Archive for the “Development” Category


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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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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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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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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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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Released at Tue, 18 Apr 2006 19:32:29 GMT by hsalis
Includes files: Hy3S-1.1.2-win32.zip (2558123 bytes, 27 downloads to date), Hy3S-1.1.2-mac-intel.tgz (4199648 bytes, 5 downloads to date), Hy3S-v1.1.2-Linux-ia64.tar.gz (15889655 bytes, 42 downloads to date), Hy3S-v1.1.2.tar.gz (62111 bytes, 162 downloads to date)
[Download] [Release Notes]

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Released at Thu, 16 Feb 2006 23:20:45 GMT by hsalis
Includes files: Hy3S-v1.1.1-Linux-ia64.tar.gz (14533573 bytes, 8 downloads to date), Hy3S-v1.1.1.tar.gz (62104 bytes, 14 downloads to date)
[Download] [Release Notes]

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Released at Fri, 28 Oct 2005 16:50:42 GMT by hsalis
Includes files: Hy3S-v1.1-Linux-i686.tar.gz (2774567 bytes, 9 downloads to date), Hy3S-v1.1-Linux-ia64.tar.gz (13593481 bytes, 4 downloads to date), Hy3S-v1.1.tar.gz (57852 bytes, 14 downloads to date)
[Download] [Release Notes]

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