Week 4 Update

I had a very productive weekly meeting with Dr. König 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. 



Comments

Post a Comment

Popular posts from this blog

Week 6 Update

Image
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.
Read more

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 Co...
Read more

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...
Read more