USE_LIBXML OFF)
-if(WITH_LIBXML)
-  if (NOT LIBXML_LIBRARY)
-    find_library(LIBXML_LIBRARY
-        NAMES libxml2.lib xml2
-        PATHS /usr/lib /usr/local/lib
-              ${LIBSBML_DEPENDENCY_DIR}/lib
-        DOC "The file name of the libxml2 library."
-                )
-  endif()
-
-  if (NOT LIBXML_INCLUDE_DIR)
-    find_path(LIBXML_INCLUDE_DIR
-        NAMES libxml/parser.h
-        PATHS ${LIBSBML_DEPENDENCY_DIR}/include
-              /usr/include /usr/local/include
-              /usr/include/libxml2
-              ${CMAKE_OSX_SYSROOT}/usr/include/libxml2
-              /usr/local/include/libxml2
-
-        DOC "The directory containing the libxml2 include files."
-              )
-  endif()
-
-  add_definitions( -DUSE_LIBXML )
-  list(APPEND SWIG_EXTRA_ARGS -DUSE_LIBXML)
-  set(USE_LIBXML ON)
-
-  set(LIBSBML_XML_LIBRARY "libxml2")
-  set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
-  set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
-
-  if(NOT EXISTS "${LIBXML_INCLUDE_DIR}/libxml/parser.h")
-        message(FATAL_ERROR
-"The include directory specified for libxml appears to be invalid.
-It should contain the file libxml/parser.h, but it does not.")
-  endif()
-endif(WITH_LIBXML)
-
-
-###############################################################################
-#
-# Locate xerces
-#
-
-if(WITH_XERCES)
-    add_definitions( -DUSE_XERCES )
-    list(APPEND SWIG_EXTRA_ARGS -DUSE_XERCES)
-
-    find_library(XERCES_LIBRARY
-        NAMES xerces-c_3.lib xerces-c
-        PATHS /usr/lib /usr/local/lib
-              ${LIBSBML_DEPENDENCY_DIR}/lib
-        DOC "The file name of the Xerces library."
-                )
-
-    find_path(XERCES_INCLUDE_DIR
-        NAMES xercesc/parsers/XercesDOMParser.hpp
-        PATHS /usr/include /usr/local/include
-              ${CMAKE_OSX_SYSROOT}/usr/include/xercesc
-              /usr/include/xercesc
-              /usr/local/include/xercesc
-              ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the Xerces include files."
-              )
-
-    if (EXISTS "${XERCES_INCLUDE_DIR}/xercesc/util/XercesVersion.hpp")
-        function(_myXercesC_GET_VERSION  version_hdr)
-            file(STRINGS ${version_hdr} _contents REGEX "^[ \t]*#define XERCES_VERSION_.*")
-            if(_contents)
-                string(REGEX REPLACE ".*#define XERCES_VERSION_MAJOR[ \t]+([0-9]+).*" "\\1" XercesC_MAJOR "${_contents}")
-                string(REGEX REPLACE ".*#define XERCES_VERSION_MINOR[ \t]+([0-9]+).*" "\\1" XercesC_MINOR "${_contents}")
-                string(REGEX REPLACE ".*#define XERCES_VERSION_REVISION[ \t]+([0-9]+).*" "\\1" XercesC_PATCH "${_contents}")
-
-                if(NOT XercesC_MAJOR MATCHES "^[0-9]+$")
-                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_MAJOR!")
-                endif()
-                if(NOT XercesC_MINOR MATCHES "^[0-9]+$")
-                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_MINOR!")
-                endif()
-                if(NOT XercesC_PATCH MATCHES "^[0-9]+$")
-                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_REVISION!")
-                endif()
-
-                set(XercesC_VERSION "${XercesC_MAJOR}.${XercesC_MINOR}.${XercesC_PATCH}" PARENT_SCOPE)
-            else()
-                message(FATAL_ERROR "Include file ${version_hdr} does not exist or does not contain expected version information")
-            endif()
-        endfunction()
-
-        _myXercesC_GET_VERSION("${XERCES_INCLUDE_DIR}/xercesc/util/XercesVersion.hpp")
-        if (XercesC_VERSION VERSION_EQUAL 2.6.0)
-         message(FATAL_ERROR
-"Xerces version ${XercesC_VERSION} contains known bugs
-and is not compatible with libSBML. Please use a newer version of
-Xerces or an alternate XML parser.")
-        endif()
-    endif ()
-
-    set(LIBSBML_XML_LIBRARY "xerces-c")
-    set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
-    set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
-
-    if(NOT EXISTS "${XERCES_INCLUDE_DIR}/xercesc/parsers/XercesDOMParser.hpp")
-        message(FATAL_ERROR
-"The include directory specified for Xerces appears to be invalid.
-It should contain the file xercesc/parsers/XercesDOMParser.hpp, but
-it does not.")
-    endif()
-
-endif(WITH_XERCES)
-
-###############################################################################
-#
-# Locate bz2
-#
-
-set(BZIP_INITIAL_VALUE)
-if (NOT LIBBZ_LIBRARY)
-find_library(LIBBZ_LIBRARY
-    NAMES bzip2.lib bz2 libbz2.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-          NO_DEFAULT_PATH
-          NO_CMAKE_ENVIRONMENT_PATH
-          NO_CMAKE_PATH
-          NO_SYSTEM_ENVIRONMENT_PATH
-          NO_CMAKE_SYSTEM_PATH
-
-          DOC "The file name of the bzip2 library."
-)
-endif()
-if (NOT LIBBZ_LIBRARY)
-find_library(LIBBZ_LIBRARY
-    NAMES bzip2.lib bz2 libbz2.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-    DOC "The file name of the bzip2 library."
-)
-endif()
-
-if(EXISTS ${LIBBZ_LIBRARY})
-    set(BZIP_INITIAL_VALUE ON)
-else()
-    set(BZIP_INITIAL_VALUE OFF)
-endif()
-
-option(WITH_BZIP2    "Enable the use of bzip2 compression."  ${BZIP_INITIAL_VALUE})
-set(USE_BZ2 OFF)
-if(WITH_BZIP2)
-
-  if (NOT LIBBZ_INCLUDE_DIR)
-    find_path(LIBBZ_INCLUDE_DIR
-        NAMES bzlib.h bzip2/bzlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-              NO_DEFAULT_PATH
-        DOC "The directory containing the bzip2 include files."
-        )
-  endif()
-
-  if (NOT LIBBZ_INCLUDE_DIR)
-      find_path(LIBBZ_INCLUDE_DIR
-        NAMES bzlib.h bzip2/bzlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the bzip2 include files."
-              )
-  endif()
-
-    set(USE_BZ2 ON)
-    add_definitions( -DUSE_BZ2 )
-  list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
-
-    # make sure that we have a valid bzip2 library
-    check_library_exists("${LIBBZ_LIBRARY}" "BZ2_bzCompressInit" "" LIBBZ_FOUND_SYMBOL)
-    if(NOT LIBBZ_FOUND_SYMBOL)
-        # this is odd, but on windows this check always fails! must be a
-        # bug in the current cmake version so for now only issue this
-        # warning on linux
-        if(UNIX)
-            message(WARNING
-"The chosen bz2 library does not appear to be valid because it is
-missing some required symbols. Please check that ${LIBBZ_LIBRARY}
-is the bzip2 library. For details about the error, please see
-${LIBSBML_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log")
-        endif()
-    endif()
-    if(NOT EXISTS "${LIBBZ_INCLUDE_DIR}/bzlib.h")
-        message(FATAL_ERROR
-"The include directory specified for the bz2 library does not
-appear to be valid.  It should contain the file bzlib.h, but
-it does not.")
-    endif()
-
-
-endif(WITH_BZIP2)
-
-
-###############################################################################
-#
-# list of additional files to link against.
-#
-
-set(EXTRA_LIBS "" CACHE STRING
-"List of additional libraries to link against.  Separate multiple
-names using semicolons." )
-set(EXTRA_INCLUDE_DIRS "" CACHE STRING
-"List of additional include directories to use during compilation.
-Separate multiple directories using semicolons." )
-
-
-###############################################################################
-#
-# Locate zlib
-#
-
-set(ZLIB_INITIAL_VALUE)
-if (NOT LIBZ_LIBRARY)
-find_library(LIBZ_LIBRARY
-    NAMES zdll.lib z zlib.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-          NO_DEFAULT_PATH
-          NO_CMAKE_ENVIRONMENT_PATH
-          NO_CMAKE_PATH
-          NO_SYSTEM_ENVIRONMENT_PATH
-          NO_CMAKE_SYSTEM_PATH
-          DOC "The file name of the zip compression library."
-    )
-endif()
-if (NOT LIBZ_LIBRARY)
-find_library(LIBZ_LIBRARY
-    NAMES zdll.lib z zlib.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-    DOC "The file name of the zip compression library."
-    )
-endif()
-
-if(EXISTS ${LIBZ_LIBRARY})
-    set(ZLIB_INITIAL_VALUE ON)
-else()
-    set(ZLIB_INITIAL_VALUE OFF)
-endif()
-option(WITH_ZLIB     "Enable the use of zip compression."    ${ZLIB_INITIAL_VALUE} )
-
-set(USE_ZLIB OFF)
-if(WITH_ZLIB)
-
-  if (NOT LIBZ_INCLUDE_DIR)
-    find_path(LIBZ_INCLUDE_DIR
-        NAMES zlib.h zlib/zlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-              NO_DEFAULT_PATH
-        DOC "The directory containing the zlib include files."
-              )
-  endif()
-    if (NOT LIBZ_INCLUDE_DIR)
-        find_path(LIBZ_INCLUDE_DIR
-        NAMES zlib.h zlib/zlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the zlib include files."
-              )
-    endif()
-    set(USE_ZLIB ON)
-    add_definitions( -DUSE_ZLIB )
-  list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB)
-
-    # make sure that we have a valid zip library
-    check_library_exists("${LIBZ_LIBRARY}" "gzopen" "" LIBZ_FOUND_SYMBOL)
-    if(NOT LIBZ_FOUND_SYMBOL)
-        # this is odd, but on windows this check always fails! must be a
-        # bug in the current cmake version so for now only issue this
-        # warning on linux
-        if(UNIX)
-            message(WARNING
-"The chosen zlib library does not appear to be valid because it is
-missing certain required symbols. Please check that ${LIBZ_LIBRARY} is
-the correct zlib library. For details about the error, please see
-${LIBSBML_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log")
-        endif()
-    endif()
-
-    if(NOT EXISTS "${LIBZ_INCLUDE_DIR}/zlib.h")
-        message(FATAL_ERROR
-"The include directory specified for zlib does not appear to be
-valid. It should contain the file zlib.h, but it does not.")
-    endif()
-
-endif(WITH_ZLIB)
-
-
-###############################################################################
-#
-# Find the C# compiler to use and set name for resulting library
-#
-
-if(WITH_CSHARP)
-    FILE(TO_CMAKE_PATH "$ENV{WINDIR}" windir)
-    find_program(CSHARP_COMPILER
-        NAMES gmcs csc mcs
-        PATHS
-            ${windir}/Microsoft.NET/Framework/v2.0.50727/
-            ${windir}/Microsoft.NET/Framework/v3.0/
-            /usr/bin
-            /usr/local/bin
-        DOC "The file name of the C# compiler for the libsbmlcs assembly."
-        )
-    find_program(CSHARP_EXAMPLE_COMPILER
-        NAMES gmcs csc mcs
-        PATHS
-            ${windir}/Microsoft.NET/Framework/v4.0.30319/
-            ${windir}/Microsoft.NET/Framework/v3.5/
-            ${windir}/Microsoft.NET/Framework/v3.0/
-            ${windir}/Microsoft.NET/Framework/v2.0.50727/
-            /usr/bin
-            /usr/local/bin
-        DOC "The file name of the C# compiler to be used for the examples."
-        )
-    if(UNIX)
-    else()
-        if(CMAKE_SIZEOF_VOID_P EQUAL 4)
-            # mark libsbml library as x86
-            set(CSHARP_EXTRA_ARGS -platform:x86 )
-        elseif(CMAKE_SIZEOF_VOID_P EQUAL 8)
-            # mark libsbml library as x64
-            set(CSHARP_EXTRA_ARGS -platform:x64 )
-        endif()
-    endif()
-
-endif(WITH_CSHARP)
-
-
-###############################################################################
-#
-# Enable support for testing ... can be invoked by running ctest
-# or make test
-#
-
-if(WITH_CHECK)
-
-    # we do use tests, that require 2.8.4
-    cmake_minimum_required(VERSION 2.8.4)
-
-    # set test timeout to 3000 as the normal time limit is not sufficient
-    # for the comp tests
-    SET(DART_TESTING_TIMEOUT "3000" CACHE STRING "" FORCE)
-
-    enable_testing()
-
-    find_library(LIBCHECK_LIBRARY
-        NAMES check libcheck
-        PATHS /usr/lib /usr/local/lib ${LIBSBML_DEPENDENCY_DIR}/lib
-        DOC "The file name of the libcheck library."
-    )
-
-    find_path(LIBCHECK_INCLUDE_DIR
-        NAMES check.h
-        PATHS /usr/include /usr/local/include  ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the libcheck include files."
-              )
-
-    if(NOT EXISTS "${LIBCHECK_INCLUDE_DIR}/check.h")
-        message(FATAL_ERROR
-"The include directory specified for the 'check' library appears to be
-invalid. It should contain the file check.h, but it does not.")
-    endif()
-
-    if(${CMAKE_GENERATOR} MATCHES "Visual Studio 6" OR ${CMAKE_GENERATOR} MATCHES "Visual Studio 7")
-        message(WARNING "Libcheck is not compatible with Visual Studio 2003 (or earlier versions).")
-    endif()
-
-  if (UNIX)
-      # setup valgrind
-      set(CMAKE_MEMORYCHECK_COMMAND valgrind)
-      set(CMAKE_MEMORYCHECK_COMMAND_OPTIONS
-         "--error-exitcode=1 --trace-children=yes --leak-check=full --show-reachable=yes --leak-resolution=high --track-origins=yes --error-limit=no ")
-
-      set(MEMCHECK_COMMAND
-         "${CMAKE_MEMORYCHECK_COMMAND} ${CMAKE_MEMORYCHECK_COMMAND_OPTIONS}")
-      separate_arguments(MEMCHECK_COMMAND)
-
-      # check that check compiles/links - needs cmake 3+
-
-      if(${CMAKE_VERSION} VERSION_GREATER 3.0.0)
-        set(CHECK_CHECK_CODE
-        "
-        #include <check.h>
-        
-        START_TEST (sanity_check)
-        {
-            fail_unless(5 == 5, \"this should succeed\");
-            fail_unless(6 == 5, \"this should fail\");
-        }
-        END_TEST
-        
-        int 
-        main(void)
-        {
-            Suite *s1 = suite_create(\"Core\");
-            TCase *tc1_1 = tcase_create(\"Core\");
-            SRunner *sr = srunner_create(s1);
-            int nf;
-        
-            suite_add_tcase(s1, tc1_1);
-            tcase_add_test(tc1_1, sanity_check);
-        
-            srunner_run_all(sr, CK_ENV);
-            nf = srunner_ntests_failed(sr);
-            srunner_free(sr);
-            ;
-            return nf == 0 ? 0 : 1;
-        }
-        " 
-        )
-
-        set(CMAKE_REQUIRED_LIBRARIES_CACHE ${CMAKE_REQUIRED_LIBRARIES})
-        unset(CHECK_CHECK_TEST CACHE)
-        unset(CHECK_CHECK_TEST2 CACHE)
-
-        set(CHECK_CHECK_TEST)
-        set(CMAKE_REQUIRED_LIBRARIES "-lcheck -lm ${EXTRA_LIBS}")
-        CHECK_C_SOURCE_COMPILES("${CHECK_CHECK_CODE}" CHECK_CHECK_TEST)
-
-        if (NOT CHECK_CHECK_TEST)
-            set(CHECK_CHECK_TEST2)
-            set(CMAKE_REQUIRED_LIBRARIES "-lcheck -lm -pthread -lrt -lsubunit ${EXTRA_LIBS}")
-            CHECK_C_SOURCE_COMPILES("${CHECK_CHECK_CODE}" CHECK_CHECK_TEST2)
-            
-            if (CHECK_CHECK_TEST2)
-                set(CHECK_TMP_LIBS "-pthread -lrt -lsubunit ${EXTRA_LIBS}")
-                string(STRIP "${CHECK_TMP_LIBS}" CHECK_TMP_LIBS)
-                set(EXTRA_LIBS "${CHECK_TMP_LIBS}" CACHE STRING
-                "List of additional libraries to link against.  Separate multiple
-                names using semicolons." FORCE)                
-                unset(CHECK_TMP_LIBS)
-                message(STATUS "Check requires the following EXTRA_LIBS : ${EXTRA_LIBS}")
-            else ()
-                message(WARNING
-"Check cannot compile tests, please specify the correct EXTRA_LIBS for your operating system.")            
-            endif (CHECK_CHECK_TEST2)
-            unset(CHECK_CHECK_TEST2 CACHE)
-
-        endif (NOT CHECK_CHECK_TEST)
-
-        unset(CHECK_CHECK_TEST CACHE)
-        set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_FLAGS_CACHE})
-
-      endif(${CMAKE_VERSION} VERSION_GREATER 3.0.0)
-
-  endif(UNIX)
-
-    include(CTest)
-
-endif(WITH_CHECK)
-
-
-###############################################################################
-#
-# Need some variables set up, such as the name for the libSBML
-# library and the Path and file separator characters. The
-# MISC_PREFIX variable will cause libsbml bindings, examples and
-# documentation to be installed in PREFIX/${MISC_PREFIX}.
-#
-
-set( MISC_PREFIX )
-if(UNIX OR CYGWIN)
-    set(PATH_SEP "/")
-    set(FILE_SEP ":")
-    set( MISC_PREFIX "${CMAKE_INSTALL_DATADIR}/libsbml/" )
-    set(LIBSBML_LIBRARY sbml)
-else()
-    set( MISC_PREFIX ".\\" )
-    set(PATH_SEP "\\")
-    set(FILE_SEP ";")
-    if(MINGW)
-        set(LIBSBML_LIBRARY sbml)
-    else()
-        set(LIBSBML_LIBRARY libsbml)
-    endif()
-endif()
-
-# On some Linux  (64bit) systems (64bit) the libraries should be installed into lib64 rather
-# than lib. It will default to 'lib' but can be overwritten.
-
-set(CMAKE_INSTALL_LIBDIR lib CACHE PATH "Full path to the library output directory")
-mark_as_advanced(CMAKE_INSTALL_LIBDIR)
-
-###############################################################################
-#
-# Set up remaining variables, add option for universal binaries
-#
-
-set(USING_INTEL)
-if (WIN32 AND CMAKE_C_COMPILER AND ${CMAKE_C_COMPILER} MATCHES ".*icl.*$")
-  message(STATUS "Detected Intel Compiler")
-  set(USING_INTEL TRUE)
-endif ()
-
-
-set(BUILD_DEFINITIONS)
-if(UNIX)
-    if(APPLE)
-        # on osx starting with xcode 4.3 the system root is in
-        # the app bundle, however cmake (up to 2.8.8) does not seem
-        # to update the path, so lets try it here
-        if (CMAKE_OSX_SYSROOT AND NOT EXISTS ${CMAKE_OSX_SYSROOT})
-          if (EXISTS "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/${CMAKE_OSX_SYSROOT}")
-            set(CMAKE_OSX_SYSROOT "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/${CMAKE_OSX_SYSROOT}" CACHE STRING "The SDK root to be used" FORCE)
-          endif()
-        endif()
-        add_definitions(-DMACOSX)
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DMACOSX")
-
-        # Since we are encountering errors with the use of libc++ on OSX
-        # this option allows to override which stdlib to use
-        if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-          option(CLANG_USE_STDLIB "Use libstdc++ rather than libc++" OFF)
-          if (CLANG_USE_STDLIB)
-            SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++" )
-          endif()
-        endif()
-
-        # On OSX it is common to build universal binaries to support multiple
-        # processor architectures. The default behavior is not to build
-        # multiple architectures, as most users might not need that.
-        option(ENABLE_UNIVERSAL
-          "Create 'universal' binaries on Mac OS X. (Not available on
-other operating systems.)" OFF)
-
-        set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING
-           "A semicolon-separated list of architectures for which libSBML should be built.")
-        if(ENABLE_UNIVERSAL)
-
-            # if universal binaries are requested and none defined so far
-            # overwrite them with all three common architectures. If the user
-            # specified their own list of architectures do not touch!
-            if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
-
-                STRING(REGEX REPLACE "^.*MacOSX([0-9]*\\.[0-9]*)\\.sdk$" "\\1"
-                       OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}")
-
-                if(OSX_SDK_VERSION  VERSION_EQUAL "10.7" OR
-                   OSX_SDK_VERSION  VERSION_GREATER "10.7" OR
-                   OSX_SDK_VERSION  VERSION_EQUAL "10.8" OR
-                   OSX_SDK_VERSION  VERSION_GREATER "10.8")
-
-                   # OSX Lion no longer supports ppc architecture
-                   set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
-                      "A semicolon-separated list of architectures for which libSBML should be built." FORCE)
-
-                elseif(OSX_SDK_VERSION AND OSX_SDK_VERSION  VERSION_LESS "10.7" )
-
-                   set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING
-                       "A semicolon-separated list of architectures for which libSBML should be built." FORCE)
-
-                else()
-
-                   set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
-                       "A semicolon-separated list of architectures for which libSBML should be built." FORCE)
-
-                endif()
-            endif()
-        endif(ENABLE_UNIVERSAL)
-    else(APPLE)
-        add_definitions(-DLINUX)
-
-        if(NOT CYGWIN)
-            # on cygwin all code is position independent so -fPIC is not needed
-            set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing -fPIC")
-            set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing -fPIC")
-        endif()
-
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DLINUX")
-    endif(APPLE)
-
-    if(WITH_CHECK)
-        if(CMAKE_VERSION VERSION_GREATER "3.0.0")
-            # https://cmake.org/cmake/help/v3.0/module/CheckCXXSourceCompiles.html
-            # CMAKE_REQUIRED_FLAGS = string of compile command line flags
-            # CMAKE_REQUIRED_DEFINITIONS = list of macros to define (-DFOO=bar)
-            # CMAKE_REQUIRED_INCLUDES = list of include directories
-            # CMAKE_REQUIRED_LIBRARIES = list of libraries to link
-            
-            # <code>       - source code to try to compile, must define 'main'
-            # <var>        - variable to store whether the source code compiled
-            # <fail-regex> - fail if test output matches this regex
-
-            # set(CMAKE_REQUIRED_LIBRARIES "${EXTRA_LIBS}")
-            # CHECK_CXX_SOURCE_COMPILES(<code> <var> [FAIL_REGEX <fail-regex>])
-
-            # set(CMAKE_REQUIRED_LIBRARIES "-lrt -lpthread -lsubunit")
-            # CHECK_CXX_SOURCE_COMPILES(<code> <var> [FAIL_REGEX <fail-regex>])
-
-            # set(CMAKE_REQUIRED_LIBRARIES "-lrt -lpthread")
-            # CHECK_CXX_SOURCE_COMPILES(<code> <var> [FAIL_REGEX <fail-regex>])
-        endif(CMAKE_VERSION VERSION_GREATER "3.0.0")
-        # plan A now extinct
-        #add_subdirectory(dev/utilities/linux-check-libs)
-        #target_link_libraries(${LIBSBML_LIBRARY} ${LIBSBML_LIBS} ${EXTRA_LIBS})
-    endif(WITH_CHECK)
-
-    
-    # not needing these defines, and they do cause warnings
-    # add_definitions( -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
-    # set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\"")
-
-else(UNIX)
-    # not needing these defines, and they do cause warnings
-    # add_definitions(-DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
-    add_definitions(-DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS)
-    set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS")
-    if(MSVC OR USING_INTEL)
-        add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE)
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -D_CRT_SECURE_NO_WARNINGS")
-        option(WITH_STATIC_RUNTIME "Compile using the static MSVC Runtime." OFF)
-        if(WITH_STATIC_RUNTIME)
-            foreach(flag_var
-                CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
-                CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
-                CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-                CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-
-                if(${flag_var} MATCHES "/MD")
-                    string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
-                endif(${flag_var} MATCHES "/MD")
-
-            endforeach(flag_var)
-        add_definitions( -D_MT)
-        endif(WITH_STATIC_RUNTIME)
-
-        # on VS enable multiprocessor build
-        SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP")
-
-        # Provide an easy way to use Visual Leak Detector (https://vld.codeplex.com)
-    option(LIBSBML_USE_VLD "When running debug builds with MSVC use Visual Leak Detector." OFF)
-    mark_as_advanced(LIBSBML_USE_VLD)
-    if (LIBSBML_USE_VLD)
-          find_path(VLD_INCLUDE_DIR
-            NAMES vld.h
-            PATHS ${LIBSBML_DEPENDENCY_DIR}/include
-            "$ENV{PROGRAMFILES}/Visual Leak Detector/include"
-            "$ENV{ProgramW6432}/Visual Leak Detector/include"
-            DOC "Directory containing VLD files."
-          )
-          if (NOT VLD_INCLUDE_DIR)
-            message(WARNING "VLD is not found on your system, please ensure you installed it correctly.")
-      else()
-        include_directories(${VLD_INCLUDE_DIR})
-      endif()
-
-      add_definitions( -DLIBSBML_USE_VLD)
-
-    endif (LIBSBML_USE_VLD)
-
-    # CMake no longer creates PDB files for static libraries after 2.8.11
-    # so we store debug information in the object files instead
-    if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
-            foreach(flag_var
-                CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
-                CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
-                CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-                CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-
-                if(${flag_var} MATCHES "/Zi")
-            STRING(REPLACE "/Zi"  "/Z7" "${flag_var}" "${${flag_var}}")
-                endif(${flag_var} MATCHES "/Zi")
-
-            endforeach(flag_var)
-        # add /bigobj to allow debug builds to work with swig and packages
-        ADD_DEFINITIONS(/bigobj)
-        SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /bigobj")
-        SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} /bigobj")
-    endif()
-
-        file(GLOB WIN32_BINARIES ${LIBSBML_DEPENDENCY_DIR}/bin/*.dll)
-        INSTALL(FILES ${WIN32_BINARIES} DESTINATION bin)
-        file(GLOB WIN32_DEPENDENCIES ${LIBSBML_DEPENDENCY_DIR}/lib/*.lib)
-        install(FILES ${WIN32_DEPENDENCIES} DESTINATION lib)
-        if(WITH_LIBXML)
-      if (EXTRA_LIBS STREQUAL "")
-        # populate EXTRA_LIBS variable
-              find_library(LIBICONV_LIBRARY
-                NAMES libiconv.lib iconv.lib iconv
-                PATHS /usr/lib /usr/local/lib
-                      ${CMAKE_OSX_SYSROOT}/usr/lib
-                      ${LIBSBML_DEPENDENCY_DIR}/lib
-                DOC "The file name of the libiconv library."
-              )
-
-        set(ADDITIONAL_LIBS)
-        if (EXISTS ${LIBICONV_LIBRARY})
-        set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBICONV_LIBRARY};")
-        endif()
-        if (EXISTS ${LIBZ_LIBRARY})
-        set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBZ_LIBRARY};")
-        endif()
-        set(EXTRA_LIBS "WS2_32.lib;${ADDITIONAL_LIBS}" CACHE STRING "List of additional libraries to link against." FORCE)
-      endif()
-    endif()
-    elseif(CYGWIN)
-        add_definitions(-DCYGWIN)
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DCYGWIN")
-    elseif(MINGW)
-        if(WITH_LIBXML)
-            # this is necessary to build with libxml2 on mingw
-            add_definitions(-DLIBXML_STATIC)
-        endif(WITH_LIBXML)
-    endif(MSVC OR USING_INTEL)
-
-endif(UNIX)
-
-
-###############################################################################
-#
-# Disable in-source build
-#
-
-if("${LIBSBML_ROOT_SOURCE_DIR}" STREQUAL "${LIBSBML_ROOT_BINARY_DIR}" )
-    message(FATAL_ERROR "In-source builds of libSBML are disabled.
-Please create a separate build directory.")
-endif()
-
-
-###############################################################################
-#
-# Add check that only one XML library was selection
-#
-
-set(LIBRARY_COUNT 0)
-if(WITH_EXPAT)
-    math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
-endif()
-if(WITH_LIBXML)
-    math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
-endif()
-if(WITH_XERCES)
-    math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
-endif()
-
-if(LIBRARY_COUNT GREATER 1)
-    message(FATAL_ERROR
-"Only one XML library should be chosen. Please select only one of the
-following options: WITH_LIBXML, WITH_EXPAT or WITH_XERCES.")
-endif()
-
-
-###############################################################################
-#
-# Add check that at least one XML library was selection
-#
-
-if(LIBRARY_COUNT EQUAL 0)
-    message(FATAL_ERROR
-"A XML library must be selected. Please select one of the following
-options: WITH_LIBXML, WITH_EXPAT or WITH_XERCES.")
-endif()
-
-###############################################################################
-#
-# Include options for all libSBML packages
-#
-set(LIBSBML_PACKAGE_INCLUDES)
-set(LIBSBML_PACKAGE_SUMMARY)
-file(GLOB PACKAGE_OPTIONS "*package.cmake")
-foreach(package ${PACKAGE_OPTIONS})
-    include(${package})
-endforeach()
-
-if (LIBSBML_PACKAGE_INCLUDES)
-  list(REMOVE_DUPLICATES LIBSBML_PACKAGE_INCLUDES)
-endif()
-
-###############################################################################
-#
-# Build the actual libSBML library
-#
-
-add_subdirectory(src)
-
-
-###############################################################################
-#
-# Build examples if specified
-#
-
-if(WITH_EXAMPLES)
-
-    # code that builds the examples
-    add_subdirectory(examples)
-
-endif(WITH_EXAMPLES)
-
-
-if(WITH_DOXYGEN)
-    add_subdirectory(docs)
-endif()
-
-
-###############################################################################
-#
-# Install documentation
-#
-
-set(DOCUMENTATION_FILES
-        COPYING.txt
-        FUNDING.txt
-        LICENSE.txt
-        NEWS.txt
-        OLD_NEWS.txt
-        README.txt
-        VERSION.txt
-)
-
-install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
-
-###############################################################################
-#
-# Write libsbml.pc
-#
-
-set (PRIVATE_LIBS "-lstdc++ -lm")
-if (WITH_ZLIB)
-set (PRIVATE_LIBS "${LIBZ_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_BZIP2)
-set (PRIVATE_LIBS "${LIBBZ_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_LIBXML)
-set (PRIVATE_LIBS "${LIBXML_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_EXPAT)
-set (PRIVATE_LIBS "${LIBEXPAT_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_XERCES)
-set (PRIVATE_LIBS "${XERCES_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-
-file(WRITE  "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Name: ${PACKAGE_NAME}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Description: A library for reading/writing/manipulating SBML\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "URL: http://sbml.org/Software/libSBML\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Version: ${PACKAGE_VERSION}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "prefix=${CMAKE_INSTALL_PREFIX}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "libdir=${CMAKE_INSTALL_FULL_LIBDIR}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "includedir=${CMAKE_INSTALL_FULL_INCLUDEDIR}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs: -L\${libdir} -lsbml\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs.private:        ${PRIVATE_LIBS}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Cflags: -I\${includedir}\n")
-if (WITH_XERCES)
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Conflicts: xerces-c = 2.6.0\n")
-endif()
-
-if (WITH_LIBXML)
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Requires.private: libxml-2.0 >= 2.6.22\n")
-endif()
-
-if (UNIX)
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc"
-        DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-endif()
-
-###############################################################################
-#
-# Print Summary
-#
-if (NOT HOSTNAME)
- site_name(HOSTNAME)
-endif()
-
-message(STATUS "
-----------------------------------------------------------------------
-libSBML version ${PACKAGE_VERSION}
-----------------------------------------------------------------------
-
-   More information and the latest version are available online at
-   http://sbml.org/Software/libSBML
-
-   Please report problems using the issue tracker at
-   http://sbml.org/Software/libsbml/issue-tracker
-
-   To contact the developers directly, email lib...@go...
-
-   Configured on host '${HOSTNAME}'
-     host type                       = ${CMAKE_SYSTEM_NAME}
-     host operating system           = ${CMAKE_SYSTEM_NAME} ${CMAKE_SYSTEM_VERSION}
-     host CPU architecture           = ${CMAKE_SYSTEM_PROCESSOR}
-
-   General build flags:
-     CC                              = ${CMAKE_C_COMPILER}
-     CXX                             = ${CMAKE_CXX_COMPILER}
-     CPPFLAGS                        = ${BUILD_DEFINITIONS}
-     CFLAGS                          = ${CMAKE_C_FLAGS}
-     CXXFLAGS                        = ${CMAKE_CXX_FLAGS}
-     LDFLAGS                         = ${CMAKE_EXE_LINKER_FLAGS}
-
-   XML parser library configuration:
-     XML library                     = ${LIBSBML_XML_LIBRARY}
-     CPPFLAGS for XML                = -I${LIBSBML_XML_LIBRARY_INCLUDE}
-     LIBS for XML                    = ${LIBSBML_XML_LIBRARY_LIBS}
-
-   Other libSBML configuration settings:
-     Installation $prefix            = ${CMAKE_INSTALL_PREFIX}")
-
-if(UNIX)
-    if(APPLE)
-        message(STATUS "     Value of $DYLD_LIBRARY_PATH     = $ENV{DYLD_LIBRARY_PATH}")
-    else()
-        message(STATUS "     Value of $LD_LIBRARY_PATH       = $ENV{LD_LIBRARY_PATH}")
-    endif()
-endif()
-
-if(WITH_SWIG)
-    message(STATUS "     Using SWIG                      = ${SWIG_EXECUTABLE} (Version ${SWIG_VERSION})")
-
-    if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
-      message(WARNING "   You are using SWIG version ${SWIG_VERSION}. We strongly recommend at least version 2.0.4.")
-    endif()
-
-endif()
-
-
-if(WITH_CSHARP)
-    message(STATUS "     Using C#                        = ${CSHARP_COMPILER}")
-endif()
-
-if(WITH_JAVA)
-    message(STATUS "     Using Java                      = ${Java_JAVA_EXECUTABLE}")
-endif()
-
-if(WITH_JAVASCRIPT)
-    message(STATUS "     Using Node.js                   = ${NODE_GYP_EXECUTABLE}")
-endif()
-
-if(WITH_PYTHON)
-    message(STATUS "     Using Python                    = ${PYTHON_EXECUTABLE}")
-endif()
-
-if(WITH_PERL)
-    message(STATUS "     Using Perl                      = ${PERL_EXECUTABLE}")
-endif()
-
-if(WITH_RUBY)
-    message(STATUS "     Using Ruby                      = ${RUBY_EXECUTABLE}")
-endif()
-
-if(WITH_OCTAVE)
-    message(STATUS "     Using Octave                    = ${MKOCTFILE_EXECUTABLE}")
-endif()
-
-if(WITH_MATLAB)
-    message(STATUS "     Using Matlab                    = ${MATLAB_ROOT_PATH}")
-endif()
-
-if(WITH_R)
-    message(STATUS "     Using R                         = ${R_INTERPRETER}")
-endif()
-
-if(WITH_PHP)
-    message(STATUS "     Using PHP                       = yes")
-endif()
-
-if(WITH_CHECK)
-    message(STATUS "     Using libcheck                  = ${LIBCHECK_LIBRARY}")
-endif()
-
-if(WITH_CPP_NAMESPACE)
-    message(STATUS "     Using C++ namespace ('libsbml') = yes")
-else()
-    message(STATUS "     Using C++ namespace ('libsbml') = no")
-endif()
-
-if(APPLE)
-    if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
-        message(STATUS "     Building 'universal' binaries   = no (using native arch)")
-    else()
-        list(REMOVE_DUPLICATES CMAKE_OSX_ARCHITECTURES)
-        list(REMOVE_ITEM CMAKE_OSX_ARCHITECTURES "")
-        list(SORT CMAKE_OSX_ARCHITECTURES)
-        list(LENGTH CMAKE_OSX_ARCHITECTURES NUM_ARCHS)
-        if(NUMARCHS EQUAL 1)
-            message(STATUS "     Building 'universal' binaries   = no (using ${CMAKE_OSX_ARCHITECTURES})")
-        else()
-            message(STATUS "     Building 'universal' binaries   = yes (using ${CMAKE_OSX_ARCHITECTURES})")
-        endif()
-    endif()
-endif()
-
-message(STATUS "")
-if(WITH_EXAMPLES)
-  message(STATUS "     Build examples                  = yes")
-else()
-  message(STATUS "     Build examples                  = no")
-endif()
-
-message(STATUS "")
-
-if(PYTHON_USE_API2_WARNINGS)
-  message(STATUS "")
-  message(STATUS "     Using Python API2 warnings      = yes")
-endif(PYTHON_USE_API2_WARNINGS)
-
-if (LIBSBML_PACKAGE_SUMMARY)
-  message(STATUS "")
-  message(STATUS "   Support for SBML Level 3 Packages: ")
-  foreach(summary ${LIBSBML_PACKAGE_SUMMARY})
-    message(STATUS "     ${summary}")
-  endforeach()
-endif(LIBSBML_PACKAGE_SUMMARY)
-
-message(STATUS "
-")
-message(STATUS "Other potentially important settings:")
-if(WITH_ZLIB)
-    message(STATUS "  Compression support is enabled for .zip and .gz files")
-else()
-    message(STATUS "
-Warning: reading/writing compressed SBML in .zip or .gz format in
-this copy of libSBML is not supported or has been disabled.
-If this was not your intention, please check the WITH_ZLIB
-option.")
-endif()
-
-if(WITH_BZIP2)
-    message(STATUS "  Compression support is enabled for .bz2 files")
-else()
-    message(STATUS "
-Warning: reading/writing compressed SBML in .bz2 format in
-this copy of libSBML is not supported or has been disabled.
-If this was not your intention, please check the WITH_BZIP2
-option.")
-endif()
-
-message(STATUS "
-----------------------------------------------------------------------")
-
-
-## Add uninstall target
-## as available from http://www.cmake.org/Wiki/RecipeAddUninstallTarget
-CONFIGURE_FILE(
-  "${CMAKE_CURRENT_SOURCE_DIR}/cmake_uninstall.cmake.in"
-  "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
-  IMMEDIATE @ONLY)
-ADD_CUSTOM_TARGET(uninstall
-  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake")
-
-if (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dev/utilities/sboTree/updateSBO.cmake")
-# add update_sbo target
-ADD_CUSTOM_TARGET(update_sbo
-  "${CMAKE_COMMAND}"
-      -DSRC_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
-      -DPYTHON_EXECUTABLE="${PYTHON_EXECUTABLE}"
-      -P "${CMAKE_CURRENT_SOURCE_DIR}/dev/utilities/sboTree/updateSBO.cmake")
-endif()
-## To compile a test program simply comment out the lines below ...
-#
-#OPTION(WITH_TEST_PROGRAM " COMPILE SMALL TEST PROGRAM " ON)
-#
-#if(WITH_TEST_PROGRAM)
-#
-#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-#
-#add_executable(libsbml_test test.cpp)
-#target_link_libraries(libsbml_test ${LIBSBML_LIBRARY}-static)
-#
-#endif()
-#

