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From: SourceForge.net <no...@so...> - 2012-02-24 00:45:53
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Support Requests item #3492571, was opened at 2012-02-23 16:45 Message generated for change (Tracker Item Submitted) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3492571&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Michael Hopkins (hopper333) Assigned to: Nobody/Anonymous (nobody) Summary: Build recommendations for Mac OS X Initial Comment: Hi all Having recently built an up-to-date SOSlib (the github version which I believe is 1.7.0 beta) I have some recommendations to make the process run smoothly. 1) use libSBML 3.4.1 and build from source because the two 3.4.1 binary installers availablel on SourceForge do not work on my 10.6.8 machine with up-to-date development tools. I built with libexpat but there are options for libxerces-c and libxml2 as well which I cannot comment upon. 2) use Sundials 2.3.0 and add the --enable-shared flag during configure or else you will get dynamic library loading errors when you run. 3) you might need 'autoconf' or perhaps 'autoreconf -i' to get the SOSlib 'configure' to work 4) there is a bug in the configure script that make one of the library search paths '/lib/'. You might need to add LDFLAGS='/usr/local/lib' if it doesn't already exist in the compiler call. Good luck! Michael ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3492571&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:49:22
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Support Requests item #2184251, was opened at 2008-10-21 04:53 Message generated for change (Comment added) made by raimc You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=2184251&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: java apai available? Initial Comment: Hello, I am writing a Java-based tool for biologists in our group wishing to run simulations and was wondering if there is a Java API binding to SOSLib - I noticed that CellDesigner and BioNessie both use Soslib and they're both Java based, but couldn't find anything on your site. Many thanks Richard Adams CSBE Group, University of Edinburgh ric...@ed... ---------------------------------------------------------------------- >Comment By: Rainer Machne (raimc) Date: 2012-02-15 06:49 Message: No, unfortunately we do not have a java api, but you may try to ask the developers of the mentioned software. Rainer ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=2184251&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:47:48
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Support Requests item #3487869, was opened at 2012-02-15 06:34 Message generated for change (Comment added) made by raimc You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3487869&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 5 Private: No Submitted By: Michael Hopkins (hopper333) Assigned to: Nobody/Anonymous (nobody) Summary: How do I get at the constants in the ODE models? Initial Comment: Hi I have looked around in the documentation and can't find the answer to this so I thought I would ask here. If I want to adjust constants in the ODE model specifications after they have been loaded, where can I find them? Are there functions for this or do I need to go inside data structures and adjust them 'manually'. Is there a specification of the internal ODE model data structure somewhere? Otherwise, which source files should I be looking in? TIA Michael ---------------------------------------------------------------------- >Comment By: Rainer Machne (raimc) Date: 2012-02-15 06:47 Message: see my previous comments, parameters and variables can be retrieved and set via the IntegratorInstance functions. Rainer ---------------------------------------------------------------------- Comment By: Rainer Machne (raimc) Date: 2012-02-15 06:46 Message: Hi Michael, the ODE Model structure itself only carries initial conidtions and initial parameter values. Actually set or retrieve current values for a simulation is done via the IntegratorInstance interface functions. This http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html may in part be outdated but most of the functions are available. Probably more then those! I guess, you have seen my previous message suggesting you use the latest version at github? it probably has more interface functions for you. In short: You need a VariableIndex which you can obtain via the ODEModel structure, then you can use this index to get and set variable or parameter values in any of the derived IntegratorInstance objects, e.g., via IntegratorInstance_getVariableValue (integratorInstance_t *engine, variableIndex_t *vi); The examples folder should have several example C programs for these interfaces. Thanks, Rainer ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3487869&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:46:28
