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A paper on SynBioSS Designer has been published in Briefings in Bioinformatics. It can be found here: SynBioSS Designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

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1.0.1 has been uploaded to Sourceforge, fixing a few bugs.

All users should upgrade as there is a bug in the way the 1.0 handles gamma-distributed reactions. Such reactions will crash the simulator. This has been fixed in 1.0.1.

Also, 1.0.1 includes new versions of all supporting libraries, including:

  • Hy3S 1.1.5
  • libSBML 3.2.0
  • SymPy 0.6.2
  • NumPy 1.1.1
  • GTK+ 2.14.1

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We’ve been published in Bioinformatics. The paper version is still on it’s way, but the you can get advanced access to the article here: SynBioSS: The Synthetic Biology Modeling Suite.

If you prefer PDFs, here is the PDF version.

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I am happy to announce that we’ve finally hit 1.0!

SynBioSS DS 1.0 fixes all of the major bugs in the previous beta version. It now presents the chemical equation for each reaction as well as the reaction name. Additionally, SBML export is now fully supported.

So, go get the Windows installer!

The source code and versions for Linux and Mac will be up shortly.

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The steady creep towards 1.0 continues with 0.9.4.6.1.

The installer can be found here: SynBioSS DS Download at SourceForge.

Please download this and test it, so we can continue to get the bugs worked out.

In this release, the following have been fixed:

  • SynBioSS DS no longer crashes when a simulation is re-run.
  • Importing from a NetCDF model allows spaces in reaction and species names.
  • Modifying a reaction no longer creates a duplicate reaction.
  • The “Export Model” button is now active. This is primarily intended for users of Hy3S on supercomputers, as it allows you to save the .nc file necessary to upload.
  • The simulation progress bar no longer jumps all the way to done immediately.
  • The internal Hy3S is now at 1.1.4 — fixing a bug in the stoichiometry code when a species is both a product and reactant.
  • The GTK, GLIB, etc libraries have been updated to their latest versions.

Examples of models can be found on the main page.

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Released at Thu, 19 Jun 2008 22:24:11 GMT by tonyhill
Includes files: SynBioSS-DS-0.9.4.6.1-x86-SLED10_SP1.tgz (16398949 bytes, 0 downloads to date), SynBioSS-DS-0.9.4.6.1-x86-Ubuntu8.04.tgz (18791492 bytes, 0 downloads to date), synbioss-0.9.4.6.1.zip (84118 bytes, 0 downloads to date), SynBioSSDSInstaller-0.9.4.6.1.exe (15213889 bytes, 0 downloads to date)
[Download] [Release Notes]

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Released at Thu, 01 May 2008 19:13:26 GMT by tonyhill
Includes files: synbioss-0.9.4.5-src.zip (83813 bytes, 0 downloads to date), SynBioSSDSInstaller-0.9.4.5.exe (15327167 bytes, 5 downloads to date)
[Download] [Release Notes]

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Don’t use 0.9.4.1. I made a mistake in the compilation and then didn’t test it enough.

The simulation exececutables run out of memory very quickly and just crash.

0.9.4.3 should fix all of this.

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Released at Thu, 17 Apr 2008 19:07:12 GMT by tonyhill
Includes files: synbioss-0.9.4-src.zip (79297 bytes, 16 downloads to date), SynBioSSDSInstaller-0.9.4.1.exe (15428170 bytes, 0 downloads to date)
[Download] [Release Notes]

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0.9.3 is short-lived. Mostly due to severe bugs in the handling of Hy3S NetCDF files and the subprocess management.

0.9.4 is out now.

Click here to download SynBioSS DS.

Report SynBioSS DS bugs here.

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