Deleted: trunk/libsbml/COPYING.html
===================================================================
--- trunk/libsbml/COPYING.html	2021-10-23 00:01:15 UTC (rev 26317)
+++ trunk/libsbml/COPYING.html	2022-07-13 16:54:48 UTC (rev 26318)
@@ -1,618 +0,0 @@
-<html>
-<body>
-
-<table width="325">
-  <tr>
-    <td width="325">
-<font size="-1">
-<center>
-<h2 align=center>GNU LESSER GENERAL PUBLIC LICENSE</h2>
-<h3 align=center>Version 2.1, February 1999</h3>
-</center>
-
-<p>
-Copyright (C) 1991, 1999 Free Software Foundation, Inc.
-51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-<p>
-Everyone is permitted to copy and distribute verbatim copies
-of this license document, but changing it is not allowed.
-
-<p>
-[This is the first released version of the Lesser GPL.  It also counts
-as the successor of the GNU Library Public License, version 2, hence
-the version number 2.1.]
-
-<p>
-<center>Preamble</center>
-
-<p>
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-Licenses are intended to guarantee your freedom to share and change
-free software--to make sure the software is free for all its users.
-
-<p>
-  This license, the Lesser General Public License, applies to some
-specially designated software packages--typically libraries--of the
-Free Software Foundation and other authors who decide to use it.  You
-can use it too, but we suggest you first think carefully about whether
-this license or the ordinary General Public License is the better
-strategy to use in any particular case, based on the explanations
-below.
-
-<p>
-  When we speak of fre...
 