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Support Requests item #3487869, was opened at 2012-02-15 06:34 Message generated for change (Comment added) made by raimc You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3487869&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Michael Hopkins (hopper333) Assigned to: Nobody/Anonymous (nobody) Summary: How do I get at the constants in the ODE models? Initial Comment: Hi I have looked around in the documentation and can't find the answer to this so I thought I would ask here. If I want to adjust constants in the ODE model specifications after they have been loaded, where can I find them? Are there functions for this or do I need to go inside data structures and adjust them 'manually'. Is there a specification of the internal ODE model data structure somewhere? Otherwise, which source files should I be looking in? TIA Michael ---------------------------------------------------------------------- >Comment By: Rainer Machne (raimc) Date: 2012-02-15 06:46 Message: Hi Michael, the ODE Model structure itself only carries initial conidtions and initial parameter values. Actually set or retrieve current values for a simulation is done via the IntegratorInstance interface functions. This http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html may in part be outdated but most of the functions are available. Probably more then those! I guess, you have seen my previous message suggesting you use the latest version at github? it probably has more interface functions for you. In short: You need a VariableIndex which you can obtain via the ODEModel structure, then you can use this index to get and set variable or parameter values in any of the derived IntegratorInstance objects, e.g., via IntegratorInstance_getVariableValue (integratorInstance_t *engine, variableIndex_t *vi); The examples folder should have several example C programs for these interfaces. Thanks, Rainer ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3487869&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:34:27
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Support Requests item #3487869, was opened at 2012-02-15 06:34 Message generated for change (Tracker Item Submitted) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3487869&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Michael Hopkins (hopper333) Assigned to: Nobody/Anonymous (nobody) Summary: How do I get at the constants in the ODE models? Initial Comment: Hi I have looked around in the documentation and can't find the answer to this so I thought I would ask here. If I want to adjust constants in the ODE model specifications after they have been loaded, where can I find them? Are there functions for this or do I need to go inside data structures and adjust them 'manually'. Is there a specification of the internal ODE model data structure somewhere? Otherwise, which source files should I be looking in? TIA Michael ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=3487869&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:20:53
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Bugs item #3487864, was opened at 2012-02-15 06:20 Message generated for change (Tracker Item Submitted) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=3487864&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: autotools compilation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Michael Hopkins (hopper333) Assigned to: Nobody/Anonymous (nobody) Summary: Current problems building 1.6 on OS X 10.6.8 Initial Comment: Hi all Just a compilation of previous OS X configure/build bugs that still appear to be present and undocumented, in case this helps anyone: (1) if the configure script gives this error ------------- configure: found SBML Library Version checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/Users/eva/Desktop/LibSBML/include -I/Users/eva/Desktop/LibSBML/include/sbml LDFLAGS= -L/Users/eva/Desktop/LibSBML/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 ----------------------------------- ...it might be because libxerces-c is not installed, not because it can't find libsbml or it's the wrong version. The configure script should be more precise about the reason for the error and should be able to solve this, especially when asked to configure with libexpat (2) you need to comment out any lines that include "malloc.h" in the source (FreeBSD also?) HTH Michael ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=3487864&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:18:02
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Support Requests item #1574416, was opened at 2006-10-10 04:29 Message generated for change (Comment added) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1574416&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Install Problem (example) Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: INstallation problem. Initial Comment: I am trying to install SBML ODE solver on a mac G5, with expat based libsbml, and sundials. I get the following message when running make after a succesful configuration. . DarwinHome:~/Desktop/SBML_odeSolver-1.6.0 ctf20$ make Making all in src if gcc -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver -I/usr/local/include - I/usr/local/include -I/usr/local/include/sbml -I. -MT integratorInstance.o -MD -MP -MF ".deps/integratorInstance.Tpo" -c -o integratorInstance.o integratorInstance.c; \ then mv -f ".deps/integratorInstance.Tpo" ".deps/integratorInstance.Po"; else rm -f ".deps/integratorInstance.Tpo"; exit 1; fi integratorInstance.c:47:20: error: malloc.h: No such file or directory make[1]: *** [integratorInstance.o] Error 1 make: *** [all-recursive] Error 1 DarwinHome:~/Desktop/SBML_odeSolver-1.6.0 ctf20$ Yours, Chrisantha ---------------------------------------------------------------------- Comment By: Michael Hopkins (hopper333) Date: 2012-02-15 06:18 Message: Still the case on OS X 10.6.8 in Feb 2012. You need to comment out all includes for "malloc.h" in the source. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1574416&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:06:24
