COMBINE Notebooks GSoC 2022 Project

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 .

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 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