[truncated message content]

[sbml-svn] SF.net SVN: sbml:[26317] trunk/project/bib/h.bib

[<luc...@us...>]

Revision: 26317
          http://sourceforge.net/p/sbml/code/26317
Author:   luciansmith
Date:     2021-10-23 00:01:15 +0000 (Sat, 23 Oct 2021)
Log Message:
-----------
Change non-ASCII character to double dash.

Modified Paths:
--------------
    trunk/project/bib/h.bib

Modified: trunk/project/bib/h.bib
===================================================================
--- trunk/project/bib/h.bib	2020-05-20 21:38:54 UTC (rev 26316)
+++ trunk/project/bib/h.bib	2021-10-23 00:01:15 UTC (rev 26317)
@@ -75,7 +75,7 @@
 }
 
 @article{hoops:2006,
-  title={COPASI\x97a complex pathway simulator},
+  title={COPASI--a complex pathway simulator},
   author={Hoops, Stefan and Sahle, Sven and Gauges, Ralph and Lee, Christine and Pahle, J{\"u}rgen and Simus, Natalia and Singhal, Mudita and Xu, Liang and Mendes, Pedro and Kummer, Ursula},
   journal={Bioinformatics},
   volume={22},

[sbml-svn] SF.net SVN: sbml:[26316] trunk/specifications/sbml-level-3/version-1/ spatial/specification/examples

[<luc...@us...>]

Revision: 26316
          http://sourceforge.net/p/sbml/code/26316
Author:   luciansmith
Date:     2020-05-20 21:38:54 +0000 (Wed, 20 May 2020)
Log Message:
-----------
Run the example files through the new validator and fix the results:
* Add the 'compartment' of reactions
* Truncate the parametric_1dom.xml parametricObject to only reference actual points (my guess is that the points were truncated earlier for the example, but the references to them were not).
* Fix the domainType ref of a SampledVolume.
* Fix a mathematical reference to a SampledFieldGeometry to instead point directly to the SampledField.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/analytic_3d.xml
    trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/parametric_1dom.xml
    trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_3d.xml
    trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_asnt.xml

Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/analytic_3d.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/analytic_3d.xml	2020-05-08 19:05:04 UTC (rev 26315)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/analytic_3d.xml	2020-05-20 21:38:54 UTC (rev 26316)
@@ -223,7 +223,7 @@
     </listOfRules>
     <listOfReactions>
       <reaction id="flux1" name="flux1" reversible="true" fast="false"
-                spatial:isLocal="true">
+                spatial:isLocal="true" compartment="Nucleus_Cytosol_membrane">
         <listOfReactants>
           <speciesReference species="s1_cyt" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -241,7 +241,7 @@
         </kineticLaw>
       </reaction>
       <reaction id="flux2" name="flux2" reversible="true" fast="false"
-                spatial:isLocal="true">
+                spatial:isLocal="true" compartment="Cytosol_Extracellular_membrane">
         <listOfReactants>
           <speciesReference species="s1_cyt" stoichiometry="1" constant="true"/>
         </listOfReactants>

Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/parametric_1dom.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/parametric_1dom.xml	2020-05-08 19:05:04 UTC (rev 26315)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/parametric_1dom.xml	2020-05-20 21:38:54 UTC (rev 26316)
@@ -160,7 +160,7 @@
           <spatial:listOfParametricObjects>
             <spatial:parametricObject spatial:id="Nucleus_polygon"
                 spatial:polygonType="triangle" spatial:domainType="Nucleus"
-                spatial:pointIndexLength="4092" spatial:compression="uncompressed"
+                spatial:pointIndexLength="1170" spatial:compression="uncompressed"
                 spatial:dataType="uint8">
                    0 1 2 3 1 0 4 1 3 3 5 4 6 7 8 7 0 2 7 6 0 6 9 0 9
 10 0 10 3 0 5 11 12 5 3 11 3 10 11 11 13 12 14 15 16 15 6 8 15 14 6 14
@@ -222,177 +222,7 @@
 197 216 199 218 219 198 218 199 219 220 199 220 200 199 220 221 200
 221 201 200 221 222 201 222 202 201 222 223 202 223 203 202 223 224
 203 224 204 203 224 225 204 225 205 204 225 226 205 226 206 205 226
-227 206 227 207 206 227 228 207 228 208 207 228 229 208 229 209 208
-229 230 209 230 210 209 230 231 210 231 211 210 231 232 211 232 212
-211 232 233 212 233 213 212 233 234 213 234 214 213 234 235 214 235
-215 214 235 236 215 236 216 215 236 217 216 237 217 236 219 238 239
-218 238 219 239 240 219 240 220 219 240 241 220 241 221 220 241 242
-221 242 222 221 242 243 222 243 223 222 243 244 223 244 224 223 244
-245 224 245 225 224 245 246 225 246 226 225 246 247 226 247 227 226
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-379 680 378 379 683 680 683 679 680 378 680 368 374 681 380 380 682
-381 681 682 380 381 683 382 682 683 381 382 683 379 
+227 206 227 207 206 227   0 207   0 208 207  
             </spatial:parametricObject>
           </spatial:listOfParametricObjects>
         </spatial:parametricGeometry>

Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_3d.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_3d.xml	2020-05-08 19:05:04 UTC (rev 26315)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_3d.xml	2020-05-20 21:38:54 UTC (rev 26316)
@@ -217,7 +217,7 @@
       </assignmentRule>
     </listOfRules>
     <listOfReactions>
-      <reaction id="flux1" name="flux1" reversible="true" fast="false" spatial:isLocal="true">
+      <reaction id="flux1" name="flux1" reversible="true" fast="false" spatial:isLocal="true" compartment="Nucleus_Cytosol_membrane">
         <listOfReactants>
           <speciesReference species="s1_cyt" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -234,7 +234,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="flux2" name="flux2" reversible="true" fast="false" spatial:isLocal="true">
+      <reaction id="flux2" name="flux2" reversible="true" fast="false" spatial:isLocal="true" compartment="Cytosol_Extracellular_membrane">
         <listOfReactants>
           <speciesReference species="s1_cyt" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -305,7 +305,7 @@
             <spatial:sampledVolume spatial:id="Extracellular2"
                  spatial:domainType="Extracellular" spatial:minValue="0"
                  spatial:maxValue="64"/>
-            <spatial:sampledVolume spatial:id="Cytosol2" spatial:domainType="Cytosol2"
+            <spatial:sampledVolume spatial:id="Cytosol1" spatial:domainType="Cytosol"
                  spatial:minValue="64" spatial:maxValue="192"/>
             <spatial:sampledVolume spatial:id="Nucleus2" spatial:domainType="Nucleus"
                  spatial:minValue="192" spatial:maxValue="256"/>

Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_asnt.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_asnt.xml	2020-05-08 19:05:04 UTC (rev 26315)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/examples/sampledfield_asnt.xml	2020-05-20 21:38:54 UTC (rev 26316)
@@ -222,7 +222,7 @@
             <plus/>
             <apply>
               <divide/>
-              <ci> img </ci>
+              <ci> imgvals </ci>
               <cn type="integer"> 2 </cn>
             </apply>
             <cn type="integer"> 3 </cn>
@@ -238,7 +238,7 @@
       </assignmentRule>
     </listOfRules>
     <listOfReactions>
-      <reaction id="flux1" name="flux1" reversible="true" fast="false" spatial:isLocal="true">
+      <reaction id="flux1" name="flux1" reversible="true" fast="false" spatial:isLocal="true" compartment="Nucleus_Cytosol_membrane">
         <listOfReactants>
           <speciesReference species="s1_cyt" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -255,7 +255,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="flux2" name="flux2" reversible="true" fast="false" spatial:isLocal="true">
+      <reaction id="flux2" name="flux2" reversible="true" fast="false" spatial:isLocal="true" compartment="Cytosol_Extracellular_membrane">
         <listOfReactants>
           <speciesReference species="s1_cyt" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -325,7 +325,7 @@
           <spatial:listOfSampledVolumes>
             <spatial:sampledVolume spatial:id="Extracellular2" spatial:domainType="Extracellular" 
                  spatial:minValue="0" spatial:maxValue="64"/>
-            <spatial:sampledVolume spatial:id="Cytosol2" spatial:domainType="Cytosol2" 
+            <spatial:sampledVolume spatial:id="Cytosol2" spatial:domainType="Cytosol" 
                  spatial:minValue="64" spatial:maxValue="192"/>
             <spatial:sampledVolume spatial:id="Nucleus2" spatial:domainType="Nucleus" 
                  spatial:minValue="192" spatial:maxValue="256"/>

[sbml-svn] SF.net SVN: sbml:[26315] branches/libsbml-experimental/src/sbml/packages/ spatial/common/CompressionUtil.h

[<luc...@us...>]

Revision: 26315
          http://sourceforge.net/p/sbml/code/26315
Author:   luciansmith
Date:     2020-05-08 19:05:04 +0000 (Fri, 08 May 2020)
Log Message:
-----------
Revert for Sarah's move to git.  Whoops!

Modified Paths:
--------------
    branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h

Modified: branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h	2020-05-08 19:02:05 UTC (rev 26314)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h	2020-05-08 19:05:04 UTC (rev 26315)
@@ -41,7 +41,6 @@
 
 #include <vector>
 #include <iostream>
-#include <cstdlib> //for malloc
 
 LIBSBML_CPP_NAMESPACE_BEGIN
 
@@ -89,7 +88,7 @@
 
   if (length > 0)
   {
-    type* data = (type*)std::malloc(sizeof(type) * length);
+    type* data = (type*)malloc(sizeof(type) * length);
     for (size_t i = 0; i < length; ++i)
     {
       data[i] = valuesVector.at(i);

[sbml-svn] SF.net SVN: sbml:[26314] branches/libsbml-experimental/src/sbml/packages/ spatial/common/CompressionUtil.h

[<luc...@us...>]

Revision: 26314
          http://sourceforge.net/p/sbml/code/26314
Author:   luciansmith
Date:     2020-05-08 19:02:05 +0000 (Fri, 08 May 2020)
Log Message:
-----------
Fix from Taraz Buck, to enable compilation on their machine.

Modified Paths:
--------------
    branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h

Modified: branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h	2020-05-06 15:41:53 UTC (rev 26313)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/common/CompressionUtil.h	2020-05-08 19:02:05 UTC (rev 26314)
@@ -41,6 +41,7 @@
 
 #include <vector>
 #include <iostream>
+#include <cstdlib> //for malloc
 
 LIBSBML_CPP_NAMESPACE_BEGIN
 
@@ -88,7 +89,7 @@
 
   if (length > 0)
   {
-    type* data = (type*)malloc(sizeof(type) * length);
+    type* data = (type*)std::malloc(sizeof(type) * length);
     for (size_t i = 0; i < length; ++i)
     {
       data[i] = valuesVector.at(i);

[sbml-svn] SF.net SVN: sbml:[26313] trunk/libsbml/dev/misc-files

[<mh...@us...>]

Revision: 26313
          http://sourceforge.net/p/sbml/code/26313
Author:   mhucka
Date:     2020-05-06 15:41:53 +0000 (Wed, 06 May 2020)
Log Message:
-----------
Add new logo artwork

Added Paths:
-----------
    trunk/libsbml/dev/misc-files/new-logo-2020/
    trunk/libsbml/dev/misc-files/new-logo-2020/README.md
    trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo-and-name.svg
    trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo.svg

Added: trunk/libsbml/dev/misc-files/new-logo-2020/README.md
===================================================================
--- trunk/libsbml/dev/misc-files/new-logo-2020/README.md	                        (rev 0)
+++ trunk/libsbml/dev/misc-files/new-logo-2020/README.md	2020-05-06 15:41:53 UTC (rev 26313)
@@ -0,0 +1,4 @@
+libSBML logo 2020
+=================
+
+Mike Hucka created this logo in early 2020.  The artwork was created using [Boxy SVG](https://boxy-svg.com) on a macOS computer.  It incorporates the "SB" logo created by Hiroshige Fukurama for the ERATO Kitano Symbiotic Systems Project.  The "SB" logo is a trademarked design ([registration number 3233845 in the US Patent and Trademark Office](http://tmsearch.uspto.gov/bin/showfield?f=doc&state=4802:xey3hy.5.30)).

Added: trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo-and-name.svg
===================================================================
(Binary files differ)

Index: trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo-and-name.svg
===================================================================
--- trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo-and-name.svg	2020-05-06 07:58:00 UTC (rev 26312)
+++ trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo-and-name.svg	2020-05-06 15:41:53 UTC (rev 26313)

Property changes on: trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo-and-name.svg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/svg+xml
\ No newline at end of property
Added: trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo.svg
===================================================================
(Binary files differ)

Index: trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo.svg
===================================================================
--- trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo.svg	2020-05-06 07:58:00 UTC (rev 26312)
+++ trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo.svg	2020-05-06 15:41:53 UTC (rev 26313)

Property changes on: trunk/libsbml/dev/misc-files/new-logo-2020/libsbml-logo.svg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/svg+xml
\ No newline at end of property

[sbml-svn] SF.net SVN: sbml:[26312] trunk/specifications/sbml-level-3/version-1/fbc/ spec

[<bg...@us...>]

Revision: 26312
          http://sourceforge.net/p/sbml/code/26312
Author:   bgoli
Date:     2020-05-06 07:58:00 +0000 (Wed, 06 May 2020)
Log Message:
-----------
updated FBC proposal text

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/fbc/spec/images/fbc_uml_src.ai
    trunk/specifications/sbml-level-3/version-1/fbc/spec/images/fbc_uml_v3.pdf
    trunk/specifications/sbml-level-3/version-1/fbc/spec/images/fbc_v3_uml_keyvalue.pdf
    trunk/specifications/sbml-level-3/version-1/fbc/spec/main.pdf
    trunk/specifications/sbml-level-3/version-1/fbc/spec/main.synctex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/syntax_user_constraints.tex

Modified: trunk/specifications/sbml-level-3/version-1/fbc/spec/images/fbc_uml_src.ai
===================================================================
--- trunk/specifications/sbml-level-3/version-1/fbc/spec/images/fbc_uml_src.ai	2020-05-05 21:55:48 UTC (rev 26311)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/images/fbc_uml_src.ai	2020-05-06 07:58:00 UTC (rev 26312)
@@ -1,12 +1,12 @@
 %PDF-1.5
 %\xE2\xE3\xCF\xD3
 1 0 obj
-<</Metadata 2 0 R/OCProperties<</D<</ON[8 0 R 170 0 R 364 0 R 571 0 R 797 0 R 1019 0 R 1440 0 R 1860 0 R 2266 0 R 2672 0 R 3078 0 R 3484 0 R 3892 0 R 4312 0 R 4732 0 R 5152 0 R 5580 0 R]/Order 5581 0 R/RBGroups[]>>/OCGs[8 0 R 170 0 R 364 0 R 571 0 R 797 0 R 1019 0 R 1440 0 R 1860 0 R 2266 0 R 2672 0 R 3078 0 R 3484 0 R 3892 0 R 4312 0 R 4732 0 R 5152 0 R 5580 0 R]>>/Pages 3 0 R/Type/Catalog>>
+<</Metadata 2 0 R/OCProperties<</D<</ON[23 0 R]/Order 24 0 R/RBGroups[]>>/OCGs[23 0 R]>>/Pages 3 0 R/Type/Catalog>>
 endobj
 2 0 obj
-<</Length 25901/Subtype/XML/Type/Metadata>>stream
+<</Length 26389/Subtype/XML/Type/Metadata>>stream
 <?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"?>
-<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Adobe XMP Core 5.6-c145 79.163499, 2018/08/13-16:40:22        ">
+<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Adobe XMP Core 6.0-c002 79.164360, 2020/02/13-01:07:22        ">
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
       <rdf:Description rdf:about=""
             xmlns:xmp="http://ns.adobe.com/xap/1.0/"
@@ -19,18 +19,19 @@
             xmlns:xmpMM="http://ns.adobe.com/xap/1.0/mm/"
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[truncated message content]

[sbml-svn] SF.net SVN: sbml:[26311] branches/libsbml-experimental/src/sbml/packages/ distrib/extension/DistribASTPlugin.cpp

[<luc...@us...>]

Revision: 26311
          http://sourceforge.net/p/sbml/code/26311
Author:   luciansmith
Date:     2020-05-05 21:55:48 +0000 (Tue, 05 May 2020)
Log Message:
-----------
Cauchy and LaPlace distributions now also allow one-child-only forms.

