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From: Mike H. <mh...@ca...> - 2003-04-20 07:01:21
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Dear SBW enthusiasts, SBW version 1.0.5 is now available for downloading from http://www.sbw-sbml.org. Most of the changes in this incremental release are minor bug fixes, but there is one new module that should be interesting to everyone: a spiffy new SBW Browser module written by Ben Kovitz. This module provides the ability to browse the SBW environment on a local host, inspect the modules and services available (much as Herbert Sauro's SBW Inspector for Windows does), and generate interface descriptions in different formats. It is portable to all architectures that SBW supports or will support in the future. Please try it out and let Ben know your comments. We are planning several feature enhancements to the SBW Browser in the near future. sys...@ca... |
From: Michael H. <mh...@ca...> - 2003-01-03 04:21:34
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TauLeapService is a module implementing Gillespie's Approximate Accelerated Stochastic Algorithm for chemically reacting systems. It is implemented as a service for SBW, and is supplied as source code and in binary form for MS windows. TauLeapService was written by Pieter van der Zee and is now available from the download page at http://www.sbw-sbml.org/sbw/software/index.html -- Mike Hucka, Ph.D. mh...@ca... Control and Dynamical Systems, MC 107-81 tel: +1.626.395.6911 Caltech, Pasadena, CA 91125, USA fax: +1.626.796.8914 Systems Biology Workbench: http://sbw.sourceforge.net |
From: Michael H. <mh...@ca...> - 2003-01-03 04:19:22
|
SBW release version 1.0.3 is now available for download. You can get it from the following locations: http://sourceforge.net/projects/sbw/ http://www.sbw-sbml.org/sbw/software/index.html Below is the list of changes in this release. === Version 1.0.3 === * The minimal installer for Windows now is much more minimal. It does not include any documentation, or debugging libraries. This reduces the size of the installer for people who only want to run applications with SBW and not do anything with SBW itself. * JDK 1.4 is now supported. * Ported "Gibson" simulator to Linux, and relaxed some of the checks for the kinds of rate laws allowed. It now allows constant rates, as well as other things, but it is not known whether this leaves the algorithm correct or not. Caveat modeler! * The C/C++ library had some bogosities related to how it determined the user's home directory and the SBW installation directory. These have been fixed. * A poor implementation of a network-related function in the Java libraries led to occasional failures on Windows systems to obtain the IP address of the machine. This caused all sorts of things to fail because SBW depends heavily on the IP address in order to name the directory where it stores runtime configuration files. The error manifested itself on Windows systems as applications not being able to connect to SBW. This particular problem should hopefully be fixed. * Dependencies should be handled much better by makefiles now, especially the C/C++ library under Linux. * The Perl library configuration attempted to install man pages and Perl-style "POD" documentation in system directories. These are typically not writable by non-root users on Unix-based systems, which lead to installation errors for most people. The makefiles are now fixed not to do that. * Makefiles should all now properly use $(MAKE) instead of 'make'. * The previous configure & Makefile setup failed to do a proper job of handling the configuration flags that let a user specify alternative locations of their Python and Numeric installations. The new scheme provides the following: --with-python=PATH The path to the Python executable. On Windows, this might be something like C:/Python22/python.exe. --with-python-includedir=DIR Adds the specific directory DIR to the list of include directories searched during compilation of the Python SBW library. This flag can be used multiple times. Here is an example of using this flag: --with-python-includedir=/home/mhucka/include/python2.2 --with-python-libdir=DIR Adds the specific directory DIR to the list of library directories used during compilation of the Python SBW library. This flag can be used multiple times. E.g.: --with-python-libdir=/home/mhucka/lib/python2.2/site-packages/Numeric Users who do not wish to use the Python library should configure with --disable-python. * Reorganized how doxygen is used to generate documentation for the C/C++ library. * Fixed bug in Broker, where it would hang if a client connected and immediately disconnected too fast for the Broker to set up its threads. -- Systems Biology Workbench team: http://sbw.sourceforge.net Control and Dynamical Systems, MC 107-81 tel: +1.626.395.6911 Caltech, Pasadena, CA 91125, USA fax: +1.626.796.8914 |
From: Michael H. <mh...@ca...> - 2002-08-20 23:02:10
|
MetaToolSBW is a wrapper around Stefan Schuster's MetaTool package. MetaTool provides a variety of functions, including facilities for computing elementary modes, null spaces and conservation vectors for an arbitrary network. MetaToolSBW can accept models from either MetaTool input files, or SBML Level 1 via the "NOM" provided with SBW. MetaToolSBW is now available from the download page at http://sbw.sourceforge.net/. -- Mike Hucka, Ph.D. mh...@ca... Control and Dynamical Systems, MC 107-81 tel: +1.626.395.6911 Caltech, Pasadena, CA 91125, USA fax: +1.626.796.8914 Systems Biology Workbench: http://sbw.sourceforge.net |