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Team:Heidelberg/OpenSource
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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 | + | <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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| + | All of us are big fans of Open Source: The availability of the source code means that one can always check for the details and features that are not perfectly documented. What is more, similar to the spirit of iGEM and the Parts Registry, Open Source leads to great software by utilizing the potential of collaborative effort. Most of us are coding on a GNU/Linux operating system. Also, for our software project (NRPSDesigner), as well as our modeling, we continuously made use of available open source code, even from previous iGEM teams. In order to also give something back to the community, we improved several of the packages we used by sending pull requests. | ||
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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> | ||
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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 <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: | + | 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: |
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<li>We fixed compilation of Python bindings and unit tests.</li> | <li>We fixed compilation of Python bindings and unit tests.</li> | ||
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| - | We fixed two bugs in the <a href=" | + | 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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<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> | ||
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Latest revision as of 11:40, 28 October 2013
Project
Notebook
Human Practice
Open Source. Because FLOSS is Awesome.
All of us are big fans of Open Source: The availability of the source code means that one can always check for the details and features that are not perfectly documented. What is more, similar to the spirit of iGEM and the Parts Registry, Open Source leads to great software by utilizing the potential of collaborative effort. Most of us are coding on a GNU/Linux operating system. Also, for our software project (NRPSDesigner), as well as our modeling, we continuously made use of available open source code, even from previous iGEM teams. In order to also give something back to the community, we improved several of the packages we used by sending pull requests.
We fixed two bugs in libSBOLc, the reference implementation of the Synthetic Biology Open Language standard, 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.