Modified Paths:
--------------
    branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribASTPlugin.cpp

Modified: branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribASTPlugin.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribASTPlugin.cpp	2020-04-18 04:13:58 UTC (rev 26310)
+++ branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribASTPlugin.cpp	2020-05-05 21:55:48 UTC (rev 26311)
@@ -54,7 +54,7 @@
 void
 DistribASTPlugin::populateNodeTypes()
 {
-  vector<unsigned int> one, two, onethree, twofour;
+  vector<unsigned int> one, two, onethree, twofour, onetwofour;
   one.push_back(1);
   two.push_back(2);
   onethree.push_back(1);
@@ -61,6 +61,9 @@
   onethree.push_back(3);
   twofour.push_back(2);
   twofour.push_back(4);
+  onetwofour.push_back(1);
+  onetwofour.push_back(2);
+  onetwofour.push_back(4);
 
   ASTNodeValues_t node;
   node.type = AST_DISTRIB_FUNCTION_NORMAL;
@@ -104,7 +107,7 @@
   node.csymbolURL = "http://www.sbml.org/sbml/symbols/distrib/cauchy";
   node.isFunction = true;
   node.allowedChildrenType = ALLOWED_CHILDREN_EXACTLY;
-  node.numAllowedChildren = twofour;
+  node.numAllowedChildren = onetwofour;
 
   mPkgASTNodeValues.push_back(node);
 
@@ -140,7 +143,7 @@
   node.csymbolURL = "http://www.sbml.org/sbml/symbols/distrib/laplace";
   node.isFunction = true;
   node.allowedChildrenType = ALLOWED_CHILDREN_EXACTLY;
-  node.numAllowedChildren = twofour;
+  node.numAllowedChildren = onetwofour;
 
   mPkgASTNodeValues.push_back(node);
 

[sbml-svn] SF.net SVN: sbml:[26310] trunk/specifications/sbml-level-3/version-1/multi /spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf

[<zha...@us...>]

Revision: 26310
          http://sourceforge.net/p/sbml/code/26310
Author:   zhangfen
Date:     2020-04-18 04:13:58 +0000 (Sat, 18 Apr 2020)
Log Message:
-----------
multi spec 1.1.2, add description about red text color, which indicates changes between Multi Version 1 Release 2 and Release 1 at the suggestion from JIB editor Falk Schreiber

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf

Added: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf
===================================================================
(Binary files differ)

Index: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf	2020-04-13 03:23:49 UTC (rev 26309)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf	2020-04-18 04:13:58 UTC (rev 26310)

Property changes on: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Apr17.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property

[sbml-svn] SF.net SVN: sbml:[26309] trunk/specifications/sbml-level-3/version-1/ distrib/jib-submission-2020/sbml-level-3-distrib-package-proposal.pdf

[<luc...@us...>]

Revision: 26309
          http://sourceforge.net/p/sbml/code/26309
Author:   luciansmith
Date:     2020-04-13 03:23:49 +0000 (Mon, 13 Apr 2020)
Log Message:
-----------
Remove 'draft' from background of title page.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-level-3-distrib-package-proposal.pdf

Modified: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-level-3-distrib-package-proposal.pdf
===================================================================
(Binary files differ)

[sbml-svn] SF.net SVN: sbml:[26308] trunk/specifications/sbml-level-3/version-1/ distrib

[<luc...@us...>]

Revision: 26308
          http://sourceforge.net/p/sbml/code/26308
Author:   luciansmith
Date:     2020-04-13 03:23:27 +0000 (Mon, 13 Apr 2020)
Log Message:
-----------
Remove 'draft' from background of title page.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.pdf
    trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex

Modified: trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.pdf
===================================================================
(Binary files differ)

Modified: trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex	2020-04-02 23:50:50 UTC (rev 26307)
+++ trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex	2020-04-13 03:23:27 UTC (rev 26308)
@@ -1,4 +1,4 @@
-\documentclass[draftspec]{sbmlpkgspec}
+\documentclass[spec]{sbmlpkgspec}
 \usepackage{tabularx}
 \usepackage{tabu}
 \usepackage{longtable}

[sbml-svn] SF.net SVN: sbml:[26307] trunk/specifications/sbml-level-3/version-1/ distrib/jib-submission-2020/orcids.txt

[<luc...@us...>]

Revision: 26307
          http://sourceforge.net/p/sbml/code/26307
Author:   luciansmith
Date:     2020-04-02 23:50:50 +0000 (Thu, 02 Apr 2020)
Log Message:
-----------
Add file with missing orcids in it.

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/orcids.txt

Added: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/orcids.txt
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/orcids.txt	                        (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/orcids.txt	2020-04-02 23:50:50 UTC (rev 26307)
@@ -0,0 +1,9 @@
+A list of orcids that are not present in your system:
+
+Stuart Moodie: 0000-0001-6191-5595
+Colin Gillespie: 0000-0003-1787-0275
+Sarah Keating: 0000-0002-3356-3542
+Chris Myers: 0000-0002-8762-8444
+Maciek Swat: (unknown)
+Darren Wilkinson: 0000-0003-0736-802X
+Michael Hucka: 0000-0001-9105-5960

[sbml-svn] SF.net SVN: sbml:[26306] trunk/specifications/sbml-level-3/version-1/ distrib/jib-submission-2020

[<luc...@us...>]

Revision: 26306
          http://sourceforge.net/p/sbml/code/26306
Author:   luciansmith
Date:     2020-04-02 20:33:23 +0000 (Thu, 02 Apr 2020)
Log Message:
-----------
Adjust author/institution list.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.pdf
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex

Modified: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.pdf
===================================================================
(Binary files differ)

Modified: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex	2020-04-02 20:21:20 UTC (rev 26305)
+++ trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex	2020-04-02 20:33:23 UTC (rev 26306)
@@ -41,27 +41,26 @@
 \jibauthor{%
   Lucian P. Smith\iref{uw},
   Stuart L. Moodie\iref{eight},
-  Frank T. Bergmann\iref{caltech},
+  Frank T. Bergmann\iref{heidelberg},
   Colin Gillespie\iref{newcastle}
-  Michael Hucka\iref{heidelberg},
   Sarah M. Keating\iref{ucl},
   Matthias K{\"o}nig\iref{humboldt}
   Chris J. Myers\iref{utah},
   Maciej J. Swat\iref{sheffield},
   Darren J. Wilkinson\iref{newcastle},
+  Michael Hucka\iref{caltech},
 }
 
 %\addjibinstitution{imbio}{IMBio, Ralf Hofest\"adt, Bielefeld University, Faculty of Technology, Bioinformatics Department, D-33501 Bielefeld, Germany, \url{http://www.imbio.de}}
 \addjibinstitution{uw}{University of Washington, US}
 \addjibinstitution{eight}{Eight Pillars Ltd,  UK}
-\addjibinstitution{caltech}{California Institute of Technology, US}
 \addjibinstitution{heidelberg}{University of Heidelberg, DE}
+\addjibinstitution{newcastle}{Newcastle University, UK}
+\addjibinstitution{ucl}{University College London, UK}
 \addjibinstitution{humboldt}{Humboldt University Berlin, DE}
-\addjibinstitution{newcastle}{Newcastle University, UK}
 \addjibinstitution{utah}{University of Utah, US}
-\addjibinstitution{ucl}{University College London, UK}
-\addjibinstitution{vbi}{Virginia Bioinformatics Institute, US}
 \addjibinstitution{sheffield}{QSP Simcyp, Sheffield, UK}
+\addjibinstitution{caltech}{California Institute of Technology, US}
 
 
 

[sbml-svn] SF.net SVN: sbml:[26305] trunk/specifications/sbml-level-3/version-1/ distrib

[<luc...@us...>]

Revision: 26305
          http://sourceforge.net/p/sbml/code/26305
Author:   luciansmith
Date:     2020-04-02 20:21:20 +0000 (Thu, 02 Apr 2020)
Log Message:
-----------
New abstract for JIB; new release note in main text.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.pdf
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex
    trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-level-3-distrib-package-proposal.pdf
    trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.pdf
    trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex

Modified: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.pdf
===================================================================
(Binary files differ)

Modified: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex	2020-04-02 20:16:20 UTC (rev 26304)
+++ trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-distrib-jib-cover-page.tex	2020-04-02 20:21:20 UTC (rev 26305)
@@ -72,7 +72,7 @@
 %\begin{adjustwidth}{}{1cm} %LS NOTE:  'adjustwidth' not recognized in my setup.
 
 \renewcommand{\baselinestretch}{1.0}
-\abstract{Biological models often contain elements that are stochastic in nature and are based on data with uncertainty. The \emph{SBML Level 3 Core} specification does not include an explicit mechanism to include stochastic elements in the mathematics of the model, nor does it provide a way to describe the uncertainty behind its constructs, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactical constructs. The SBML \emph{Distributions} package for SBML Level 3 adds the necessary features to allow the encoding of models with stochastic elements, by allowing new math constructs to draw values from predefined distributions. It also allows the modeler to encode the uncertainty of observations such as the standard deviation or the range of elements in the model with mathematical meaning.}
+\abstract{Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The \emph{SBML Level~3 Core} specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactic constructs. The SBML \emph{Distributions} package for SBML Level~3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.}
 
 %\end{adjustwidth} % please do not change %LS NOTE:  'adjustwidth' not recognized in my setup.
 

Modified: trunk/specifications/sbml-level-3/version-1/distrib/jib-submission-2020/sbml-level-3-distrib-package-proposal.pdf
===================================================================
(Binary files differ)

Modified: trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.pdf
===================================================================
(Binary files differ)

Modified: trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex	2020-04-02 20:16:20 UTC (rev 26304)
+++ trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex	2020-04-02 20:21:20 UTC (rev 26305)
@@ -152,6 +152,8 @@
 0.25 (Draft) & July 2019 & Lucian Smith & The \token{id} of a \UncertParameter no longer has mathematical meaning in any other context.\\
 \midrule
 0.26 (Release Candidate) & March 2020 & Lucian Smith & Add validation rules, and other corrections for release candidate.\\
+\midrule
+1.0 (Release) & April 2020 & Lucian Smith & Add qual example and adjust wording based on feedback from SBML Editors.\\
 \bottomrule
 \end{edtable}
 \end{table}

[sbml-svn] SF.net SVN: sbml:[26304] trunk/specifications/sbml-level-3/version-1/ distrib

[<luc...@us...>]

Revision: 26304
          http://sourceforge.net/p/sbml/code/26304
Author:   luciansmith
Date:     2020-04-02 20:16:20 +0000 (Thu, 02 Apr 2020)
Log Message:
-----------
Updates based on SBML Editors' suggestions.  Final version, to submit to JIB.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/distrib/apdx-validation.tex
    trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.pdf
    trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex

Modified: trunk/specifications/sbml-level-3/version-1/distrib/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/apdx-validation.tex	2020-03-31 16:48:07 UTC (rev 26303)
+++ trunk/specifications/sbml-level-3/version-1/distrib/apdx-validation.tex	2020-04-02 20:16:20 UTC (rev 26304)
@@ -312,8 +312,16 @@
 on an \UncertSpan object. (Reference: SBML Level~3 Specification for
 Distributions, Version~1, \sec{uncertainty-class}.)}
 
+\validRule{distrib-20450}{An \Uncertainty object may have only one or zero \UncertParameter children of each of the following types: \val{distribution},
+\val{coeffientOfVariation}, \val{kurtosis},
+\val{mean}, \val{median}, \val{mode}, \val{sampleSize}, \val{skewness},
+\val{standardDeviation}, \val{stan\-dard\-Er\-ror}, or \val{variance}.
+(Reference: SBML Level~3 Specification for Distributions, Version~1, \sec{uncertainty-class}.)}
 
+\validRule{distrib-20451}{An \Uncertainty object may have only one or zero \UncertSpan children of each of the following types: \val{confidence\-Interval}, \val{credible\-Interval}, \val{in\-ter\-quar\-tile\-Range} or \val{range}.
+(Reference: SBML Level~3 Specification for Distributions, Version~1, \sec{uncertainty-class}.)}
 
+
 \subsubsection*{Rules for \class{UncertSpan} object}
 
 \validRule{distrib-20501}{An \UncertSpan object may have the optional

Modified: trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.pdf
===================================================================
(Binary files differ)

Modified: trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex	2020-03-31 16:48:07 UTC (rev 26303)
+++ trunk/specifications/sbml-level-3/version-1/distrib/sbml-level-3-distrib-package-proposal.tex	2020-04-02 20:16:20 UTC (rev 26304)
@@ -51,15 +51,15 @@
 
 
 \packageTitle{The Distributions Package\\for SBML Level 3}
-\packageVersion{Version \changed{0.26} (Release Candidate)}
-\packageVersionDate{\changed{March 26, 2020}}
-%\packageGeneralURL{http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Distributions_and_Ranges}
-%\packageThisVersionURL{}
+\packageVersion{Version 1, Release 1}
+\packageVersionDate{April 2, 2020}
+\packageGeneralURL{http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/distrib}
+\packageThisVersionURL{https://co.mbine.org/specifications/sbml.level-3.version-1.distrib.version-1.release-1}
 
 \author{%
   \begin{tabular}{c>{\hspace{20pt}}c}
   \multicolumn{2}{c}{\Large\bf{Authors}}\\
-\\ Lucian P Smith           &Stuart L Moodie
+\\ Lucian P Smith           & Stuart L Moodie
 \\ University of Washington & Eight Pillars Ltd
 \\ Seattle, WA, USA         & Edinburgh, UK
 \\
@@ -88,10 +88,10 @@
 \end{tabular}
 }
 
-\frontNotice{Disclaimer: This is a working draft of the SBML Level 3
-  ``distrib'' package specification. It is not a normative document.  Please
-  send comments and other feedback to the mailing list:
-  \mailto{sbm...@li....}}
+%\frontNotice{Disclaimer: This is a working draft of the SBML Level 3
+%  ``distrib'' package specification. It is not a normative document.  Please
+%  send comments and other feedback to the mailing list:
+%  \mailto{sbm...@li....}}
 
 \maketitlepage
 \maketableofcontents
@@ -193,7 +193,7 @@
 
 \subsection{This document}
 
-This draft specification describes the consensus view of workshop participants and subscribers to the sbml-distrib mailing list. Although it was written by the listed authors, it does not solely reflect their views nor is it their proposal alone. Rather, it is their understanding of the consensus view of what the \distrib package should do and how it should do it. The contributors listed have made significant contributions to the development and writing of this specification and are credited accordingly, but a more comprehensive attribution is provided in the acknowledgements (\sec{sec:acknowledgements}).
+This draft specification describes the consensus view of workshop participants and subscribers to the sbml-distrib mailing list. Although it was written by the listed authors, it does not solely reflect their views nor is it their proposal alone. Rather, it is their understanding of the consensus view of what the \distrib package should do and how it should do it. The contributors listed have made significant contributions to the development and writing of this specification and are credited accordingly, but a more comprehensive attribution is provided in the acknowledgments (\sec{sec:acknowledgments}).
 
 %\subsection{Conventions used in this document}
 
@@ -897,6 +897,8 @@
 
 The \Uncertainty class is a collection of zero or more statistical measures related to the uncertainty of the parent SBML element.  It may only contain one of each type of measurement, which means that each of its \UncertParameter children must have a unique \token{type} attribute for every value but \val{externalParameter}.  Each \UncertParameter child with a \token{type} of \val{externalParameter} must, in turn, have a unique \token{definitionURL} value.  If a given SBML element has multiple measures of the same \token{type} (for example, as measured from different sources or different experiments), it should be given multiple \Uncertainty children.  Each \Uncertainty child must be a unique set of statistical measures.
 
+These statistical measures do not numerically affect simulation of the model.  They are, in essence, a controlled annotation format specifically designed for this sort of information.  Tools may use this information as they wish, just as they can with other annotation information.
+
 Note that for elements that change in value over time, the described uncertainty applies only to the element's initial state, and not to how it changes in time.  For typical simulations, this means the element's initial assignment.
 
 The child \UncertParameter children are named according to their class, so any \UncertSpan child will have the element name \token{uncertSpan}, and any \UncertParameter base class child will have the element name \token{uncertParameter}.
@@ -1284,7 +1286,7 @@
 \end{example}
 
 
-It is also possible to create even more complex structures with the \UncertParameter scheme.  In this example, we define a categorical distribution based on data from three patients.  The parent \UncertParameter is defined to be the 'categorical' distribution, with three 'category' children, each with two child 'value' and 'probability' parameters.  Collectively, they define a distribution where a value of 1.01 has a probability of 50\%, a value of 2.24 has a probability of 25\%, and a value of 1.72 has a probability of 25\%.  (The \token{definitionURL} examples here were made up for the purposes of this example, to be readable.  In an actual SBML document, they would point to external ontologies.)
+It is also possible to create even more complex structures with the \UncertParameter scheme.  In this example, we define a categorical distribution based on data from three patients.  The parent \UncertParameter is defined to be the 'categorical' distribution, with three 'category' children, each with two child 'value' and 'probability' parameters.  Collectively, they define a distribution where a value of 1.01 has a probability of 50\%, a value of 2.24 has a probability of 25\%, and a value of 1.72 has a probability of 25\%.  (The \token{definitionURL} examples here were made up for the purposes of this example, to be readable.  In an actual SBML document, they would point to existing external ontologies.)
 
 \clearpage
 
@@ -1460,6 +1462,56 @@
 Another change between SBML Level~3 Version~1 and Version~2 is that in Version~2, core elements and core \Math may refer to package \token{ids} with mathematical meaning.  However, \distrib \UncertParameter elements do not have mathematical meaning, and may not be used in this fashion. Instead, the \token{var} attribute should be used to connect the element to a core \Parameter, instead of using the \token{value} attribute.  This approach has the advantage of working both in Version~1 and Version~2 of SBML Core.
 
