Team:Heidelberg/OpenSource

From 2013.igem.org

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                     We fixed two bugs in the <a href="http://http://opencobra.sourceforge.net/">COBRA toolbox for MATLAB</a>, the de-facto standard for constraints based modeling such as flux balance analysis (FBA) of genome-scale metabolic models, used in our project for modeling of delftibactin production and gold recycling:
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                     We fixed two bugs in the <a href="http://opencobra.sourceforge.net/">COBRA toolbox for MATLAB</a>, the de-facto standard for constraints based modeling such as flux balance analysis (FBA) of genome-scale metabolic models, used in our project for modeling of delftibactin production and gold recycling:
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                     <ul>
                         <li>SBML compatibility <a href="https://github.com/opencobra/cobratoolbox/pull/3">was improved.</a></li>
                         <li>SBML compatibility <a href="https://github.com/opencobra/cobratoolbox/pull/3">was improved.</a></li>

Revision as of 17:55, 26 October 2013

Open Source.Because FLOSS is awesome.

We fixed two bugs in libSBOLc, the reference implementation of the , which we use in the NRPSDesigner C++ command-line executable for output of the designed NRPSs:
  • We fixed compilation of Python bindings and unit tests.
  • We fixed a crash occurring when changing the description of a DNAComponent.
Additionally, we fixed a bug in libSBOLpy, the Python wrapper to libSBOLc, which is used by the NRPSDesigner web interface:
  • A memory leak due to the C object not being deleted upon destruction of the Python object.
We fixed a bug in antismash, the Secondary Metabolites Analysis Shell, NRPSDesigner's backend for NRPS domain recognition and substrate specificity prediction:
  • Maximal overlaps between domains were not computed correctly.
We fixed a bug in Gibthon, the Gibson assembly protocol designer by iGEM Cambridge 2010 and 2011, used within the NRPSDesigner for plasmid and primer design:
  • Import of BioBricks from the PartsRegistry did not work.
Additionally, Gibthon's GenBank output was enhanced to contain fragment and primer annotations and SBOL output functionality was added.
We fixed two bugs in the COBRA toolbox for MATLAB, the de-facto standard for constraints based modeling such as flux balance analysis (FBA) of genome-scale metabolic models, used in our project for modeling of delftibactin production and gold recycling:
  • SBML compatibility was improved.
  • Added check for empty cells in the function that creates smaller, context-specific models out of global genome-scale metabolic models.
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