Pysces / News: Recent posts

I am pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS version 0.9.6.
This is mostly a bugfix release that adds SciPy 1.0 compatability.

I am pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS version 0.9.5.
This release contains new functionality and support for the PyscesToolbox

I am pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS version 0.9.3.

This release contains new functionality (response coefficients of moiety conserved cycles), bugfixes (assignment rules) and updates (SED-ML and COMBINE archive export)

Tracing regulatory routes in metabolism using generalised supply-demand analysis
Carl D. Christensen, Jan-Hendrik S. Hofmeyr and Johann M. Rohwer

http://www.biomedcentral.com/1752-0509/9/89

PySCeS 0.9.1

We are happy to release a new version of PySCeS. This release includes bugfixes, optimizations and extended support for COMBINE archives. More news on the PySCeS website (http://pysces.sourceforge.net)

PySCeS 0.9.0 has has been released

I am happy to announce a way overdue release of the Python Simulator for Cellular Systems (http://pysces.sf.net). This release has many bug fixes and introduces new functionality that includes:
- cross platform parallel parameter scanning (using iPython)
- generalized supply demand analysis
- exporting simulations as SED-ML, including COMBINE archives, (using libSEDML or web services)
- support for scanning moiety totals
- more flexible plotting support... read more

I am happy to announce a way overdue release of the Python Simulator for Cellular Systems (http://pysces.sf.net). This release introduces some new features, has many bugfixes and extends the PySCeS MDL to include new model types.

Enjoy
Brett G. Olivier

The PySCeS (http://pysces.sf.net) documentation is now also available on the Python Packages Site - http://packages.python.org/PySCeS/

I am happy to report that as of version 0.7.4 PySCeS natively builds and installs on an Apple running OS 10.6. Brett

I've cleaned up the package structure a bit. As a result it is now possible for me to build Ubuntu binary packages (try python-pysces-0.7.4-test.deb).

We are pleased to announce the PySCeS 0.7 release.

This release has many new features including: support for multi-compartment models, enhanced SBML support, a new plotting module and an almost complete overhaul of the core analysis algorithms.

We have also created all new Sphinx based documentation including new Users and Input File Guides and hope you have as much fun using this new PySCeS as much as we have had in creating it.... read more

We are extremely pleased to announce the next release of PySCeS - The Python Simulator for Cellular Systems (http://pysces.sourceforge.net)

This release introduces a number of enhancements and new features including:

- updated documentation (available from the PySCeS website or as a package download)
- the introduction of the distributed framework PySCeS/Kraken
- support for libSBML 3.0

Please take a look at the release notes and CHANGELOG file for more specific details of the new functionality and package structure. ... read more

We are extremely pleased to announce the next release of PySCeS - The Python Simulator for Cellular Systems (http://pysces.sourceforge.net)

This release introduces a number of significant changes to PySCeS include:
- use only NumPy and SciPy 0.5+ (available at http://scipy.org\)
- uses Matplotlib for interactive plotting and so no longer requires GnuPlot (http://matplotlib.sf.net)
- Removed dependencies on ScientificPython and Numeric.
- simplified build/installation process... read more

We are extremely pleased to announce the latest release of PySCeS - The Python Simulator for Cellular Systems (http://pysces.sourceforge.net)

Now available for download from SourceForge.net (https://sourceforge.net/project/showfiles.php?group_id=13917)

This release expands PySCeS functionality (Generic MultiParameter Scanner, Response Coefficient Analysis) contains some bugfixes (elementory modes) and introduces some new features that we are trying out (MCA attribute collection classes).... read more

Hi

I've recently moved all PySCeS code onto the SF subversion server and plan to update it as soon as new features are added, bugs fixed etc.

In this weeks update I've included alpha versions of two PySCeS contrib modules that can be used for visualisation (based on code from PySBML) and to access services provided by the Systems Biology Workbench (SBW).

Both these modules can be accessed as add-in modules (simply delete the relevant directories from pysces/contrib/ to uninstall) using the PySCeS module loader:
contrib = pysces.LoadContrib()... read more

We are extremely pleased to announce the latest release of PySCeS (the Python Simulator for Cellular Systems) now available for download from SourceForge (http://pysces.sourceforge.net).

The major change to PySCeS is that it can now be used with Numpy and new SciPy. We have implemented improvements to the model loading interface, as well as numerous bugfixes and minor improvements. PySCeS is now available via Subversion.... read more

We are extremely pleased to announce the latest release of PySCeS (the Python Simulator for Cellular Systems) now available for download from SourceForge (http://pysces.sourceforge.net) .

In this release, all methods have been provided with docstrings that explain: how to call the function, a basic description and an explanation of the arguments.

The PySCeS website has recently been updated and includes a documentation section with a new PyDoc generated "class reference" as well as other user manuals and referencing information: (http://pysces.sourceforge.net/documentation.html)... read more

We are extremely pleased to announce the latest release of the PySCeS (Python Simulator for Cellular Systems) available for download at http://pysces.sourceforge.net

This release includes:
- enhanced input file syntax
- improved SBML conversion/writing
- an updated structural analysis module

See the changelog for more information regarding this release and the release notes for the latest infomation on installing PySCeS. ... read more

We are happy to announce the release of the latest version of PySCecS (Python Simulator for Cellular Systems) available for download at http://pysces.sourceforge.net

This release includes:
- allowing the definition of forcing functions in the input file
- improved SBML export capabilites
- development of an extension framework for add-in modules

See the CHANGELOG for more information regarding this release. Enjoy!... read more

Hi
The PySCeS (http://pysces.sourceforge.net) documemtation has been updated to be compatible with PySCeS versions 0.1.5 and newer.

The PySCeS development team

Hi

We are happy to announce that the Python Simulator for Cellular Systems (PySCeS) version 0.1.5 has been released. This release adds Systems Biology Markup Language (SBML - http://www.sbml.org\) support as well as significant enhancements to PySCeS simulation capabilites. Many other functions and fixes have also been implemented.

The PySCeS development team.

Hi

I am pleased to announce the release of PySCeS-0.1.4 (http://pysces.sourceforge.net).

This release smooths out some bugs and adds some new functionality to the modelling and plotting classes

Brett

Hi

I am pleased to announce the release of PySCeS-0.1.3 (http://pysces.sourceforge.net).

This release smooths out some bugs and adds a Timer class. Upgrading from all older versions is strongly recommended.

Brett

I am happy to announce the next point release of PySCeS: the Python Simulator for Cellular Systems.

This release fixes some bugs, adjusts a few default values and adds some new functions, see the changelog for details.

PySCeS 0.1.1 has been released. This release adds a few new features and fixes a some bugs found in the initial release.