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Team:Heidelberg/OpenSource
From 2013.igem.org
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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> | <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/9/9b/Heidelberg_SBOLlogo_-_no_text.png" style="width:100%"></div> | ||
<div class="col-sm-10 jumbotron"> | <div class="col-sm-10 jumbotron"> | ||
| - | 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: | + | We fixed <a href="https://github.com/SynBioDex/libSBOLc/pull/1">two bugs in libSBOLc</a>, the reference implementation of the <a href="http://www.sbolstandard.org/"Synthetic Biology Open Language standard</a>, which we use in the NRPSDesigner C++ command-line executable for output of the designed NRPSs: |
<ul> | <ul> | ||
<li>We fixed compilation of Python bindings and unit tests.</li> | <li>We fixed compilation of Python bindings and unit tests.</li> | ||
<li>We fixed a crash occurring when changing the description of a DNAComponent.</li> | <li>We fixed a crash occurring when changing the description of a DNAComponent.</li> | ||
</ul> | </ul> | ||
| - | Additionally, we fixed <a href="https://github.com/SynBioDex/libSBOLpy/pull/1">a bug in libSBOLpy</a>, the Python wrapper to libSBOLc: | + | Additionally, we fixed <a href="https://github.com/SynBioDex/libSBOLpy/pull/1">a bug in libSBOLpy</a>, the Python wrapper to libSBOLc, which is used by the NRPSDesigner web interface: |
<ul> | <ul> | ||
<li>A memory leak due to the C object not being deleted upon destruction of the Python object.</li> | <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> | <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/e/e7/Heidelberg_antismash.png" style="width:100%"></div> | ||
<div class="col-sm-10 jumbotron"> | <div class="col-sm-10 jumbotron"> | ||
| - | 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: | + | 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 <a href="http://www.secondarymetabolites.org/">Secondary Metabolites Analysis Shell</a>, NRPSDesigner's backend for NRPS domain recognition and substrate specificity prediction: |
<ul> | <ul> | ||
| - | <li> | + | <li>Maximal overlaps between domains were not computed correctly.</li> |
</ul> | </ul> | ||
<blockquote class="twitter-tweet"><p>Just merged the first pull request to <a href="https://twitter.com/search?q=%23antiSMASH2&src=hash">#antiSMASH2</a>. Someone found a bug and fixed it for us. <a href="https://twitter.com/search?q=%23OpenSource&src=hash">#OpenSource</a> is awesome!</p>— Kai Blin (@kaiblin) <a href="https://twitter.com/kaiblin/statuses/381650799249481728">September 22, 2013</a></blockquote> | <blockquote class="twitter-tweet"><p>Just merged the first pull request to <a href="https://twitter.com/search?q=%23antiSMASH2&src=hash">#antiSMASH2</a>. Someone found a bug and fixed it for us. <a href="https://twitter.com/search?q=%23OpenSource&src=hash">#OpenSource</a> is awesome!</p>— Kai Blin (@kaiblin) <a href="https://twitter.com/kaiblin/statuses/381650799249481728">September 22, 2013</a></blockquote> | ||
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<div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/7/72/Heidelberg_Gibthon2.0beta.png" style="width:100%"></div> | <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/7/72/Heidelberg_Gibthon2.0beta.png" style="width:100%"></div> | ||
<div class="col-sm-10 jumbotron"> | <div class="col-sm-10 jumbotron"> | ||
| - | 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: | + | We fixed <a href="https://github.com/haydnKing/Gibthon/pull/36">a bug in Gibthon</a>, the <a href="http://gibthon.org/">Gibson assembly protocol designer by iGEM Cambridge 2010 and 2011</a>, used within the NRPSDesigner for plasmid and primer design: |
<ul> | <ul> | ||
<li>Import of BioBricks from the PartsRegistry did not work.</li> | <li>Import of BioBricks from the PartsRegistry did not work.</li> | ||
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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> | <div class="col-sm-2"><img src="https://static.igem.org/mediawiki/2013/5/52/Heidelberg_cobra.png" style="width:100%"></div> | ||
<div class="col-sm-10 jumbotron"> | <div class="col-sm-10 jumbotron"> | ||
| - | We fixed two bugs in | + | 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: |
<ul> | <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 17:54, 26 October 2013
Project
Notebook
Human Practice
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.
- 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.
Just merged the first pull request to #antiSMASH2. Someone found a bug and fixed it for us. #OpenSource is awesome!
— Kai Blin (@kaiblin) September 22, 2013
Great example why #opensource is awesome: @igem_heidelberg is using modified version of #antiSMASH2 in their project http://t.co/mdmT7YlBrJ
— Kai Blin (@kaiblin) October 21, 2013
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.
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.