New Release of SBW 2.8.3

This is to announce the release of a new version of SBW (Systems Biology Workbench). To those who are not familiar with it, SBW is a collection of collaborating tools for carrying out simulations of biochemical networks.

Download here

The four main tools are Jarnac, JDesigner, ‘General Purpose Simulation Tool’ and the translators (eg Matlab). All tools can load and save SBML. The list below summarizes the changes in this latest release.

I am also glad to report that we will be receiving 4 more years of NIH support to continue the development of SBW. In particular we will be focusing in model reproducibility (in relation to SED-ML), model publishing in journals, full cross-platform support, version control and model change tracking. I will therefore be offering a number of positions in my lab to support this effort. If anyone is interested in modeling, SBML, visualization, programming and developing a single cross-platform tool with a plugin interface to consolidate SBW into one main tool, please get in touch at hsauro at u.washington.edu and I can send you further details.

Changes in Version 2.8.3
===========================

Jarnac:

- New graphing module now gives more control and smoother lines
- Changed augr and augc to take variable arguments
- Added new function, cv2m() to convert a vector to a matrix
- Added quick button to copy model to SBML (clipboard or file)
- Added option to display line numbers in editor
- Added simple find function to the editor
- Added two sample models that can be loaded from the menu

JDesigner

- Fixed typo Tablular to Tabular in tabular display
- Added scroll bar to HTML edit window
- When creating alias node, node is now placed near selected node
- The parameter list in the scan window woudl sometimes hold old parameter names,
due to a bug in serializing the edge objects
- i/o error 103 sometimes in saving selection lists, not sure if fixed
(difficult to reproduce) but try/finally blocks were not quite right which is now fixed
- Bug in commit parameter changes when paramter grid did not have focus
- Added ability to copy the results from the end of a time course
simulation to the model so that the state can be saved to file

SBML Layout

- limited support for libsbgn AF and ER

SBRML

- updated parsing of CSV files to support a wider variety of files

libSedML

- updated to latest changes,
- support for CellML,
- support for Validation

Simulation Tool

- updated to .net framework 4
- fix issue with the plugin system on some systems
- updated to iron python 2.7

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