GSoC 2020: Simulation of systems biology models in Java

[HEMIL PANCHIWALA]

Dear all,

My name is Hemil Panchiwala, a 2nd-year undergraduate CSE student at the Indian Institute of Technology, Roorkee, India. I am currently participating in the Google Summer of Code 2020 with NRNB as a mentoring organization.

My project is “Simulation of systems biology models in Java: support for new features” mentored by Dr. Andreas Dräger, Dr. Matthias König, Mykola Zakharchuk, and Shalin Shah.

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

My project aims to update SBSCL. We aim

• to support the SBML Level 3 Version 2 and the FBC Version 3

• add the stochastic simulations in SBSCL

• improve support for the simulation of SBML models with comp extension

• testing SBSCL against the SBML Test Suite, BioModels Database as well as BiGG Models database, and

• update the documentation for the SBSCL repository.

More details about my project can be found in my proposal [Link].

Project Idea: https://github.com/nrnb/GoogleSummerOfCode/issues/141

GitHub repository: https://github.com/draeger-lab/SBSCL

Project Blog: https://gsoc20hemil.blogspot.com/

Thanks and regards

Hemil Panchiwala

[Miguel de Alba]

Hi Hemil,

that really sounds exciting. I have not heard of SBSCL before. Does it overlap with SED-ML or replaces it? It is really interesting for me as jlibsedml is not updated very often and having a simulation library with the same libraries and dependencies that SBML would be very handy.

Cheers,

Miguel

[HEMIL PANCHIWALA]

Hi,

Thanks for the greetings! SBSCL currently overlaps with SED-ML and its backend for SED-ML depends on the jLibSEDML library only. However, I think there is an open project for GSoC JSEDML(https://github.com/nrnb/GoogleSummerOfCode/issues/101) which once get developed can become an effective replacement for jLibSEDML.