 
+\subsection{Other SBML Level~3 Packages}
+This package may be used seamlessly with other SBML Level~3 packages that have \Math elements, and/or that have elements with mathematical meaning.  It would be possible, for example, to use a \distribshort \token{csymbol} in the \Math of a 'Qualitative Models' \token{<functionTerm>}.  In this example, the \token{functionTerm} returns true when a quantity 'A' is greater than or equal to a value drawn from a uniform distribution:
+
+\begin{example}
+<qual:transition qual:id="tr_B">
+  [...]
+  <qual:listOfFunctionTerms>
+    <qual:functionTerm qual:resultLevel="1">
+      <math xmlns="http://www.w3.org/1998/Math/MathML"> 
+        <!-- A >= uniform(0,2)-->
+        <apply>
+          <geq/>
+          <ci>A</ci>
+          <apply>
+            <csymbol definitionURL="http://www.sbml.org/sbml/symbols/distrib/uniform"
+                     encoding="text"> uniform </csymbol>
+            <cn type="integer"> 0 </cn>
+            <cn type="integer"> 2 </cn>
+          </apply>
+        </apply>
+      </math>
+    </qual:functionTerm>
+    <qual:defaultTerm qual:resultLevel="0"/>
+  </qual:listOfFunctionTerms>
+</qual:transition>
+\end{example}
+
+A Qualitative Species could also be given a child \Uncertainty.  Here, the value of A is described as coming from a poisson distribution:
+
+\begin{example}
+<qual:qualitativeSpecies qual:compartment="cytosol" qual:constant="false" 
+                         qual:id="A" qual:maxLevel="6">
+  <distrib:listOfUncertainties>
+    <distrib:uncertainty>
+      <distrib:uncertParameter distrib:type="distribution">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <csymbol definitionURL="http://www.sbml.org/sbml/symbols/distrib/poisson"
+                     encoding="text"> poisson </csymbol>
+            <cn type="integer"> 0 </cn>
+          </apply>
+        </math>
+      </distrib:uncertParameter>
+    </distrib:uncertainty>
+  </distrib:listOfUncertainties>
+</qual:qualitativeSpecies>
+\end{example}
+
+These constructs can be used in identical ways in other SBML Level~3 packages.
+
 \section{Use-cases and examples}
 
 The following examples are more fleshed out than the ones in the main text, and/or illustrate features of this package that were not previously illustrated.
@@ -1523,8 +1575,8 @@
 \input{apdx-validation.tex}
 
 
-\section{Acknowledgements}
-\label{sec:acknowledgements}
+\section{Acknowledgments}
+\label{sec:acknowledgments}
 
 Much of the initial concrete work leading to this proposal document
 was carried out at the Statistical Models Workshop in Hinxton in 2011,

[sbml-svn] SF.net SVN: sbml:[26303] trunk/specifications/sbml-level-3/version-1/multi

[<zha...@us...>]

Revision: 26303
          http://sourceforge.net/p/sbml/code/26303
Author:   zhangfen
Date:     2020-03-31 16:48:07 +0000 (Tue, 31 Mar 2020)
Log Message:
-----------
cover letter (PDF and latex) to submit multi to JIB 

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/
    trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/jib.cls
    trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.pdf
    trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.tex

Added: trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/jib.cls
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/jib.cls	                        (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/jib.cls	2020-03-31 16:48:07 UTC (rev 26303)
@@ -0,0 +1,276 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{jib}[2016/11/11 v3.0 by Stephan Weise and Bjorn Sommer]
+\DeclareOption*{%
+   \PassOptionsToClass{\CurrentOption}{article}}
+\ProcessOptions
+%  article.cls Version: 2004/02/16 v1.4f
+%  jib.cls Version: 2016/11/11 v3.0f for de Gruyter
+\LoadClass[12pt]{article}
+% calc -> Tools Package
+% textcomp -> base Package
+% url -> ltxmisc Package
+\RequirePackage{calc}[1998/07/07 v4.1b Infix arithmetic (KKT,FJ)]
+\RequirePackage{url}[2004/03/15 ver 3.1 Verb mode for urls, etc.]
+\RequirePackage{listings}[2004/09/07 1.3 Carsten Heinz]
+\RequirePackage{caption}[2004/07/16 v3.0c Customising captions (AS)]
+\RequirePackage{textcomp}[2004/02/22 v1.99f Standard LaTeX package]
+\RequirePackage{helvet}[2004/02/22 v1.99f Standard LaTeX package]
+% graphicx -> graphics Package
+% epsfig -> graphics Package
+\RequirePackage{graphicx}[1999/02/16 v1.0f  Enhanced LaTeX Graphics (DPC,SPQR)]
+\RequirePackage{epsfig}[1999/02/16 v1.7a (e)psfig emulation (SPQR)]
+% vmargin Package
+\RequirePackage{vmargin}[2004/07/15 V2.5 set document margins (VK)]
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% In Case of using latex compiler (Standard)
+%\RequirePackage[dvipdfm]{hyperref}[2003/11/30 v6.74m Hypertext links for LaTeX]
+
+% Set default font to Helvetica (Arial)
+\usepackage{helvet}
+\renewcommand{\familydefault}{\sfdefault}
+
+% In Case of using pdflatex compiler
+\RequirePackage{hyperref}[2003/11/30 v6.74m Hypertext links for LaTeX]
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Required for tabulator support for section titles
+\usepackage{titlesec}
+
+
+
+%\usepackage[scaled]{helvet}
+
+\hypersetup{
+  naturalnames=true,
+  hypertexnames=false,
+  pageanchor=false,
+  plainpages=false,
+  breaklinks=true,
+  colorlinks=true,
+  linkcolor=black,
+  citecolor=black,
+  urlcolor=black,
+  filecolor=black,
+  bookmarks=true,
+  bookmarksopen=true,
+}
+
+\RequirePackage{eso-pic}
+
+\pagenumbering{gobble}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Titelseitendefinition
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\newenvironment{jibtitlepage}{%
+  \sffamily% 
+  \newcounter{institution}
+  \renewcommand{\theinstitution}{\arabic{institution}}
+  \newcommand{\addjibinstitution}{%
+    \@ifstar{\@addjibinstitution}
+            {\@addjibinstitutionwithreference}}
+  \newcommand{\@addjibinstitution}[1]{
+    \begin{center}{\small ##1}\end{center}}
+  \newcommand{\@addjibinstitutionwithreference}[2]{%
+    \begin{center}%
+    \refstepcounter{institution}\label{##1}%
+    \textsuperscript{\scriptsize{\theinstitution}}{\small ##2}%
+    \end{center}}
+    
+  \newcommand{\jibtitle}[1]{\begin{center}\large\bfseries ##1\end{center}}
+  \newcommand{\iref}[2][]{\textsuperscript{\scriptsize{\ref{##2}##1}}}
+  \newcommand{\jibauthor}[1]{\begin{center}\small\bfseries ##1\end{center}}
+  
+  \newcommand{\jibfootnotemark}{}
+  \newcommand{\jibfurtherfootnotes}{}
+  \renewcommand{\@makefnmark}{\textsuperscript{\scriptsize{\jibfootnotemark\jibfurtherfootnotes}}}%
+  \renewcommand\@makefntext[1]{%
+    \parindent 1em%
+    \noindent
+    \hb@xt@1.8em{\hss\textsuperscript{\scriptsize{\jibfootnotemark}}}##1}
+  \newcommand{\jibauthorfootnote}[3][]{%
+    \renewcommand{\jibfurtherfootnotes}{##1}%
+    \renewcommand{\jibfootnotemark}{##2}%
+    \footnote{##3}}
+}
+{\setcounter{footnote}{0}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Definition des Satzspiegels und Seitenlayouts
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\setpapersize{A4}
+%\setlength{\paperwidth}{210mm}
+%\setlength{\paperheight}{297mm}
+\setmarginsrb{2.5cm}%{1in}%Rand links
+             {2.5cm}%{12.5mm}%Rand oben
+             {2.5cm}%{1in}%Rand rechts
+             {1.25cm}%{12.5mm}%Rand unten
+             {0cm}%Kopfhoehe
+             {0cm}%Kopfabstand
+             {1.25cm}%{2cm}%Fusshoehe
+             {1.25cm}%{2.25cm}%Fussabstand
+             
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{1.5ex plus.2ex minus.2ex}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	URL-Definitionen und Anpassungen
+%%  Infos: Package url
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\url@emailstyle{%
+ \@ifundefined{selectfont}{\def\UrlFont{\sf}}{\def\UrlFont{\sffamily}}}
+\DeclareUrlCommand\email{\urlstyle{email}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Header/Footer-Definition
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\jibvolume#1{\gdef\@jibvolume{#1}}\jibvolume{00}
+\def\jibissue#1{\gdef\@jibissue{#1}}\jibissue{00}
+\def\jibpages#1{\gdef\@jibpages{#1}}\jibpages{0000}
+\def\jibyear#1{\def\@jibyear{#1}}\jibyear{0000}
+
+\def\jibfooter{\footnotesize\sffamily doi:10.2390/biecoll-jib-\@jibyear-\@jibpages \hfil \thepage}
+
+\def\ps@jibheadings{%
+%     \renewcommand{\@oddfoot}{\jibfooter}%
+% 	\renewcommand{\@evenfoot}{\jibfooter}%
+%     \renewcommand{\@evenhead}{\leftmark\hfil\rightmark}%
+%     \renewcommand{\@oddhead}{\leftmark\hfil\rightmark}%
+    }
+
+\newcommand{\makeHeaderFooter}[1]{
+\markboth{\footnotesize\sffamily Journal of Integrative Bioinformatics,
+\@jibvolume(\@jibissue):\@jibpages, \@jibyear}{\href{http://journal.imbio.de/}{\footnotesize\sffamily http://journal.imbio.de/}}}
+\makeHeaderFooter{}
+\pagestyle{jibheadings}
+
+% Copyright
+% \AddToShipoutPictureFG{%
+%    \put(635,60){%
+%       \rotatebox{90}{\scriptsize{
+%         \begin{minipage}[t]{200mm}
+%             \textcolor[rgb]{0.67,0.67,0.67}{Copyright \@jibyear~The Author(s). Published by Journal of Integrative Bioinformatics. \\
+%           This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/).}
+%         \end{minipage}
+%       }}%
+%    }%
+% }
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Abstract ohne Indent
+%%  - nutzt intern die Quotation-Umgebung zum Erzeugen des Abstracts
+%%    (im notitlepage und onecolumn Modus)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% \renewcommand{\abstractname}{Summary}
+% \renewenvironment{quotation}
+%                {\list{}{\listparindent 0em%
+%                         \itemindent    \listparindent
+%                         \rightmargin   \leftmargin
+%                         \parsep        \z@ \@plus\p@}%
+%                 \item\relax}
+%                {\endlist}
+
+\newcounter{abstract}
+\setcounter{abstract}{-1}
+\renewcommand\abstract{
+
+%\setlength{\rightskip}{1cm}
+
+% The \@startsection{⟨name ⟩}{⟨level ⟩}{ ⟨indent ⟩}{⟨beforeskip ⟩}
+% {⟨afterskip⟩}{⟨style⟩}*[⟨altheading⟩ ]{⟨heading⟩} command is the mother of all
+% the user level sectioning commands. The part after the *, including the * is optional.
+\@startsection {abstract}{0}	{\z@}
+								{1ex}                                    
+                                {0.8ex}%
+                                {\normalfont\sffamily\large\bfseries}*{Abstract}}
+                 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Font-Anpassung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+% \renewcommand\section{			\def\@seccntformat##1{\csname
+% the##1\endcsname\hspace{1.02cm \@minus.2ex}} \@startsection {section}{1}{\z@}%
+% 									{1ex}
+%                                    	{0.8ex}%
+%                                     {\normalfont\sffamily\large\bfseries}}
+% \renewcommand\subsection{		\def\@seccntformat##1{\csname the##1\endcsname\hspace{0.71cm \@minus.2ex}} 
+% 								\@startsection{subsection}{2}{\z@}%
+% 									 {-3.25ex\@plus -1ex \@minus -.2ex}%
+%                                      {1.5ex \@plus .2ex}%
+%                                      {\normalfont\sffamily\normalsize\bfseries}}
+% \renewcommand\subsubsection{	\def\@seccntformat##1{\csname the##1\endcsname\hspace{0.35cm \@minus.2ex}} 
+% 								\@startsection{subsubsection}{3}{\z@}%
+% 									{-3.25ex\@plus -1ex \@minus -.2ex}%
+%                                    	{1.5ex \@plus .2ex}%
+%                                     {\normalfont\sffamily\normalsize}}
+% \renewcommand\paragraph{		\def\@seccntformat##1{\csname the##1\endcsname\hspace{1.0cm \@minus.2ex}} 
+% 								\@startsection {paragraph}{4}{\z@}%
+% 									{3.25ex \@plus1ex \@minus.2ex}%
+%                                    	{-1em}%
+%                                     {\normalfont\sffamily\normalsize\bfseries}}
+% \renewcommand\subparagraph{ 	\def\@seccntformat##1{\csname the##1\endcsname\hspace{1.0cm \@minus.2ex}} 
+% 								\@startsection {subparagraph}{5}{\z@}%
+% 									{3.25ex \@plus1ex \@minus .2ex}%
+%                                    	{-1em}%
+%                                     {\normalfont\sffamily\normalsize\bfseries}} 
+
+ 
+% \renewcommand\section{\@startsection{section}{1}{\z@}%
+% 										{-3.5ex \@plus -1ex \@minus -.2ex}%
+% 										{2.3ex \@plus.2ex}%
+% 										{\normalfont\sffamily\large\bfseries}}
+
+
+
+% \renewcommand\section{\@startsection{section}										% name
+% 										{1}		 									% level
+% 										{\z@}										% indent
+% 										{-3.5ex \@plus -1ex \@minus -.2ex}			% beforeskip
+% 										{2.3ex \@plus.2ex}							% afterskip
+% 										{\normalfont\sffamily\large\bfseries}}		% font type
+% \renewcommand\subsection{\@startsection{subsection}{2}{\z@}
+% 										{-3.25ex\@plus -1ex \@minus -.2ex}
+% 										{1.5ex \@plus .2ex}
+% 										{\normalfont\sffamily\normalsize\bfseries}}
+% \renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}
+% 										{-3.25ex\@plus -1ex \@minus -.2ex}
+% 										{1.5ex \@plus .2ex}
+% 										{\normalfont\sffamily\normalsize}}
+% \renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}
+% 										{3.25ex \@plus1ex \@minus.2ex}
+% 										{-1em}
+% 										{\normalfont\sffamily\normalsize\bfseries}}
+% \renewcommand\subparagraph{\@startsection{subparagraph}{5}{\parindent}
+% 										{3.25ex \@plus1ex \@minus .2ex}
+% 										{-1em}
+% 										{\normalfont\sffamily\normalsize\bfseries}}
+
+\titleformat{\section}{\normalfont\large\bfseries}{\makebox[40pt][l]{\thesection}}{0pt}{} 
+\titleformat{\subsection}{\normalfont\large\bfseries}{\makebox[40pt][l]{\thesubsection}}{0pt}{}
+\titleformat{\subsubsection}{\normalfont\large\mdseries}{\makebox[40pt][l]{\thesubsubsection}}{0pt}{}
+
+\linespread{2}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Caption Anpassung fuer Bild- und Tabellenunterschriften
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\captionsetup{font={footnotesize,bf},%
+              margin=0.7cm,%
+              parskip=5pt,%
+              aboveskip=0pt,%
+              belowskip=0pt}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%	Sonderzeichenanpassung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% \texorpdfstring{...}, weil z.B. \textreg eventuell in section, subsection etc. genutzt wird
+%% und hyperref bzw. in bookmarks Probleme mit Sonderzeichen auftreten
+%% werden die originalen Befehle, wie \textregistered etc., verwendet, treten keine Probleme auf
+\newcommand{\textreg}{\texorpdfstring{\textsuperscript{\textregistered}}{\textregistered}}
+\newcommand{\textcright}{\texorpdfstring{\textsuperscript{\textcopyright}}{\textcopyright}}

Added: trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.pdf
===================================================================
(Binary files differ)

Index: trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.pdf
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.pdf	2020-03-31 13:43:27 UTC (rev 26302)
+++ trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.pdf	2020-03-31 16:48:07 UTC (rev 26303)

Property changes on: trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.tex	                        (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/multi/jib-submission-2020/sbml-multi-jib-cover-page-03312020.tex	2020-03-31 16:48:07 UTC (rev 26303)
@@ -0,0 +1,116 @@
+\documentclass{jib}
+\newlength{\platz}
+\setlength{\platz}{15pt}
+\RequirePackage{listings}
+
+\usepackage{changepage} %test, TODO remove
+
+\lstset{%
+  basicstyle=\ttfamily,
+  fontadjust,
+  flexiblecolumns=true,
+  frame=L,
+  xleftmargin=15pt,
+  framesep=5pt,
+  emphstyle=\rmfamily\itshape}
+
+\usepackage{pdfpages}  
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% JIB Header/Footer
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\jibvolume{XX} % insert volume
+%\jibissue{X}   % insert issue
+%\jibpages{XXX} % insert article ID
+%\jibyear{XXXX} % insert year
+%\makeHeaderFooter{} % leave as is
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{document}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Title Page
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{jibtitlepage}
+
+\jibtitle{SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 2}
+
+
+%We did not provide author(s) nor author footnote(s), please complete as applicable.
+% Please make sure to use unique footnote characters for each author
+
+\jibauthor{ 
+  Fengkai Zhang\iref{niaid},
+  Lucian P. Smith\iref{uw},
+  Michael L. Blinov\iref{uconn},
+  James Faeder\iref{upitt},
+  William S. Hlavacek\iref{lanl},
+  Jose Juan Tapia\iref{upitt},
+  Sarah M. Keating\iref{ebi},
+  Nicolas Rodriguez\iref{babraham},
+  Andreas Dr{\"a}ger\iref{tuebingen},
+  Leonard A. Harris\iref{vusm},
+  Andrew Finney\iref{aul},
+  Bin Hu\iref{lanl},
+  Michael Hucka\iref{caltech},
+  Martin Meier-Schellersheim\iref{niaid}
+}
+
+
+\addjibinstitution{niaid}{NIAID/NIH, US}
+\addjibinstitution{uw}{University of Washington, US}
+\addjibinstitution{uconn}{UConn Health, US}
+\addjibinstitution{upitt}{University of Pittsburgh, US}
+\addjibinstitution{lanl}{Los Alamos National Laboratory, US}
+\addjibinstitution{ebi}{European Bioinformatics Institute, GB}
+\addjibinstitution{babraham}{Babraham Institute, GB}
+\addjibinstitution{tuebingen}{University of T{\"u}bingen, DE}
+\addjibinstitution{vusm}{Vanderbilt University School of Medicine, US}
+\addjibinstitution{aul}{Anasys UK Ltd, GB}
+\addjibinstitution{caltech}{California Institute of Technology, US}
+
+
+
+\end{jibtitlepage}
+
+
+% \begin{abstract}
+% 
+% This document is a short description of the \LaTeX\ \emph{document class} \emph{jib} and its use. It shall be used to submit \LaTeX\ articles to the \emph{Journal of Integrative Bioinformatics} and at the same time may be used to check whether your \LaTeX\ installation can compile output files according to the guidelines of the journal.
+% 
+% \end{abstract}
+
+% adjusts the width of the abstract, please do not change!
+\begin{adjustwidth}{}{1cm}                 
+
+\abstract{
+Rule-based modeling is an approach that permits constructing reaction
+networks based on the specification of rules for molecular
+interactions and transformations. These rules can encompass details
+such as the interacting sub-molecular 
+domains (components) and the
+states such as phosphorylation and binding  
+status of the involved
+components. Conceptually, fine-grained spatial information such as the locations of
+the molecular components relative to a membrane (e.g. whether a
+modeled molecular domain is embedded into the inner leaflet of the 
+cellular plasma membrane) can also be provided. Through ``wildcards''
+representing component states, entire families of molecule complexes
+sharing certain properties can be specified as patterns. This can
+significantly simplify the definition of models involving species with
+multiple components, multiple states, and multiple compartments. 
+The SBML Level~3 \emph{Multi} Package (Multistate, Multicomponent and
+Multicompartment Species Package for SBML Level~3) Version~1 extends the SBML Level~3 Version 1
+\emph{core} with the ``type'' concept in the Species and Compartment classes. Therefore, 
+reaction rules may contain species that can be patterns
+and exist in multiple locations. 
+Multiple software tools such as \emph{Simmune} and \emph{BioNetGen} support the SBML
+Level~3 \emph{Multi} package that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level~3 \emph{Multi} package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications. All the completed example models in this specification have been validated by the validation rules of SBML Level 3 Version 1 core and SBML Level 3 Multi package Version 1 using the libSBML library.
+}
+
+\end{adjustwidth} % please do not change
+
+\end{document}

[sbml-svn] SF.net SVN: sbml:[26302] trunk/specifications/sbml-level-3/version-1/multi /spec

[<zha...@us...>]

Revision: 26302
          http://sourceforge.net/p/sbml/code/26302
Author:   zhangfen
Date:     2020-03-31 13:43:27 +0000 (Tue, 31 Mar 2020)
Log Message:
-----------
multi spec V1R2, minor update about M.L.B.

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex	2020-03-31 12:49:25 UTC (rev 26301)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex	2020-03-31 13:43:27 UTC (rev 26302)
@@ -6,7 +6,7 @@
 This work was supported by the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health.
 
 We sincerely thank all the contributors and their funding agencies. L.P.S., S.M.K, N.R., A.D., F.B. and M.H. were supported by the National Institute of General Medical Sciences (NIGMS, US) grant R01~GM070923. In addition, A.D. was supported by the DZIF (German Center for Infection Research) and by infrastructural funding from the \emph{Deutsche Forschungsgemeinschaft} (DFG, German Research Foundation), Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections; and F.B. was supported by the Bundesministerium f\"{u}r Bildung und Forschung (BMBF, DE) grant de.NBI~ModSim1, 031L0104A.
-M.L.B. was supported by NIH (US) grant P41~GM103313 and R01~GM095485.
+M.L.B. was supported by NIH (US) grant P41~GM103313 and R24~GM134211.
 J.F. and J.J.T. were supported by National Institutes of Health (NIH, US) grant P41~GM103712 to the National Center for Multiscale Modeling of Biological Systems (MMBioS).
 W.S.H was supported by the National Institute of General Medical Sciences (NIGMS, US) grant R01~ GM111510.
 