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Bugs item #1807109, was opened at 2007-10-03 11:50 Message generated for change (Comment added) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 9 Private: No Submitted By: Eva (eva_1983) Assigned to: Nobody/Anonymous (nobody) Summary: Prolem Installing SBML Ode Solver on Mac Initial Comment: Hi all, I am trying to install SBML_odeSolver-1.6.0 on a Mac OSX 10.4.10. I already installed the libraries: Sundials 2.1.1 in: /Users/eva/Desktop/Code/sundials/lib and libSBML 2.3.5 in: /Users/eva/Desktop/LibSBML I tried to configure the SBML ODE Solver by: ./configure --with-libsbml="/Users/eva/Desktop/LibSBML" --with-sundials="/Users/eva/Desktop/Code/sundials/lib" But it does not find my SBML Library. Here is the output: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking build system type... powerpc-apple-darwin8.10.0 checking host system type... powerpc-apple-darwin8.10.0 checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for autoconf... /usr/bin/autoconf checking for aclocal... /usr/bin/aclocal checking for make... /usr/bin/make checking for ar... /usr/bin/ar checking for swig... swig checking for perl... /usr/bin/perl checking for SBML Library Version... expr: syntax error expr: syntax error expr: syntax error ./configure: line 4175: test: -eq: unary operator expected configure: found SBML Library Version checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/Users/eva/Desktop/LibSBML/include -I/Users/eva/Desktop/LibSBML/include/sbml LDFLAGS= -L/Users/eva/Desktop/LibSBML/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 Someone can please help me? Thanks, Eva. ---------------------------------------------------------------------- Comment By: Michael Hopkins (hopper333) Date: 2012-02-15 06:06 Message: I believe the error message is misinformation here; it probably can't continue because it can't find the other required library i.e. libxerces-c. This appears to still be the case on OS X 10.6.8 in Feb 2012, even when libexpat is installed and requested at the configure stage. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 14:02:06
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Bugs item #1575411, was opened at 2006-10-11 09:49 Message generated for change (Comment added) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1575411&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: autotools compilation Group: None Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: configure fails under Mac OS 10.4 Initial Comment: There are several issues compiling SOSlib under Mac OS X: The configure script does not correctly indentify the version of the installed SBML library. Replacing the filename suffix ".so" by ".dylib" in library file names in lines 4146 and 4148 is a possible workaround. Even after that, the configure script fails: configure: found SBML Library Version 2.3.4 checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/usr/local/include -I/usr/local/include/ sbml LDFLAGS=-L/sw/lib -L/usr/local/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 System information: Mac OS 10.4.8, libSBML 2.3.4 built with expat Bug submitted by Hendrik Fuss <fu...@ul...> ---------------------------------------------------------------------- Comment By: Michael Hopkins (hopper333) Date: 2012-02-15 06:02 Message: I can confirm that in Feb 2012 on OS X 10.6.8 this is still the case unless libxerces-c is installed. ---------------------------------------------------------------------- Comment By: Christoph Flamm (chfl) Date: 2006-11-23 03:11 Message: Logged In: YES user_id=1113720 Originator: NO removed libSBML version check from the configure process. added configure dispatch between xerces-c and expat. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1575411&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2012-02-15 13:59:55
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Bugs item #1510023, was opened at 2006-06-21 07:38 Message generated for change (Comment added) made by hopper333 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1510023&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Installation on Mac Os X 10.3 Initial Comment: Hi, I could not install the OdeSolver until I removed all includes for the malloc.h from the source code. But afterwards everything works fine. Might be the case for all FreeBSD systems. Best regards Marvin Schulz sch...@mo... ---------------------------------------------------------------------- Comment By: Michael Hopkins (hopper333) Date: 2012-02-15 05:59 Message: I can confirm that this is still the case on OS X 10.6.8 in February 2012. I guess it should be dealt with at the configure stage. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1510023&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2010-10-05 02:02:24
