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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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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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A lot has been fixed in this release — we still have a bit to go, though.

Most notably, the SBML import code should be more robust, and we’ve included the new adaptive simulation algorithms described here: http://link.aip.org/link/?JCPSA6/128/014103/1.

Please uninstall any old versions before installing this one.

Download here:
http://sourceforge.net/project/showfiles.php?group_id=203655&package_id=242861&release_id=592425

Report bugs here:
http://sourceforge.net/tracker/?atid=986464&group_id=203655&func=browse

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We’re under heavy development right now, and we’re finally at a place where we feel like it’s time to make a public beta release!

Version 0.9.2 is now available as a Windows binary installer as well as source code. The Windows installer takes care of all dependencies. Just run it and a new shortcut will appear in your Start Menu. The source code takes a little more work to get all the dependencies taken care of.

Without further ado, here is the download link:
http://sourceforge.net/project/showfiles.php?group_id=203655&package_id=242861

Please report all bugs here:
http://sourceforge.net/tracker/?atid=986464&group_id=203655&func=browse

Check back soon for more beta releases as we close in on 1.0.

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