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex	2020-03-31 12:49:25 UTC (rev 26301)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex	2020-03-31 13:43:27 UTC (rev 26302)
@@ -8,7 +8,7 @@
   USA						& USA \\
   \\
   Michael L. Blinov			   	& Andreas Dr\"ager \\[0.25em]
-  University of Connecticut Health Center  	& Universtiy of Tuebingen \\
+  UConn Health  	& Universtiy of Tuebingen \\
   USA     				   	& Germany \\
   \\
   James Faeder 					& Andrew Finney \\[0.25em]

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf
===================================================================
(Binary files differ)

[sbml-svn] SF.net SVN: sbml:[26301] trunk/specifications/sbml-level-3/version-1/multi /spec

[<zha...@us...>]

Revision: 26301
          http://sourceforge.net/p/sbml/code/26301
Author:   zhangfen
Date:     2020-03-31 12:49:25 +0000 (Tue, 31 Mar 2020)
Log Message:
-----------
multi spec acknowledgments, minor update 

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex	2020-03-31 04:56:07 UTC (rev 26300)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex	2020-03-31 12:49:25 UTC (rev 26301)
@@ -5,8 +5,8 @@
 
 This work was supported by the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health.
 
-We sincerely thank all the contributors and their funding agencies. L.P.S., S.M.K, N.R., A.D., F.B. and M.H. were supported by the National Institute of General Medical Sciences(NIGMS, US) grant R01~GM070923. In addition, A.D. was supported by the DZIF (German Center for Infection Research) and by infrastructural funding from the \emph{Deutsche Forschungsgemeinschaft} (DFG, German Research Foundation), Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections; and F.B. was supported by the Bundesministerium f\"{u}r Bildung und Forschung (BMBF, DE) grant de.NBI~ModSim1, 031L0104A.
+We sincerely thank all the contributors and their funding agencies. L.P.S., S.M.K, N.R., A.D., F.B. and M.H. were supported by the National Institute of General Medical Sciences (NIGMS, US) grant R01~GM070923. In addition, A.D. was supported by the DZIF (German Center for Infection Research) and by infrastructural funding from the \emph{Deutsche Forschungsgemeinschaft} (DFG, German Research Foundation), Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections; and F.B. was supported by the Bundesministerium f\"{u}r Bildung und Forschung (BMBF, DE) grant de.NBI~ModSim1, 031L0104A.
 M.L.B. was supported by NIH (US) grant P41~GM103313 and R01~GM095485.
 J.F. and J.J.T. were supported by National Institutes of Health (NIH, US) grant P41~GM103712 to the National Center for Multiscale Modeling of Biological Systems (MMBioS).
-W.S.H was supported by the National Institute of General Medical Sciences(NIGMS, US) grant R01~ GM111510.
+W.S.H was supported by the National Institute of General Medical Sciences (NIGMS, US) grant R01~ GM111510.
 

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf
===================================================================
(Binary files differ)

[sbml-svn] SF.net SVN: sbml:[26300] trunk/specifications/sbml-level-3/version-1/multi /spec/sbml-multi_spec_1.1.2_release_2020Mar23.pdf

[<zha...@us...>]

Revision: 26300
          http://sourceforge.net/p/sbml/code/26300
Author:   zhangfen
Date:     2020-03-31 04:56:07 +0000 (Tue, 31 Mar 2020)
Log Message:
-----------
multi spec V1R2, delete the version of 2020Mar23 to avoid confusion and duplication with the most recent one 2020Mar31

Removed Paths:
-------------
    trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar23.pdf

Deleted: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar23.pdf
===================================================================
(Binary files differ)

[sbml-svn] SF.net SVN: sbml:[26299] trunk/specifications/sbml-level-3/version-1/multi /spec

[<zha...@us...>]

Revision: 26299
          http://sourceforge.net/p/sbml/code/26299
Author:   zhangfen
Date:     2020-03-31 04:47:22 +0000 (Tue, 31 Mar 2020)
Log Message:
-----------
multi spec acknowledgments update based on the SBML L3 paper and inputs from A.D. and W.S.H

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex	2020-03-27 23:53:49 UTC (rev 26298)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/acknowledgments.tex	2020-03-31 04:47:22 UTC (rev 26299)
@@ -4,3 +4,9 @@
 
 
 This work was supported by the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health.
+
+We sincerely thank all the contributors and their funding agencies. L.P.S., S.M.K, N.R., A.D., F.B. and M.H. were supported by the National Institute of General Medical Sciences(NIGMS, US) grant R01~GM070923. In addition, A.D. was supported by the DZIF (German Center for Infection Research) and by infrastructural funding from the \emph{Deutsche Forschungsgemeinschaft} (DFG, German Research Foundation), Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections; and F.B. was supported by the Bundesministerium f\"{u}r Bildung und Forschung (BMBF, DE) grant de.NBI~ModSim1, 031L0104A.
+M.L.B. was supported by NIH (US) grant P41~GM103313 and R01~GM095485.
+J.F. and J.J.T. were supported by National Institutes of Health (NIH, US) grant P41~GM103712 to the National Center for Multiscale Modeling of Biological Systems (MMBioS).
+W.S.H was supported by the National Institute of General Medical Sciences(NIGMS, US) grant R01~ GM111510.
+

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex	2020-03-27 23:53:49 UTC (rev 26298)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex	2020-03-31 04:47:22 UTC (rev 26299)
@@ -3,7 +3,7 @@
 \section{Background and context}
 \label{def:Background}
 
-Rule-base, domain-detailed modeling has been extremely valuable in systems biology related studies [\cite{ref:nathan2015} and \cite{ref:jamesFader2013}]. Rule-based, domain-detailed modeling approaches (\BioNetGen\ [\cite{ref:bionetgen2009}], \Kappa\ [\cite{ref:kappa2004}], and \Simmune\ [\cite{ref:simmune2012, ref:simmune2006}]) define rules for \mBlockChangedBegin{\revTwentyTwentyMarch}transformations of molecular domains and \mBlockChangedEnd{\revTwentyTwentyMarch}interactions between pairs of molecule domains, specifying how the \mBlockChangedBegin{\revTwentyTwentyMarch}transformations/\mBlockChangedEnd{\revTwentyTwentyMarch}interactions depend on particular states of the molecules (pattern) and their locations in specific compartments. In order to generate networks of biochemical reactions these rules are applied to the molecular components of the systems to be modeled, either at the beginning of the modeling (simulation) process or ``on the fly'' (as molecule complexes emerge from the interaction rules). Expressing such rule-based, domain-detailed reaction networks using the concepts of \Species and \Compartment in SBML (L3 core and L2) can be difficult for rules and molecule sets that lead to large numbers of resulting molecular complexes. It would therefore be desirable to have an SBML standard for encoding rule-based, domain-detailed \smodels\ using their ``native'' concepts for describing reactions instead of having to apply the rules and unfold the networks prior to encoding in an SBML format.
+Rule-based, domain-detailed modeling has been extremely valuable in systems biology related studies [\cite{ref:nathan2015} and \cite{ref:jamesFader2013}]. Rule-based, domain-detailed modeling approaches (\BioNetGen\ [\cite{ref:bionetgen2009}], \Kappa\ [\cite{ref:kappa2004}], and \Simmune\ [\cite{ref:simmune2012, ref:simmune2006}]) define rules for \mBlockChangedBegin{\revTwentyTwentyMarch}transformations of molecular domains and \mBlockChangedEnd{\revTwentyTwentyMarch}interactions between pairs of molecule domains, specifying how the \mBlockChangedBegin{\revTwentyTwentyMarch}transformations/\mBlockChangedEnd{\revTwentyTwentyMarch}interactions depend on particular states of the molecules (pattern) and their locations in specific compartments. In order to generate networks of biochemical reactions these rules are applied to the molecular components of the systems to be modeled, either at the beginning of the modeling (simulation) process or ``on the fly'' (as molecule complexes emerge from the interaction rules). Expressing such rule-based, domain-detailed reaction networks using the concepts of \Species and \Compartment in SBML (L3 core and L2) can be difficult for rules and molecule sets that lead to large numbers of resulting molecular complexes. It would therefore be desirable to have an SBML standard for encoding rule-based, domain-detailed \smodels\ using their ``native'' concepts for describing reactions instead of having to apply the rules and unfold the networks prior to encoding in an SBML format.
 
 We proposed a revised proposal of the \multi\ package: ``Multistate, Multicomponent and Multicompartment Species Package for SBML Level 3''  (abbreviated as Multi) [\cite{ref:revisedMulti} and \cite{ref:multiproposal280}] which takes the scopes and some data structures developed in \multiOneProposalWC\ and addresses main issues arising from a rule-based, domain-detailed modeling point of view with the data structures consistent with that used in the available rule-based, domain-detailed modeling tools. 
 

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex	2020-03-27 23:53:49 UTC (rev 26298)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/contributors.tex	2020-03-31 04:47:22 UTC (rev 26299)
@@ -3,11 +3,11 @@
 \begin{large}\textbf{Contributors}\end{large} \\
 \begin{center}
   \begin{tabular}{l @{\hspace{20 pt}} l}
-  Bastian Angermann				& Frank Bergmann \\[0.25em]
+  Bastian R. Angermann				& Frank Bergmann \\[0.25em]
   NIAID/NIH		     			& California Institute of Technology \\
   USA						& USA \\
   \\
-  Michael Blinov			   	& Andreas Dr\"ager \\[0.25em]
+  Michael L. Blinov			   	& Andreas Dr\"ager \\[0.25em]
   University of Connecticut Health Center  	& Universtiy of Tuebingen \\
   USA     				   	& Germany \\
   \\
@@ -15,7 +15,7 @@
   University of Pittsburgh School of Medicine	& University Hertfordshire \\
   USA						& United Kingdom \\
   \\
-  Leonard Harris 				& William Hlavacek \\[0.25em]
+  Leonard A. Harris 				& William S. Hlavacek \\[0.25em]
   University of Pittsburgh School of Medicine	& Los Alamos National Laboratory \\
   USA						& USA\\
   \\
@@ -23,7 +23,7 @@
   Virginia Tech 				& Los Alamos National Laboratory \\
   USA	 					& USA \\
   \\
-  Michael Hucka 				& Sarah Keating\\[0.25em]
+  Michael Hucka 				& Sarah M. Keating\\[0.25em]
   California Institute of Technology		& European Bioinformatics Institute \\
   USA						& United Kingdom \\
   \\
@@ -31,7 +31,7 @@
   Babraham Institute				& European Bioinformatics Institute \\
   United Kingdom				& United Kingdom \\
   \\
-  Nicolas Rodriguez 				& Lucian Smith \\[0.25em]
+  Nicolas Rodriguez 				& Lucian P. Smith \\[0.25em]
   European Bioinformatics Institute		& University of Washington\\
   United Kingdom				& USA\\
   \\

Added: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf
===================================================================
(Binary files differ)

Index: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf	2020-03-27 23:53:49 UTC (rev 26298)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf	2020-03-31 04:47:22 UTC (rev 26299)

Property changes on: trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar31.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property

[sbml-svn] SF.net SVN: sbml:[26298] trunk/specifications/sbml-level-3/version-1/multi /spec

[<zha...@us...>]

Revision: 26298
          http://sourceforge.net/p/sbml/code/26298
Author:   zhangfen
Date:     2020-03-27 23:53:49 +0000 (Fri, 27 Mar 2020)
Log Message:
-----------
multi spec version 1 Release 2 update, including spec PDF file and latex source files

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/apdx-validation.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/bionetgen_egfr_simple.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_patternSpecies_sum.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_speciesReferenceAtt_species.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_002_CompartmentSpeciesTypeSpecies.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_015_SimpleSpeciesReference.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_SpeciesFeatureExample.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/kappa_introduction_syntax.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/simmune_Ecad.xml
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/intro.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/macros.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/multi.tex
    trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/syntax.tex

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2_release_2020Mar23.pdf

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/apdx-validation.tex	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/apdx-validation.tex	2020-03-27 23:53:49 UTC (rev 26298)
@@ -21,7 +21,6 @@
 
 For convenience and brevity, we use the shorthand ``\token{multi:x}'' to stand for an attribute or element name \token{x} in the namespace for the \multi\ package, using the namespace prefix \token{multi}. We use ``\token{multi:x}'' because it is shorter than to write a full explanation everywhere we refer to an attribute or element in the \multi\ package namespace.
 
-\changed{Attributes from this package are listed in these rules as having the \val{multi:} prefix, but as is convention for SBML packages, this prefix is optional for elements that this specification defines, and is required for elements from SBML Core that this specification extends (\Compartment, \Species, \SimpleSpeciesReference, and within \textbf{\class{MathML}}\xspace).}
 
 \subsection*{General rules about the \multi\ package}
 

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/background.tex	2020-03-27 23:53:49 UTC (rev 26298)
@@ -3,13 +3,13 @@
 \section{Background and context}
 \label{def:Background}
 
-Rule-base, domain-detailed modeling has been extremely valuable in systems biology related studies [\cite{ref:nathan2015} and \cite{ref:jamesFader2013}]. Rule-based, domain-detailed modeling approaches (\BioNetGen\ [\cite{ref:bionetgen2009}], \Kappa\ [\cite{ref:kappa2004}], and \Simmune\ [\cite{ref:simmune2012, ref:simmune2006}]) define rules for interactions between pairs of molecule domains, specifying how the interactions depend on particular states of the molecules (pattern) and their locations in specific compartments. In order to generate networks of biochemical reactions these rules are applied to the molecular components of the systems to be modeled, either at the beginning of the modeling (simulation) process or ``on the fly'' (as molecule complexes emerge from the interaction rules). Expressing such rule-based, domain-detailed reaction networks using the concepts of \Species and \Compartment in SBML (L3 core and L2) can be difficult for rules and molecule sets that lead to large numbers of resulting molecular complexes. It would therefore be desirable to have an SBML standard for encoding rule-based, domain-detailed \smodels\ using their ``native'' concepts for describing reactions instead of having to apply the rules and unfold the networks prior to encoding in an SBML format.
+Rule-base, domain-detailed modeling has been extremely valuable in systems biology related studies [\cite{ref:nathan2015} and \cite{ref:jamesFader2013}]. Rule-based, domain-detailed modeling approaches (\BioNetGen\ [\cite{ref:bionetgen2009}], \Kappa\ [\cite{ref:kappa2004}], and \Simmune\ [\cite{ref:simmune2012, ref:simmune2006}]) define rules for \mBlockChangedBegin{\revTwentyTwentyMarch}transformations of molecular domains and \mBlockChangedEnd{\revTwentyTwentyMarch}interactions between pairs of molecule domains, specifying how the \mBlockChangedBegin{\revTwentyTwentyMarch}transformations/\mBlockChangedEnd{\revTwentyTwentyMarch}interactions depend on particular states of the molecules (pattern) and their locations in specific compartments. In order to generate networks of biochemical reactions these rules are applied to the molecular components of the systems to be modeled, either at the beginning of the modeling (simulation) process or ``on the fly'' (as molecule complexes emerge from the interaction rules). Expressing such rule-based, domain-detailed reaction networks using the concepts of \Species and \Compartment in SBML (L3 core and L2) can be difficult for rules and molecule sets that lead to large numbers of resulting molecular complexes. It would therefore be desirable to have an SBML standard for encoding rule-based, domain-detailed \smodels\ using their ``native'' concepts for describing reactions instead of having to apply the rules and unfold the networks prior to encoding in an SBML format.
 
 We proposed a revised proposal of the \multi\ package: ``Multistate, Multicomponent and Multicompartment Species Package for SBML Level 3''  (abbreviated as Multi) [\cite{ref:revisedMulti} and \cite{ref:multiproposal280}] which takes the scopes and some data structures developed in \multiOneProposalWC\ and addresses main issues arising from a rule-based, domain-detailed modeling point of view with the data structures consistent with that used in the available rule-based, domain-detailed modeling tools. 
 
 \label{def:OtherRuleBasedModels}
-\noticeFont{Note: \\
-This specification was developed with the main goal of taking into account bi-molecular interactions mediated through specific binding domains (or sites). Models without such detailed description of the molecular interactions can be encoded as well if the other features in this specification such as \SpeciesFeatureType, \SpeciesFeature, and extended \ExCompartment satisfy the model requirements.
+\noticeFont{Note: \notice\\
+This specification was developed with the main goal of taking into account \mBlockChangedBegin{\revTwentyTwentyMarch}molecular transformations and \mBlockChangedEnd{\revTwentyTwentyMarch}bi-molecular interactions mediated through specific binding domains (or sites). Models without such detailed description of the molecular interactions can be encoded as well if the other features in this specification such as \SpeciesFeatureType, \SpeciesFeature, and extended \ExCompartment satisfy the model requirements.
 }
 
 
@@ -50,47 +50,63 @@
 
 \newcommand{\mVersionTileFont}[1]{\textbf{#1}}
 
+
 \subsubsection{Release(s)}
 
 \begin{itemize}
-\mBlockChangedBegin{1.1.1}
- \item \mVersionTileFont{Version: 1.1.1, this version} 
- \label{def:v1_1_1}
-\mBlockChangedEnd{1.1.1} 
- \end{itemize}
+%  \mBlockChangedBegin{1.1.2}
+%    \item \mVersionTileFont{Version: 1.1.2, this version} 
+%    \label{def:v1_1_2}
+%  \mBlockChangedEnd{1.1.2} 
+  \mBlockChangedBegin{\revTwentyTwentyMarch}
+    \item \mVersionTileFont{Version: \revTwentyTwentyMarch}, this version
+    \label{def:v1_2}
+    \begin{itemize}
+     \item Fix issues raised by the community after ``Version 1 release 1''.
+     \item Revise parts of the text.
+     \item Add a paragraph to clarify ``XML Namespace use''(see \sec{def:xml_namespace_use}).
+     \item Validate the complete models and add ``demonstration only'' notes to those ``incomplete'' models in the example section (see \sec{def:Examples}).
+    \end{itemize}
 
+  \mBlockChangedEnd{\revTwentyTwentyMarch} 
 
+  \mBlockChangedBegin{1.1.1}
+    \item \mVersionTileFont{Version: 1.1.1, March 2017} 
+    \label{def:v1_1_1}
+  \mBlockChangedEnd{1.1.1} 
+\end{itemize}
+
+
 \subsubsection{Release Candidates}
 
 \begin{itemize}
-\mBlockChangedBegin{1.1.rc5}
- \item \mVersionTileFont{Version: 1.1.rc5 (release candidate), March 2017} 
- \label{def:v1_1_rc5}
-  \begin{itemize}
-  \item Add two validation rules \defRef{multi-21213}{validation:species:21213} and \defRef{multi-21214}{validation:species:21214} to check the \speciesTypeAtt\ attribute of a \species\ with \listOfOutwardBindingSites\ and/or \listOfSpeciesFeatures\. (See \sec{def:ExSpecies}.)
-  \item Add a constraint to the \relationAtt\ attribute of a \subListOfSpeciesFeatures\ having a \speciesFeature\ child referencing a \speciesFeatureType\ with \val{occur > 1}. (See \sec{def:SubListOfSpeciesFeatures:relation} and \sec{validation:species:21215}.)
-  \item Enforce the \SubListOfSpeciesFeatures class to have at least two \speciesFeature s and set \relationAtt\ as a required attribute. (See \sec{def:SubListOfSpeciesFeatures}.)
- \end{itemize}
- 
+  \mBlockChangedBegin{1.1.rc5}
+  \item \mVersionTileFont{Version: 1.1.rc5 (release candidate), March 2017} 
+  \label{def:v1_1_rc5}
+    \begin{itemize}
+      \item Add two validation rules \defRef{multi-21213}{validation:species:21213} and \defRef{multi-21214}{validation:species:21214} to check the \speciesTypeAtt\ attribute of a \species\ with \listOfOutwardBindingSites\ and/or \listOfSpeciesFeatures\. (See \sec{def:ExSpecies}.)
+      \item Add a constraint to the \relationAtt\ attribute of a \subListOfSpeciesFeatures\ having a \speciesFeature\ child referencing a \speciesFeatureType\ with \val{occur > 1}. (See \sec{def:SubListOfSpeciesFeatures:relation} and \sec{validation:species:21215}.)
+      \item Enforce the \SubListOfSpeciesFeatures class to have at least two \speciesFeature s and set \relationAtt\ as a required attribute. (See \sec{def:SubListOfSpeciesFeatures}.)
+    \end{itemize}
 \mBlockChangedEnd{1.1.rc5} 
 
- \item \mVersionTileFont{Version: 1.1.rc4 (release candidate), March 2017} \\
- \label{def:v1_1_rc4}
- More updates on validation rule numbers, line breaks, and the example about \SubListOfSpeciesFeatures. 
+  \item \mVersionTileFont{Version: 1.1.rc4 (release candidate), March 2017} \\
+  \label{def:v1_1_rc4}
+  More updates on validation rule numbers, line breaks, and the example about \SubListOfSpeciesFeatures. 
 