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Bugs item #3081242, was opened at 2010-10-05 11:02 Message generated for change (Tracker Item Submitted) made by alizeeshan You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=3081242&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: autotools compilation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Ali Zeeshan Ijaz (alizeeshan) Assigned to: Nobody/Anonymous (nobody) Summary: drawGraph compilation issue Initial Comment: after performing ./configure which completed well.. "make" gave this error: drawGraph.c: In function ‘drawModelTxt’: drawGraph.c:854: error: ‘ModifierSpeciesReference_t’ undeclared (first use in this function) drawGraph.c:854: error: (Each undeclared identifier is reported only once drawGraph.c:854: error: for each function it appears in.) drawGraph.c:854: error: ‘mref’ undeclared (first use in this function) drawGraph.c:885: warning: assignment from incompatible pointer type drawGraph.c:908: warning: assignment from incompatible pointer type ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=3081242&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2009-03-23 16:51:30
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Bugs item #2706607, was opened at 2009-03-23 16:51 Message generated for change (Tracker Item Submitted) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=2706607&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: autotools compilation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: installation failed when compiling drawGragh Initial Comment: ./configure passed well. When "make" drawGraph.c it complained in function 'drawModel': drawGraph.c: In function 'drawModel': drawGraph.c:606: error: 'ModifierSpeciesReference_t' undeclared (first use in this function) drawGraph.c:606: error: (Each undeclared identifier is reported only once drawGraph.c:606: error: for each function it appears in.) drawGraph.c:606: error: 'mref' undeclared (first use in this function) drawGraph.c:666: warning: passing argument 2 of 'Model_getSpeciesById' makes pointer from integer without a cast drawGraph.c:722: warning: assignment from incompatible pointer type drawGraph.c:765: warning: assignment from incompatible pointer type make[1]: *** [drawGraph.o] Error 1 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=2706607&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-10-21 11:53:07
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Support Requests item #2184251, was opened at 2008-10-21 11:53 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=2184251&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: java apai available? Initial Comment: Hello, I am writing a Java-based tool for biologists in our group wishing to run simulations and was wondering if there is a Java API binding to SOSLib - I noticed that CellDesigner and BioNessie both use Soslib and they're both Java based, but couldn't find anything on your site. Many thanks Richard Adams CSBE Group, University of Edinburgh ric...@ed... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=2184251&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-09-30 12:12:38
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Bugs item #2138052, was opened at 2008-09-30 13:18 Message generated for change (Comment added) made by raimc You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=2138052&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: time and delay in simplifyAST Initial Comment: simplifyAST in processAST.c,v 1.62 2008/09/24 14:10:10 looses AST_NAME_TIME types. Shouldn't 1923 ASTNode_setName(simple, ASTNode_getName(f)); be followed by ASTNode_setType(simple, ASTNode_getType(f)); (like in copyAST and indexAST)? ---------------------------------------------------------------------- >Comment By: Rainer Machne (raimc) Date: 2008-09-30 14:12 Message: Correct! This bug had been supressed until recently because sosLib explicitly interpreted nodes with names "time", "Time" or "TIME" as AST_NAME_TIME. This has been removed to strictly adhere to SBML definitions. Thanks for catching that! In CVS now. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=2138052&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-09-30 11:18:31
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Bugs item #2138052, was opened at 2008-09-30 11:18 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=2138052&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: time and delay in simplifyAST Initial Comment: simplifyAST in processAST.c,v 1.62 2008/09/24 14:10:10 looses AST_NAME_TIME types. Shouldn't 1923 ASTNode_setName(simple, ASTNode_getName(f)); be followed by ASTNode_setType(simple, ASTNode_getType(f)); (like in copyAST and indexAST)? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=2138052&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-05-30 19:16:28
