The BEGINNING



Greetings!

So yesterday was my first official meeting with the mentors. I have four mentors assigned to my project, Matthias König and Andreas Dräger, the two main mentors of the project and Sarah Keating and Lucian Smith, as two backup mentors in case of any emergency due to COVID-19. The meeting was scheduled for May 14th, 15:30 UTC, and the objective was to discuss how am I expected to proceed in the project. This was the first time I was talking live with someone outside the Indian boundaries, so I was a little nervous. But as soon as we all (me, Andreas and Matthias. Sarah and Lucian were warmly invited for the meeting, but were not obligated to join it) entered in the live video, they made the atmosphere so light and familiar that I felt so easy talking with them. They first summarized the project, discussed why is that important and further instructed me on how should I start with it. I was first required to solve a few issues to get a more better insight, discuss with them the approach and finalize it, and finally, how should I go to update the codebase and make the pull request. They provided me some more resources and instructed on how should I contact them on slack or via email. I was also required to summarise the meeting which we are going to have every week so that if any mentor was unable to join one, he can follow it afterward. We agreed that it would be nice if I do so in the project's blogpost itself which I am going to write every week. So this is what I have done until now. Let me now give you a short description of my project.

About the Project

The Systems Biology Markup Language (SBML) is the main language for representation and exchange of computational models in biology. JSON is the main data format of the web. Currently, many issues exist with the JSON representation of SBML used by tools like cobrapy, escher, ModelPolisher or the BiGG database.

The idea of this project is to update the JSON scheme to have a full coverage of features important for constraint-based methods, i.e. SBML core and the additional SBML packages like fbc and groups. In addition, existing issues related to SBML-JSON will be solved. The project will be implemented as part of COBRApy with main focus on the following:

1. Annotation and meta-data support will be implemented.
2. Validation of JSON-SBML files will be performed.
3. Roundtripping SBML-JSON-SBML without information loss will be implemented.
4. JSON (SBML) scheme and scheme validation will be implemented.

Hence, a full-featured JSON exchange format for SBML will improve the web-integration and exchange of SBML models on web.

That's all for this blog.

Thanks you.
Location: Rewari, Haryana, India

Comments

  1. anweshaOctober 27, 2020 at 8:20 PM

    Hi!
    So I am trying to find projects for GSoC'21 and the tech stack of this project is familiar to me. So, can you suggest the future scope for this project. Like, a few improvements that I can do or features that I can add to it this year?

    ReplyDelete

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