- \item \mVersionTileFont{Version: 1.1.rc3 (release candidate), Febrary 2017} \\
- \label{def:v1_1_rc3}
- Modify the numbers of several rules to be consistent with the general SBML validation rule conventions. 
+  \item \mVersionTileFont{Version: 1.1.rc3 (release candidate), Febrary 2017} \\
+  \label{def:v1_1_rc3}
+  Modify the numbers of several rules to be consistent with the general SBML validation rule conventions. 
 
- \item \mVersionTileFont{Version: 1.1.rc2 (release candidate), January 2017} \\
- \label{def:v1_1_rc2}
- Add a new validation rule \defRef{multi-22006}{def:validationRule:22006} to prevent circular referencing among the extended \ExCompartment objects.
+  \item \mVersionTileFont{Version: 1.1.rc2 (release candidate), January 2017} \\
+  \label{def:v1_1_rc2}
+  Add a new validation rule \defRef{multi-22006}{def:validationRule:22006} to prevent circular referencing among the extended \ExCompartment objects.
  
- Revise the specification text with minor changes towards a version of the official release candidate. 
+  Revise the specification text with minor changes towards a version of the official release candidate. 
 
- \item \mVersionTileFont{Version: 1.1.rc1 (release candidate), November 2016} \\
- \label{def:v1_1_rc1}
- Revise the specification text with minor changes towards a version of the official release candidate. 
+  \item \mVersionTileFont{Version: 1.1.rc1 (release candidate), November 2016} \\
+  \label{def:v1_1_rc1}
+  Revise the specification text with minor changes towards a version of the official release candidate. 
 
 \end{itemize}
 

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/bionetgen_egfr_simple.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/bionetgen_egfr_simple.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/bionetgen_egfr_simple.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -2,12 +2,14 @@
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
    xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" multi:required="true">
 
+    <!-- Note: this model has been validated agains multi validation rules without errors -->
+    
    <model name="bionetgen_example_egfr_simple">
 
       <listOfUnitDefinitions>
          <unitDefinition id="molecules_per_mol">
             <listOfUnits>
-               <unit kind="mole" scale="0" mulitplier="1" exponent="-1" />
+               <unit kind="mole" scale="0" multiplier="1" exponent="-1" />
             </listOfUnits>
          </unitDefinition>
       </listOfUnitDefinitions>
@@ -14,9 +16,9 @@
 
       <!-- compartments -->
       <listOfCompartments>
-         <compartment id="Vo" constant="true" spatialDimensions="3" units="liter" 
+         <compartment id="Vo" constant="true" spatialDimensions="3" units="litre" 
             multi:isType="false" />
-         <compartment id="V" constant="true" spatialDimensions="3" units="liter" 
+         <compartment id="V" constant="true" spatialDimensions="3" units="litre" 
             multi:isType="false" />
       </listOfCompartments>
 
@@ -27,7 +29,7 @@
          <multi:bindingSiteSpeciesType multi:id="st_EGF_bs_R" />
          <multi:speciesType multi:id="st_EGF">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="R" multi:speciesType="st_EGF_bs_R" />
+               <multi:speciesTypeInstance multi:id="R" multi:speciesType="st_EGF_bs_R" />
             </multi:listOfSpeciesTypeInstances>
          </multi:speciesType>
 
@@ -36,7 +38,7 @@
          <multi:bindingSiteSpeciesType multi:id="st_EGFR_bs_CR1" />
          <multi:bindingSiteSpeciesType multi:id="st_EGFR_bs_Y1068">
             <multi:listOfSpeciesFeatureTypes>
-               <multi:speciesFeatureType multi:id="sft_Y1068">
+               <multi:speciesFeatureType multi:id="sft_Y1068" multi:occur="1">
                   <multi:listOfPossibleSpeciesFeatureValues>
                      <multi:possibleSpeciesFeatureValue multi:id="U" />
                      <multi:possibleSpeciesFeatureValue multi:id="P" />
@@ -46,9 +48,9 @@
          </multi:bindingSiteSpeciesType>
          <multi:speciesType multi:id="st_EGFR">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="L" multi:speciesType="st_EGFR_bs_L" />
-               <multi:component multi:id="CR1" multi:speciesType="st_EGFR_bs_CR1" />
-               <multi:component multi:id="Y1068" multi:speciesType="st_EGFR_bs_Y1068" />
+               <multi:speciesTypeInstance multi:id="L" multi:speciesType="st_EGFR_bs_L" />
+               <multi:speciesTypeInstance multi:id="CR1" multi:speciesType="st_EGFR_bs_CR1" />
+               <multi:speciesTypeInstance multi:id="Y1068" multi:speciesType="st_EGFR_bs_Y1068" />
             </multi:listOfSpeciesTypeInstances>
          </multi:speciesType>
 
@@ -55,8 +57,8 @@
          <!-- EGFR dimer: [EGFR(CR1!1).EGFR(CR1!1)] -->
          <multi:speciesType multi:id="st_EGFR_dimer">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="EGFR1" multi:speciesType="st_EGFR" />
-               <multi:component multi:id="EGFR2" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="EGFR1" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="EGFR2" multi:speciesType="st_EGFR" />
             </multi:listOfSpeciesTypeInstances>
             <multi:listOfSpeciesTypeComponentIndexes>
                <multi:speciesTypeComponentIndex multi:id="EGFR1CR1"
@@ -73,10 +75,10 @@
          <!-- EGFR-EGF dimer: [EGF(R!1).EGF(R!2).EGFR(L!1,CR1!3).EGFR(L!2,CR1!3)] -->
          <multi:speciesType multi:id="st_EGFR_EGF_dimer">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="EGF1" multi:speciesType="st_EGF" />
-               <multi:component multi:id="EG2" multi:speciesType="st_EGF" />
-               <multi:component multi:id="EGFR1" multi:speciesType="st_EGFR" />
-               <multi:component multi:id="EGFR2" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="EGF1" multi:speciesType="st_EGF" />
+               <multi:speciesTypeInstance multi:id="EGF2" multi:speciesType="st_EGF" />
+               <multi:speciesTypeInstance multi:id="EGFR1" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="EGFR2" multi:speciesType="st_EGFR" />
             </multi:listOfSpeciesTypeInstances>
             <multi:listOfSpeciesTypeComponentIndexes>
                <multi:speciesTypeComponentIndex multi:id="EGF1R"
@@ -104,8 +106,8 @@
          <multi:bindingSiteSpeciesType multi:id="st_Grb2_bs_SH3" />
          <multi:speciesType multi:id="st_Grb2">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="SH2" multi:speciesType="st_Grb2_bs_SH2" />
-               <multi:component multi:id="SH3" multi:speciesType="st_Grb2_bs_SH3" />
+               <multi:speciesTypeInstance multi:id="SH2" multi:speciesType="st_Grb2_bs_SH2" />
+               <multi:speciesTypeInstance multi:id="SH3" multi:speciesType="st_Grb2_bs_SH3" />
             </multi:listOfSpeciesTypeInstances>
          </multi:speciesType>
 
@@ -113,18 +115,18 @@
          <multi:bindingSiteSpeciesType multi:id="st_Sos1_bs_PxxP" />
          <multi:speciesType multi:id="st_Sos1">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="PxxP" multi:speciesType="st_Sos1_bs_PxxP" />
+               <multi:speciesTypeInstance multi:id="PxxP" multi:speciesType="st_Sos1_bs_PxxP" />
             </multi:listOfSpeciesTypeInstances>
          </multi:speciesType>
 
          <!-- Trash -->
-         <multi:speciesType multi:id="trash" />
+         <multi:speciesType multi:id="st_trash" />
 
          <!-- Grb2-Sos1 -->
          <multi:speciesType multi:id="st_Grb2_Sos1">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="Grb2" multi:speciesType="st_Grb2" />
-               <multi:component multi:id="Sos1" multi:speciesType="st_Sos1" />
+               <multi:speciesTypeInstance multi:id="Grb2" multi:speciesType="st_Grb2" />
+               <multi:speciesTypeInstance multi:id="Sos1" multi:speciesType="st_Sos1" />
             </multi:listOfSpeciesTypeInstances>
             <multi:listOfInSpeciesTypeBonds>
                <multi:inSpeciesTypeBond multi:bindingSite1="SH3" multi:bindingSite2="PxxP" />
@@ -134,9 +136,9 @@
          <!-- EGFR(Y1068!1).Grb1(SH2!1,SH3!2).Sos1(PxxP!2) -->
          <multi:speciesType multi:id="st_EGFR_Grb2_Sos1">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="EGFR" multi:speciesType="st_EGFR" />
-               <multi:component multi:id="Grb2" multi:speciesType="st_Grb2" />
-               <multi:component multi:id="Sos1" multi:speciesType="st_Sos1" />
+               <multi:speciesTypeInstance multi:id="EGFR" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="Grb2" multi:speciesType="st_Grb2" />
+               <multi:speciesTypeInstance multi:id="Sos1" multi:speciesType="st_Sos1" />
             </multi:listOfSpeciesTypeInstances>
             <multi:listOfInSpeciesTypeBonds>
                <multi:inSpeciesTypeBond multi:bindingSite1="Y1068" multi:bindingSite2="SH2" />
@@ -147,8 +149,8 @@
          <!-- EGFR(L!1).EGF(R!1) -->
          <multi:speciesType multi:id="st_EGFR_EGF">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="EGFR" multi:speciesType="st_EGFR" />
-               <multi:component multi:id="EGF" multi:speciesType="st_EGF" />
+               <multi:speciesTypeInstance multi:id="EGFR" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="EGF" multi:speciesType="st_EGF" />
             </multi:listOfSpeciesTypeInstances>
             <multi:listOfInSpeciesTypeBonds>
                <multi:inSpeciesTypeBond multi:bindingSite1="L" multi:bindingSite2="R" />
@@ -158,8 +160,8 @@
          <!-- EGFR(Y1068!1).Grb2(SH2!1) -->
          <multi:speciesType multi:id="st_EGFR_Grb2">
             <multi:listOfSpeciesTypeInstances>
-               <multi:component multi:id="EGFR" multi:speciesType="st_EGFR" />
-               <multi:component multi:id="Grb2" multi:speciesType="st_Grb2" />
+               <multi:speciesTypeInstance multi:id="EGFR" multi:speciesType="st_EGFR" />
+               <multi:speciesTypeInstance multi:id="Grb2" multi:speciesType="st_Grb2" />
             </multi:listOfSpeciesTypeInstances>
             <multi:listOfInSpeciesTypeBonds>
                <multi:inSpeciesTypeBond multi:bindingSite1="Y1068" multi:bindingSite2="SH2" />
@@ -171,16 +173,16 @@
       <!-- species -->
       <listOfSpecies>
 
-         <species id="sp_EGF_free" name="EGF(R)" multi:speciesType="st_EGF" 
-            hasOnlySubstanceUnits="false"
-            boundaryCondition="false" constant="false">
+         <species id="sp_EGF_free" name="EGF(R)" compartment="Vo" multi:speciesType="st_EGF" 
+            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="R" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
 
-         <species id="sp_EGFR_free_U" name="EGFR(L,CR1,Y1068~U)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_free_U" name="EGFR(L,CR1,Y1068~U)" compartment="V" 
+            multi:speciesType="st_EGFR" hasOnlySubstanceUnits="false" 
+            boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="L" multi:bindingStatus="unbound" />
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="unbound" />
@@ -187,7 +189,7 @@
                <multi:outwardBindingSite multi:component="Y1068" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="U" />
                   </multi:listOfSpeciesFeatureValues>
@@ -194,7 +196,7 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_Grb2_free" name="Grb2(SH2,SH3)" multi:speciesType="st_Grb2"
+         <species id="sp_Grb2_free" name="Grb2(SH2,SH3)" compartment="Vo" multi:speciesType="st_Grb2"
             hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="SH2" multi:bindingStatus="unbound" />
@@ -201,7 +203,7 @@
                <multi:outwardBindingSite multi:component="SH3" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_Grb2_SH2" name="Grb2(SH2)" multi:speciesType="st_Grb2" 
+         <species id="sp_Grb2_SH2" name="Grb2(SH2)" compartment="V" multi:speciesType="st_Grb2" 
             hasOnlySubstanceUnits="false"
             boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
@@ -208,7 +210,7 @@
                <multi:outwardBindingSite multi:component="SH2" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_Grb2_SH3" name="Grb2(SH3)" multi:speciesType="st_Grb2" 
+         <species id="sp_Grb2_SH3" name="Grb2(SH3)" compartment="V" multi:speciesType="st_Grb2" 
             hasOnlySubstanceUnits="false"
             boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
@@ -215,25 +217,27 @@
                <multi:outwardBindingSite multi:component="SH3" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_Sos1_free" name="Sos1(PxxP)" multi:speciesType="st_Sos1"
+         <species id="sp_Sos1_free" name="Sos1(PxxP)" compartment="V" multi:speciesType="st_Sos1"
             hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="PxxP" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_EGF_tot" name="EGF()" multi:speciesType="st_EGF" 
+         <species id="sp_EGF_tot" name="EGF()" compartment="Vo" multi:speciesType="st_EGF" 
             hasOnlySubstanceUnits="false"
             boundaryCondition="false" constant="false" />
-         <species id="sp_EGFR_dimerized" name="EGFR(CR1!+)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_dimerized" name="EGFR(CR1!+)" compartment="V" 
+            multi:speciesType="st_EGFR" hasOnlySubstanceUnits="false" boundaryCondition="false" 
+            constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="bound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_EGFR_U" name="EGFR(Y1068~P!?)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_U" name="EGFR(Y1068~P!?)" compartment="V" 
+            multi:speciesType="st_EGFR" hasOnlySubstanceUnits="false" boundaryCondition="false" 
+            constant="false">
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="P" />
                   </multi:listOfSpeciesFeatureValues>
@@ -240,7 +244,7 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_EGFR_L_CR1" name="EGFR(L,CR1)" multi:speciesType="st_EGFR"
+         <species id="sp_EGFR_L_CR1" name="EGFR(L,CR1)" compartment="V" multi:speciesType="st_EGFR"
             hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="L" multi:bindingStatus="unbound" />
@@ -247,20 +251,22 @@
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_EGFR_EGF_CR1" name="EGFR(L!1,CR1).EGF(R!1)" multi:speciesType="st_EGFR_EGF"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_EGF_CR1" name="EGFR(L!1,CR1).EGF(R!1)" compartment="V" 
+            multi:speciesType="st_EGFR_EGF" hasOnlySubstanceUnits="false" boundaryCondition="false" 
+            constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_EGFR_bL_CR1" name="EGFR(L!+,CR1)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_bL_CR1" name="EGFR(L!+,CR1)" compartment="V" 
+            multi:speciesType="st_EGFR" hasOnlySubstanceUnits="false" boundaryCondition="false" 
+            constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="L" multi:bindingStatus="bound" />
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_EGFR_dimer_bL" name="EGFR(L!+,CR1!1).EGFR(L!+,CR1!1)" 
+         <species id="sp_EGFR_dimer_bL" name="EGFR(L!+,CR1!1).EGFR(L!+,CR1!1)" compartment="V" 
             multi:speciesType="st_EGFR_dimer"
             hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
@@ -270,18 +276,18 @@
                   multi:bindingStatus="bound" />
             </multi:listOfOutwardBindingSites>
          </species>
-         <species id="sp_EGFR_EGF_dimer" name="EGF(R!1).EGF(R!2).EGFR(L!1,CR1!3).EGFR(L!2,CR1!3)"
-            multi:speciesType="st_EGFR_EGF_dimer" hasOnlySubstanceUnits="false" 
-            boundaryCondition="false"
-            constant="false" />
-         <species id="sp_EGFR_bCR1_Y1068_U" name="EGFR(CR1!+,Y1068~U)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_EGF_dimer" name="EGF(R!1).EGF(R!2).EGFR(L!1,CR1!3).EGFR(L!2,CR1!3)" 
+            compartment="V" multi:speciesType="st_EGFR_EGF_dimer" hasOnlySubstanceUnits="false" 
+            boundaryCondition="false" constant="false" />
+         <species id="sp_EGFR_bCR1_Y1068_U" name="EGFR(CR1!+,Y1068~U)" compartment="V" 
+            multi:speciesType="st_EGFR" hasOnlySubstanceUnits="false" boundaryCondition="false" 
+            constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="bound" />
                <multi:outwardBindingSite multi:component="Y1068" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="U" />
                   </multi:listOfSpeciesFeatureValues>
@@ -288,14 +294,14 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_EGFR_bCR1_Y1068_P" name="EGFR(CR1!+,Y1068~P)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_bCR1_Y1068_P" name="EGFR(CR1!+,Y1068~P)" multi:speciesType="st_EGFR" 
+            compartment="V" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="CR1" multi:bindingStatus="bound" />
                <multi:outwardBindingSite multi:component="Y1068" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="P" />
                   </multi:listOfSpeciesFeatureValues>
@@ -302,13 +308,13 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_EGFR_Y1068_P" name="EGFR(Y1068~P)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_Y1068_P" name="EGFR(Y1068~P)" multi:speciesType="st_EGFR" 
+            compartment="V" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="Y1068" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="P" />
                   </multi:listOfSpeciesFeatureValues>
@@ -315,13 +321,13 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_EGFR_Y1068_U" name="EGFR(Y1068~U)" multi:speciesType="st_EGFR"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+         <species id="sp_EGFR_Y1068_U" name="EGFR(Y1068~U)" multi:speciesType="st_EGFR" 
+            compartment="V" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfOutwardBindingSites>
                <multi:outwardBindingSite multi:component="Y1068" multi:bindingStatus="unbound" />
             </multi:listOfOutwardBindingSites>
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="U" />
                   </multi:listOfSpeciesFeatureValues>
@@ -328,11 +334,11 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_EGFR_Grb2_P" name="EGFR(Y1068~P!1).Grb2(SH2!1)" 
+         <species id="sp_EGFR_Grb2_P" name="EGFR(Y1068~P!1).Grb2(SH2!1)"  compartment="V"
             multi:speciesType="st_EGFR_Grb2"
             hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
             <multi:listOfSpeciesFeatures>
-               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068">
+               <multi:speciesFeature multi:speciesFeatureType="sft_Y1068" multi:occur="1">
                   <multi:listOfSpeciesFeatureValues>
                      <multi:speciesFeatureValue multi:value="P" />
                   </multi:listOfSpeciesFeatureValues>
@@ -339,10 +345,11 @@
                </multi:speciesFeature>
             </multi:listOfSpeciesFeatures>
          </species>
-         <species id="sp_Grb2_Sos1" name="Grb2(SH3!1).Sos1(PxxP!1)" multi:speciesType="st_Grb2_Sos1"
-            hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+         <species id="sp_Grb2_Sos1" name="Grb2(SH3!1).Sos1(PxxP!1)" compartment="V" 
+            multi:speciesType="st_Grb2_Sos1" hasOnlySubstanceUnits="false" 
+            boundaryCondition="false" constant="false" />
 