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Bugs item #1979339, was opened at 2008-05-30 16:05 Message generated for change (Comment added) made by raimc You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1979339&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Michael Lawrence (larman) Assigned to: Nobody/Anonymous (nobody) Summary: sink reactions not supported? Initial Comment: When a reaction only has reactants, most SBML simulators treat them as a sink, i.e. they decrease the concentrations of the reactants, even though there are no products. It seems SOSLib does not do this. It would be nice if it did :) See HG in BIOMD0000000015 for an example. ---------------------------------------------------------------------- >Comment By: Rainer Machne (raimc) Date: 2008-05-30 21:16 Message: Logged In: YES user_id=1124477 Originator: NO was not a bug, but a misinterpretation of inorganic phosphate Pi for the constant pi during preprocessing of the SBML file. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1979339&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-05-30 14:05:43
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Bugs item #1979339, was opened at 2008-05-30 14:05 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1979339&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Michael Lawrence (larman) Assigned to: Nobody/Anonymous (nobody) Summary: sink reactions not supported? Initial Comment: When a reaction only has reactants, most SBML simulators treat them as a sink, i.e. they decrease the concentrations of the reactants, even though there are no products. It seems SOSLib does not do this. It would be nice if it did :) See HG in BIOMD0000000015 for an example. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1979339&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-05-06 09:54:09
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Bugs item #1951462, was opened at 2008-04-25 10:24 Message generated for change (Comment added) made by ch_li You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chen (ch_li) Assigned to: Nobody/Anonymous (nobody) Summary: Compartment size could be absent Initial Comment: Hello, I have a model, which compartment was not used by any species or reactions. For instance, in the model I attached, its species has intialAmount and hasOnlySubstanceUnits is TRUE. The whole model's reactions doesn't nothing with the compartment. For this model, it should be able to be simulated without given compartment size. Regards, Chen ---------------------------------------------------------------------- >Comment By: Chen (ch_li) Date: 2008-05-06 10:54 Message: Logged In: YES user_id=1712101 Originator: YES Hi, James, > Looks like SOSlib returns a fatal error message "No value found for > compartment cell" in this case? Yes, I got that error. In this model, all reactions do nothing with that compartment. It was there, only because species need to be defined in at least one compartment according to SBML spec. So in this case, my humble opinion is, SOSlib should not throw that error. Regards, Chen ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2008-04-28 09:50 Message: Logged In: NO hi Chen: Looks like SOSlib returns a fatal error message "No value found for compartment cell" in this case? BTW, it seems MathSBML integrates the model correctly, but it does so with the complaint that value for compartment is absent. James ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-04-28 08:50:31
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Bugs item #1951462, was opened at 2008-04-25 02:24 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chen (ch_li) Assigned to: Nobody/Anonymous (nobody) Summary: Compartment size could be absent Initial Comment: Hello, I have a model, which compartment was not used by any species or reactions. For instance, in the model I attached, its species has intialAmount and hasOnlySubstanceUnits is TRUE. The whole model's reactions doesn't nothing with the compartment. For this model, it should be able to be simulated without given compartment size. Regards, Chen ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2008-04-28 01:50 Message: Logged In: NO hi Chen: Looks like SOSlib returns a fatal error message "No value found for compartment cell" in this case? BTW, it seems MathSBML integrates the model correctly, but it does so with the complaint that value for compartment is absent. James ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-04-25 09:24:25
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Bugs item #1951462, was opened at 2008-04-25 10:24 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chen (ch_li) Assigned to: Nobody/Anonymous (nobody) Summary: Compartment size could be absent Initial Comment: Hello, I have a model, which compartment was not used by any species or reactions. For instance, in the model I attached, its species has intialAmount and hasOnlySubstanceUnits is TRUE. The whole model's reactions doesn't nothing with the compartment. For this model, it should be able to be simulated without given compartment size. Regards, Chen ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1951462&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2008-03-24 12:23:24
