Team:Heidelberg/OpenSource

From 2013.igem.org

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                <h1><span style="font-size:150%;color:#074E0B;">Open Source.</span><span class="text-muted" style="font-size:90%">Because FLOSS is awesome.</span></h1>
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                <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/9/9b/Heidelberg_SBOLlogo_-_no_text.png" style="width:100%"></div>
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                <div class="col-sm-10 jumbotron">
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                    We fixed <a href="https://github.com/SynBioDex/libSBOLc/pull/1">two bugs in libSBOLc</a>, the reference implementation of the Synthetic Biology Open Language standard:
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                    <ul>
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                        <li>We fixed compilation of Python bindings and unit tests.</li>
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                        <li>We fixed a crash occurring when changing the description of a DNAComponent.</li>
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                    </ul>
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                    Additionally, we fixed <a href="https://github.com/SynBioDex/libSBOLpy/pull/1">a bug in libSBOLpy</a>, the Python wrapper to libSBOLc:
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                    <ul>
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                        <li>A memory leak due to the C object not being deleted upon destruction of the Python object.</li>
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                <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/e/e7/Heidelberg_antismash.png" style="width:100%"></div>
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                <div class="col-sm-10 jumbotron">
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                    We fixed <a href="https://bitbucket.org/antismash/antismash2/pull-request/1/correctly-define-max-overlap-based-on/diff">a bug in antismash</a>, the Secondary Metabolites Analysis Shell:
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                    <ul>
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                        <li>Overlaps between domains were not computed correctly</li>
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                    </ul>
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                    <blockquote class="twitter-tweet"><p>Just merged the first pull request to <a href="https://twitter.com/search?q=%23antiSMASH2&amp;src=hash">#antiSMASH2</a>. Someone found a bug and fixed it for us. <a href="https://twitter.com/search?q=%23OpenSource&amp;src=hash">#OpenSource</a> is awesome!</p>&mdash; Kai Blin (@kaiblin) <a href="https://twitter.com/kaiblin/statuses/381650799249481728">September 22, 2013</a></blockquote>
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                    <blockquote class="twitter-tweet"><p>Great example why <a href="https://twitter.com/search?q=%23opensource&amp;src=hash">#opensource</a> is awesome: <a href="https://twitter.com/igem_heidelberg">@igem_heidelberg</a> is using modified version of <a href="https://twitter.com/search?q=%23antiSMASH2&amp;src=hash">#antiSMASH2</a> in their project <a href="http://t.co/mdmT7YlBrJ">http://t.co/mdmT7YlBrJ</a></p>&mdash; Kai Blin (@kaiblin) <a href="https://twitter.com/kaiblin/statuses/392329255335374848">October 21, 2013</a></blockquote>
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                    We fixed <a href="https://github.com/haydnKing/Gibthon/pull/36">a bug in Gibthon</a>, the Gibson assembly protocol designer by iGEM Cambridge 2010 and 2011:
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                    <ul>
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                        <li>Import of BioBricks from the PartsRegistry did not work.</li>
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                    Additionally, Gibthon's GenBank output was enhanced to contain fragment and primer annotations and SBOL output functionality was added.
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                <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/5/52/Heidelberg_cobra.png" style="width:100%"></div>
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                    We fixed two bugs in openCOBRA, the open source Cnstraints Based Reconstruction and Analysis toolbox:
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                    <ul>
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                        <li>SBML compatibility <a href="https://github.com/opencobra/cobratoolbox/pull/3">was improved.</a></li>
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                        <li><a href="https://github.com/opencobra/cobratoolbox/pull/4">Added check</a> for empty cells in the function that creates smaller, context-specific models out of global genome-scale metabolic models.</li>
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Revision as of 17:44, 26 October 2013

Open Source.Because FLOSS is awesome.

We fixed two bugs in libSBOLc, the reference implementation of the Synthetic Biology Open Language standard:
  • 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:
  • 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:
  • Overlaps between domains were not computed correctly
We fixed a bug in Gibthon, the Gibson assembly protocol designer by iGEM Cambridge 2010 and 2011:
  • 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 openCOBRA, the open source Cnstraints Based Reconstruction and Analysis toolbox:
  • 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.
Retrieved from "http://2013.igem.org/Team:Heidelberg/OpenSource"