-         <species id="sp_Trash" name="Trash()" multi:speciesType="st_Trash" 
+         <species id="sp_Trash" name="Trash()" compartment="V" multi:speciesType="st_trash" 
             hasOnlySubstanceUnits="false"
             boundaryCondition="false" constant="false" />
       </listOfSpecies>
@@ -365,10 +372,10 @@
       </listOfParameters>
 
       <!-- intiialAssignments -->
-      <listOfIntialAssignments>
+      <listOfInitialAssignments>
 
          <initialAssignment symbol="Vo">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <times />
                   <ci>f</ci>
@@ -377,7 +384,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="V">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <times />
                   <ci>f</ci>
@@ -386,7 +393,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="kp1">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <divide />
                   <cn>9.02e7</cn>
@@ -399,7 +406,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="kp2">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <divide />
                   <cn>1.0e7</cn>
@@ -412,7 +419,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="kp4">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <divide />
                   <cn>1.5e6</cn>
@@ -425,7 +432,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="kp5">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <divide />
                   <cn>1.0e7</cn>
@@ -438,7 +445,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="sp_EGF_free">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <times />
                   <cn>20</cn>
@@ -449,7 +456,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="sp_EGFR_free_U">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <times />
                   <ci>f</ci>
@@ -458,7 +465,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="sp_Grb2_free">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <times />
                   <ci>f</ci>
@@ -467,7 +474,7 @@
             </math>
          </initialAssignment>
          <initialAssignment symbol="sp_Sos1_free">
-            <math xmls="http://www.w3.org/1998/Math/MathML">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <apply>
                   <times />
                   <ci>f</ci>
@@ -475,7 +482,7 @@
                </apply>
             </math>
          </initialAssignment>
-      </listOfIntialAssignments>
+      </listOfInitialAssignments>
 
       <!-- reactions -->
       <listOfReactions>
@@ -660,4 +667,4 @@
          </reaction>
       </listOfReactions>
    </model>
-</sbml>
\ No newline at end of file
+</sbml>

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_patternSpecies_sum.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_patternSpecies_sum.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_patternSpecies_sum.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -24,7 +24,7 @@
       </math>
       <listOfLocalParameters>
          <localParameter id="k1" ... />
-         <localParameter id="k2" .... />
+         <localParameter id="k2" ... />
       </listOfLocalParameters>
    </kineticLaw>
 </reaction>
\ No newline at end of file

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_speciesReferenceAtt_species.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_speciesReferenceAtt_species.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/ci_speciesReferenceAtt_species.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -6,9 +6,7 @@
             <times />
             <ci> k </ci>
             <ci multi:speciesReference="r1"> spA </ci>
-            <ci multi:speciesReference="m1"> spM </ci>
             <ci multi:speciesReference="r2"> spA </ci>
-            <ci multi:speciesReference="m2"> spM </ci>
          </apply>
       </math>
       <listOfLocalParameters>
@@ -15,4 +13,5 @@
          <localParameter id="k" value="0.1" ... />
       </listOfLocalParameters>
    </kineticLaw>
-</reaction>
\ No newline at end of file
+</reaction>
+ 
\ No newline at end of file

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_002_CompartmentSpeciesTypeSpecies.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_002_CompartmentSpeciesTypeSpecies.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_002_CompartmentSpeciesTypeSpecies.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -1,3 +1,5 @@
+<!-- Note: this example is for the purpose of demonstration; it s not a complete model-->
+
 <listOfCompartments>
    <compartment id="ct" multi:isType="true" />
    <compartment id="cct" multi:isType="true">

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_015_SimpleSpeciesReference.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_015_SimpleSpeciesReference.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_015_SimpleSpeciesReference.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -9,7 +9,6 @@
 </listOfCompartments>
 <multi:listOfSpeciesTypes>
    <multi:bindingSiteSpeciesType multi:id="stA" multi:compartment="c" />
-   <multi:speciesType multi:id="stM" multi:compartment="c" />
    <multi:speciesType multi:id="stAA" multi:compartment="cc">
       <multi:listOfSpeciesTypeInstances>
          <multi:speciesTypeInstance multi:id="stiA1" multi:speciesType="stA"
@@ -24,20 +23,18 @@
 </multi:listOfSpeciesTypes>
 <listOfSpecies>
    <species id="spA" multi:speciesType="stA" compartment="c" ... />
-   <species id="spM" multi:speciesType="stM" compartment="c" ... />
    <species id="spAA" multi:speciesType="stAA" compartment="cc" ... />
 </listOfSpecies>
-<reaction id="reaction" ...>
-   <listOfReactants>
-      <speciesReference id="r1" species="spA" multi:compartmentReference="cr1" ... />
-      <speciesReference id="r2" species="spA" multi:compartmentReference="cr2" ... />
-   </listOfReactants>
-   <listOfProducts>
-      <speciesReference species="spAA" ... />
-   </listOfProducts>
-   <listOfModifiers>
-      <modifierSpeciesReference id="m1" species="spM" multi:compartmentReference="cr1" />
-      <modifierSpeciesReference id="m2" species="spM" multi:compartmentReference="cr2" />
-   </listOfModifiers>
+<listOfReactions>
+   <reaction id="reaction" ...>
+      <listOfReactants>
+         <speciesReference id="r1" species="spA" multi:compartmentReference="cr1" ... />
+         <speciesReference id="r2" species="spA" multi:compartmentReference="cr2" ... />
+      </listOfReactants>
+      <listOfProducts>
+         <speciesReference species="spAA" ... />
+      </listOfProducts>
+      ...
+   </reaction>
    ...
-</reaction>
+</listOfReactions>
\ No newline at end of file

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_SpeciesFeatureExample.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_SpeciesFeatureExample.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/code_SpeciesFeatureExample.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -1,59 +1,57 @@
 <multi:listOfSpeciesTypes>
-   <multi:bindingSiteSpeciesType multi:id="st_B">
+   <multi:bindingSiteSpeciesType multi:id="st_A">
       <multi:listOfSpeciesFeatureTypes>
-         <multi:speciesFeatureType multi:id="fB" multi:occur="1">
+         <multi:speciesFeatureType multi:id="fA" multi:occur="1">
             <multi:listOfPossibleSpeciesFeatureValues>
-               <multi:possibleSpeciesFeatureValue multi:id="fb1" />
-               <multi:possibleSpeciesFeatureValue multi:id="fb2" />
+               <multi:possibleSpeciesFeatureValue multi:id="v1" />
+               <multi:possibleSpeciesFeatureValue multi:id="v2" />
             </multi:listOfPossibleSpeciesFeatureValues>
          </multi:speciesFeatureType>
       </multi:listOfSpeciesFeatureTypes>
    </multi:bindingSiteSpeciesType>
-   <multi:bindingSiteSpeciesType multi:id="st_C">
+   <multi:bindingSiteSpeciesType multi:id="st_B">
       <multi:listOfSpeciesFeatureTypes>
-         <multi:speciesFeatureType multi:id="fC" multi:occur="1">
+         <multi:speciesFeatureType multi:id="fB1" multi:occur="1">
             <multi:listOfPossibleSpeciesFeatureValues>
-               <multi:possibleSpeciesFeatureValue multi:id="fc1" />
-               <multi:possibleSpeciesFeatureValue multi:id="fc2" />
+               <multi:possibleSpeciesFeatureValue multi:id="v3" />
+               <multi:possibleSpeciesFeatureValue multi:id="v4" />
             </multi:listOfPossibleSpeciesFeatureValues>
          </multi:speciesFeatureType>
-      </multi:listOfSpeciesFeatureTypes>
-   </multi:bindingSiteSpeciesType>
-   <multi:speciesType multi:id="st_A">
-      <multi:listOfSpeciesFeatureTypes>
-         <multi:speciesFeatureType multi:id="fA" multi:occur="1">
+         <multi:speciesFeatureType multi:id="fB2" multi:occur="1">
             <multi:listOfPossibleSpeciesFeatureValues>
-               <multi:possibleSpeciesFeatureValue multi:id="fa1" />
-               <multi:possibleSpeciesFeatureValue multi:id="fa2" />
+               <multi:possibleSpeciesFeatureValue multi:id="v5" />
+               <multi:possibleSpeciesFeatureValue multi:id="v6" />
             </multi:listOfPossibleSpeciesFeatureValues>
          </multi:speciesFeatureType>
       </multi:listOfSpeciesFeatureTypes>
+   </multi:bindingSiteSpeciesType>
+   <multi:speciesType multi:id="st_X">
       <multi:listOfSpeciesTypeInstances>
+         <multi:speciesTypeInstance multi:id="sti_A" multi:speciesType="st_A" />
          <multi:speciesTypeInstance multi:id="sti_B" multi:speciesType="st_B" />
-         <multi:speciesTypeInstance multi:id="sti_C" multi:speciesType="st_C" />
       </multi:listOfSpeciesTypeInstances>
    </multi:speciesType>
 </multi:listOfSpeciesTypes>
 <listOfSpecies>
    <species id="sp_A1" multi:speciesType="st_A" .>
-      <!-- [fa1] and [fb1] and [fc1] -->
-      <multi:listOfSpeciesFeatures multi:relation="and">
+      <!-- [v1] AND [v3] AND [v5] -->
+      <multi:listOfSpeciesFeatures>
          <multi:speciesFeature multi:speciesFeatureType="fA" multi:occur="1"
-            multi:component="st_A">
+            multi:component="sti_A">
             <multi:listOfSpeciesFeatureValues>
-               <multi:speciesFeatureValue multi:value="fa1" />
+               <multi:speciesFeatureValue multi:value="v1" />
             </multi:listOfSpeciesFeatureValues>
          </multi:speciesFeature>
-         <multi:speciesFeature multi:speciesFeatureType="fB" multi:occur="1"
+         <multi:speciesFeature multi:speciesFeatureType="fB1" multi:occur="1"
             multi:component="sti_B">
             <multi:listOfSpeciesFeatureValues>
-               <multi:speciesFeatureValue multi:value="fb1" />
+               <multi:speciesFeatureValue multi:value="v3" />
             </multi:listOfSpeciesFeatureValues>
          </multi:speciesFeature>
-         <multi:speciesFeature multi:speciesFeatureType="fC" multi:occur="1"
-            multi:component="sti_C">
+         <multi:speciesFeature multi:speciesFeatureType="fB2" multi:occur="1"
+            multi:component="sti_B">
             <multi:listOfSpeciesFeatureValues>
-               <multi:speciesFeatureValue multi:value="fc1" />
+               <multi:speciesFeatureValue multi:value="v5" />
             </multi:listOfSpeciesFeatureValues>
          </multi:speciesFeature>
       </multi:listOfSpeciesFeatures>
@@ -62,48 +60,20 @@
     </multi:listOfOutwardBindingSites>
    </species>
    <species id="sp_A2" multi:speciesType="st_A" .>
-      <!-- {[fa1] and [fb1]) and [fc1]} or {[fa2] and [fb2] and [fc2]} -->
-      <multi:listOfSpeciesFeatures multi:relation="or">
-         <multi:subListOfSpeciesFeatures multi:relation="and">
-            <multi:speciesFeature multi:speciesFeatureType="fA" multi:occur="1"
-               multi:component="st_A">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fa1" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-            <multi:speciesFeature multi:speciesFeatureType="fB" multi:occur="1"
-               multi:component="sti_B">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fb1" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-            <multi:speciesFeature multi:speciesFeatureType="fC" multi:occur="1"
-               multi:component="sti_C">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fc1" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-         </multi:subListOfSpeciesFeatures>
-         <multi:subListOfSpeciesFeatures multi:relation="and">
-            <multi:speciesFeature multi:speciesFeatureType="fA" multi:occur="1"
-               multi:component="st_A">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fa2" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-            <multi:speciesFeature multi:speciesFeatureType="fB" multi:occur="1"
-               multi:component="sti_B">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fb2" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-            <multi:speciesFeature multi:speciesFeatureType="fC" multi:occur="1"
-               multi:component="sti_C">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fc2" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-         </multi:subListOfSpeciesFeatures>
+      <!-- [v1] AND [v3] -->
+      <multi:listOfSpeciesFeatures>
+         <multi:speciesFeature multi:speciesFeatureType="fA" multi:occur="1"
+            multi:component="sti_A">
+            <multi:listOfSpeciesFeatureValues>
+               <multi:speciesFeatureValue multi:value="v1" />
+            </multi:listOfSpeciesFeatureValues>
+         </multi:speciesFeature>
+         <multi:speciesFeature multi:speciesFeatureType="fB1" multi:occur="1"
+            multi:component="sti_B">
+            <multi:listOfSpeciesFeatureValues>
+               <multi:speciesFeatureValue multi:value="v3" />
+            </multi:listOfSpeciesFeatureValues>
+         </multi:speciesFeature>
       </multi:listOfSpeciesFeatures>
       <multi:listOfOutwardBindingSites>
          ...
@@ -110,28 +80,25 @@
     </multi:listOfOutwardBindingSites>
    </species>
    <species id="sp_A3" multi:speciesType="st_A" .>
-      <!-- {[fa1] and [fb1] and [fc2]} or {[fa1] and [fb2] and [fc2]} or {[fa1] and [fb2] and [fc1]} -->
-      <multi:listOfSpeciesFeatures multi:relation="and">
+      <!-- [v1] AND NOT([v3] and [v5]) -->
+      <multi:listOfSpeciesFeatures>
          <multi:speciesFeature multi:speciesFeatureType="fA" multi:occur="1"
-            multi:component="st_A">
+            multi:component="sti_A">
             <multi:listOfSpeciesFeatureValues>
-               <multi:speciesFeatureValue multi:value="fa1" />
+               <multi:speciesFeatureValue multi:value="v1" />
             </multi:listOfSpeciesFeatureValues>
          </multi:speciesFeature>
-         <multi:subListOfSpeciesFeatures multi:relation="not">
-
-            <multi:speciesFeature multi:speciesFeatureType="fB" multi:occur="1"
-               multi:component="sti_B">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fb1" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
-            <multi:speciesFeature multi:speciesFeatureType="fC" multi:occur="1"
-               multi:component="sti_C">
-               <multi:listOfSpeciesFeatureValues>
-                  <multi:speciesFeatureValue multi:value="fc1" />
-               </multi:listOfSpeciesFeatureValues>
-            </multi:speciesFeature>
+         <multi:subListOfSpeciesFeatures multi:id="sf_B" multi:relation="not" multi:component="sti_B">
+	         <multi:speciesFeature multi:speciesFeatureType="fB1" multi:occur="1">
+	            <multi:listOfSpeciesFeatureValues>
+	               <multi:speciesFeatureValue multi:value="v3" />
+	            </multi:listOfSpeciesFeatureValues>
+	         </multi:speciesFeature>
+	         <multi:speciesFeature multi:speciesFeatureType="fB2" multi:occur="1">
+	            <multi:listOfSpeciesFeatureValues>
+	               <multi:speciesFeatureValue multi:value="v5" />
+	            </multi:listOfSpeciesFeatureValues>
+	         </multi:speciesFeature>
          </multi:subListOfSpeciesFeatures>
       </multi:listOfSpeciesFeatures>
       <multi:listOfOutwardBindingSites>

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/kappa_introduction_syntax.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/kappa_introduction_syntax.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/kappa_introduction_syntax.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -2,6 +2,8 @@
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
    xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" multi:required="true">
 
+   <!-- Note: this example is for the purpose of demonstration; it is not a complete model-->
+    
    <model name="An Introduction to Kappa Syntax">
       ...
       <!-- speciesType -->
@@ -10,7 +12,7 @@
          <!-- A:Site1 -->
          <multi:bindingSiteSpeciesType multi:id="st_A_Site1">
             <multi:listOfSpeciesFeatureTypes>
-               <multi:speciesFeatureType multi:id="phosphorylation">
+               <multi:speciesFeatureType multi:id="phosphorylation" multi:occur="1">
                   <multi:listOfPossibleSpeciesFeatureValues>
                      <multi:possibleSpeciesFeatureValue multi:id="U" />
                      <multi:possibleSpeciesFeatureValue multi:id="P" />
@@ -111,4 +113,4 @@
          ...
       </listOfReactions>
    </model>
-</sbml>
\ No newline at end of file
+</sbml>

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/simmune_Ecad.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/simmune_Ecad.xml	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/examples/simmune_Ecad.xml	2020-03-27 23:53:49 UTC (rev 26298)
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
    xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" multi:required="true">
+    
+   <!-- Note: this model has been validated against multi validation rules without errors -->
+    
    <model name="E-cadherin_mediated_adhesion">
 
       <!-- Definitions -->
@@ -498,4 +501,4 @@
          </multi:intraSpeciesReaction>
       </listOfReactions>
    </model>
-</sbml>
\ No newline at end of file
+</sbml>

Modified: trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/intro.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/intro.tex	2020-03-27 23:47:56 UTC (rev 26297)
+++ trunk/specifications/sbml-level-3/version-1/multi/spec/latex_src/intro.tex	2020-03-27 23:53:49 UTC (rev 26298)
@@ -6,7 +6,7 @@
 \section{Introduction}
 \label{def:Introduction}
 
-This Multistate, Multicomponent and Multicompartment Species (Multi) package provides an extension of \SbmlLevelThreeWC\ that supports encoding \smodels\ with molecular complexes that have multiple components and can exist in multiple states and in multiple \compartments. One of its goals also is to provide a platform for sharing \smodels\ based on the specifications of bi-molecular interactions and the rules governing such interactions [\cite{ref:simmune2012, ref:scienceSignaling2006, ref:FeretPnas2009, ref:modeler2013}]. This specification covers the goals and features described in \multiOneProposalWC\ for extending SBML to carry the information for \textit{multistate multicomponent} \species\ with revised data structure. In addition, this specification includes the feature for \textit{multicompartment} \species\ as described in the releases of the Multi proposal [\cite{ref:multiproposal280}, \cite{ref:revisedMulti}].
+This Multistate, Multicomponent and Multicompartment Species (Multi) package provides an extension of \SbmlLevelThreeWC\ that supports encoding \smodels\ with molecular complexes that have multiple components and can exist in multiple states and in multiple \compartments. One of its \mBlockChangedBegin{\revTwentyTwentyMarch}goals is\mBlockChangedEnd{\revTwentyTwentyMarch} to provide a platform for sharing \smodels\ based on the specifications of \mBlockChangedBegin{\revTwentyTwentyMarch} molecular transformations/interactions and the rules governing such reactions\mBlockChangedEnd{\revTwentyTwentyMarch} [\cite{ref:simmune2012, ref:scienceSignaling2006, ref:FeretPnas2009, ref:modeler2013}]. This specification covers the goals and features described in \multiOneProposalWC\ for extending SBML to carry the information for \textit{multistate multicomponent} \species\ w...
 
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