Week 6 Update

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.


Comments

Post a Comment

Popular posts from this blog

COMBINE Notebooks GSoC Project Preparation

Image
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of various community standards and formats in systems biology and related fields. The goal of this project is to create several interactive Jupyter notebooks that showcase these standards and their libraries around one common theme; the repressilator model. More information about this project can be found on the Github issue ( https://github.com/nrnb/GoogleSummerOfCode/issues/192 ). I am preparing myself for this project and being mentored by  Dr. Matthias König . The first month of learning taught me some great things, some new and some known (e.g. the COMBINE structure, history, abstract and core ideas). I have gone through the following resources have reached a good understanding of the core ideas: COMBINE webpage: http://co.mbine.org/standards https://pypi.org/project/libsbgnpy/ (accessed 02-April-2022) https://pypi.org/project/python-libsbml/ (accessed 02-April-2022) https://p
Read more

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
Read more