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nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
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Update JSON scheme and implementation for SBML #137

Closed matthiaskoenig closed 4 years ago

matthiaskoenig commented 4 years ago

Background

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. E.g.

https://github.com/opencobra/cobrapy/issues/706 https://github.com/opencobra/cobrapy/issues/720 https://github.com/opencobra/cobrapy/issues/736 https://github.com/opencobra/cobrapy/issues/856

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 fbc and groups. In addition existing issues should be solved (see above). The project will be implemented as part of cobrapy.

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

Goal

Update the cobra(py) JSON scheme and implementation. Existing issues should be fixed and a complete coverage of SBML core and the SBML fbc and SBML groups package should be implemented.

Difficulty Level X

The level is a basic bioinformatic project focusing on easy-to-medium skills, i.e., python and JSON.

Skills

JSON, Python (essential) SBML (nice to have)

Public Repository

https://github.com/opencobra/cobrapy https://escher.readthedocs.io/en/latest/index.html http://bigg.ucsd.edu/models

Potential Mentors

Matthias König

Contact

Matthias König

Hemant27031999 commented 4 years ago

Hi @matthiaskoenig , I'm Hemant from the Indian Institute of Technology, Roorkee, India. I find this issue quite interesting. I have gone through the listed issues of cobrapy and have got an insight of them. I have dig some of them quite deeper also, understanding where the issue actually points by discussing them with the members of cobrapy. If NRNB made it possible to GSoC this time, I would like to work on it.

But as there is some time left until the final GSoC list, I was thinking to have an understanding of SBML core and SBML packages which are a part of this project. Can you help me a little about where should I start with and what else can I do before that? Thanks.

Hemant27031999 commented 4 years ago

@matthiaskoenig , is this issue open for GSoC 2020?

matthiaskoenig commented 4 years ago

@Hemant27031999 Yes, I answered you via email.

dukkee commented 4 years ago

@matthiaskoenig Hello. Is this issue still open and without any interns?

matthiaskoenig commented 4 years ago

@dukkee We already have a student who is working on this issue and wrote a very good proposal. I would look for another issue

khanspers commented 4 years ago

Active project for GSoC 2020, closing here.