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Bugs item #1924288, was opened at 2008-03-24 13:23 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1924288&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: solver malfunction Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Gabriel Plantat (gabrieljps) Assigned to: Nobody/Anonymous (nobody) Summary: Only one timepoint Initial Comment: Hello, I have in fact two problems, and i think that i need the solution to only one of them :) I'm trying to install the verison 1.6.0 on a Kubuntu (Linux) operating system. I have installed the libsbml.2.3.4 (compiled with the expat library) and sundials.2.3.0 libraries in a local directory, and when i compile the SBML_odeSolver, it crashes. I have set the --with-libsbml option to the directory where the libraries are, and it produces the error: checking for SBML Library Version... expr: syntax error expr: syntax error expr: syntax error ./configure: line 4175: test: -eq: unary operator expected configure: found SBML Library Version checking correct functioning of SBML... yes ./configure: line 4278: test: -eq: unary operator expected checking correct functioning of SUNDIALS CVODE... no: CFLAGS=-g -O2 -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0//include LDFLAGS= -L/home/gabrieljps/trabajos/synthbio2/genetdes_3.0//lib LIBS= -lsundials_kinsol -lsundials_cvodes -lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm configure: error: Can not link to SUNDIALS CVODE Library If i change the directory to where the files .so are (the same directory with a /lib appended), it gives this error: checking for SBML Library Version... configure: found SBML Library Version 2.3.4 checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/include -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/include/sbml LDFLAGS= -Wl,-rpath,/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/lib -L/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 So i began using the 1.6pre version, which compiles. But doesn't seem to be working properly. I have tried the integrate exemple file with the MAPK.xml file, and when i expect all the results from the integration, it just gives me one time. I have printed the results->timepoints variable and it is set to 1. Even further, in this file the third parameter to be given is supposed to be the number of time steps, but if the number of steps is greater than the ending time, it crashes. On the contrary, if it is not, it doesn't, even if the number of steps is lower than 1 (0.1 for exemple)! Anyway, i have used the MAPK.xml file given as an exemple with the library, and i get only the initial conditions, and no other point of the integration. I think that if i can integrate the function or intall the 1.6.0 version, i will have the problem solved. Thank you for your help! Gabriel PLANTAT. Ecole Polytechnique's student. gab...@gm... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1924288&group_id=139893 |
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From: Rainer M. <ra...@tb...> - 2007-10-26 18:15:17
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Rainer Machne wrote: > ToDos before release: > > * libSBML has a completely reworked handling of SBML parse and > validation errors. These should be accomodated, in parallel to generally > stream-lining and refactor SOSlib error handling. > > * make objective function related structures independent of odeModel_t > structure > > * implement new features of SBML L2V3: > constraints, initialAssignments etc. > > * implement variable Compartment sizes I forgot: * test and submit the new excellent Swig and (so far) Perl bindings :) * finally check and repair odeSolverBatch function to fully cycle through varySettings Please tell us your requests and priorities for other things you'd like to see in the next release! Rainer |
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From: Rainer M. <ra...@tb...> - 2007-10-26 18:07:37
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Hi All, SOSlib has switched to libSBML 3.0.1, new code is in CVS now. Some minor bugs had to be fixed in libSBML. To avoid potential problems, you should thus preferably use the current CVS version of libSBML, but 3.0.1 should in principle also work. However, in the latter case DON'T use SBML Version 1 models, as these are not correctly translated (imho) in the 3.0.1 release of libSBML. I have not tested the 3.0.0 release. Also a well-hidden but potentially harmful bug of the compiled r.h.s functions for the sensitivity and adjoint solvers has been removed. Some equations where misinterpreted. The bug could have lead to wrong sensitivities for species with hasOnlySubstanceUnits=true, or for predefined rateRules. Feedback welcome. ToDos before release: * libSBML has a completely reworked handling of SBML parse and validation errors. These should be accomodated, in parallel to generally stream-lining and refactor SOSlib error handling. * make objective function related structures independent of odeModel_t structure * implement new features of SBML L2V3: constraints, initialAssignments etc. * implement variable Compartment sizes Rainer |
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From: Stefan M. <ste...@oe...> - 2007-10-19 11:00:01
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no. if it still works afterwards :) s Am Freitag, 19. Oktober 2007 10:17 schrieb Rainer Machne: > Hi, > > I plan to switch SOSlib code to libsbml 3.0.1 today. Any objections? > > Rainer > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: Rainer M. <ra...@tb...> - 2007-10-19 08:17:56
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Hi, I plan to switch SOSlib code to libsbml 3.0.1 today. Any objections? Rainer |
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