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Week 13 Update - Wrapping Up

This is the last week of Google Summer of Code. I am happy to share that we have met most of the goals outlined in our proposal. I am thankful to my mentor Dr. Matthias  König  for his guidance and supervision throughout the summer. I hope the NRNB community finds our project useful and I'll continue to be a part of the open-source world forever.  An update on the current project status: GSoC final submission is due before September 12 (Monday). Work submission guidelines are  here . We must move the complete code from the libsbml-notebook branch to the main branch. Github CI is failing. We need to sort it out. Combine archive created. Need review. LibOmexMeta - too complex; I think we can skip this. Hosting notebooks on google colab. Need review. Pending code tasks: CellML: Code written, some minor issues to discuss: math equations, the syntax for public_interface, and connections between two components. SBOL: Waiting for response from Gonzalo. Standard Code Status Jupyter noteboo
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Week 12 Update

We are in the final stretch of GSoC program.  Submitted abstract CellML: Code written, some minor issues to discuss: math equations, the syntax for public_interface, and connections between two components. Asked on the group list, no response yet. BioPax: Code complete, need help in saving the model. Jupyter notebooks: Created for SBML, SBGN, SED-ML, antimony, BioPax, SBMLutils. SBOL: Waiting for response from Gonzalo. Pending tasks:  Standard Code Status Jupyter notebook Validation code SBML Yes Yes Yes CellML Yes NeuroML SBGN Yes Yes SED-ML Yes Yes SBOL Antimony Yes Yes Yes BioPax Yes Yes SBMLUtils Yes Yes Yes Also, figure out LibOmexMeta and Archive .
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Week 11 Update

This past week we covered a lot of ground. I wrote an abstract for presenting a lightning talk at the ICSB Satellite event on COMBINE, to be held in Berlin, Germany in October this year.  Matthias confirmed that we can't use SBML2SBGN converter in its current form (issue: https://groups.google.com/g/sbml-discuss/c/x2thfIeL5l4 )  We continued work on CellML. (issues: https://github.com/cellml/libcellml/issues/1017  and https://github.com/cellml/libcellml/issues/1024 ) Basically, we can't figure out a way to code mathematical equations for repressilators using CellML. Biopax: issue -  https://github.com/indralab/pybiopax/issues/36  " The main issue on our side is to figure out which parameters to provide in the constructors, because all the kwargs are directed to parent (and grandparent, ... ) classes in combination with composition. " - Matthias Finally, I tried working on SBOL (issue: https://github.com/combine-org/combine-notebooks/issues/5  ) and created a POC for c
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Weeks 7 - 10 Updates

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A lot of progress has been made in the last 4 weeks.  cellml writing script for repressilator using libcellml on windows machine sbgn moved the python script into functions similar to the SBML added the nested glyphs Downloaded and tried the example:  http://sbfc.sourceforge.net/mediawiki/index.php/SBML2SBGNML  (SBML 2 SBGN conversion). Facing some issues, will discuss them in today's meeting. biopax installed python library trying to read an example file sedml python-libsedml library https://github.com/SED-ML/sed-ml/blob/master/specification/level-1-version-4/examples/repressilator/repressilator.xml
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Week 6 Update

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This past week I worked on writing a script for a repressilator using SBGN. It was interesting, as, besides the usual text output, I also utilized Newt editor to see a visual output of the repressilator. The next step is implementing SBML to CellML using antimony, and SBML to SBGN.
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Week 5 Update

In our last meeting, Dr. König and I discussed the implementation of CellML and NeuroML. I worked on CellML this past week but ran into issues while importing. I have been discussing this with the community, and it seems to be a rpath issue. I am hoping that it will be resolved in our today's meeting so that I can be back on track for the project.
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Week 4 Update

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I had a very productive weekly meeting with Dr. K ö nig last week. We finished setting up testing and continuous integration and completed the coding of repressilator using sbml. This week will focus on creating scripts using CellML and neuroml. 
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