Starting Google Summer of Code 2020

-

Hi,

I am Hemil Panchiwala, 2nd year CSE student at the Indian Institute of Technology, Roorkee, India. I am incredibly excited to share that I was selected in the Google Summer of Code (GSoC) this year with the National Resource for Network Biology (NRNB) as a mentoring organization. I will be working on the project "Simulation of system biology models in Java: support for new features" in this program. I am incredibly thankful to the wonderful mentors, namely Dr. Andreas Dräger, Dr. Matthias König, Mykola Zakharchuk, and Shalin Shah, who helped me to get selected and will guide me throughout this project.

This blog series is dedicated mainly to share my progress for the project. The official coding period starts from 1st June, and the community bonding period has currently begun. In this period, I will be exploring the codebase with solving some small issues and will discuss the implementation details with the mentors and finalize them.

What is NRNB?

The aim of the National Resource for Network Biology (NRNB) to advance the new science of Biological Networks through analytic tools, visualizations, databases, and computing resources. Biomedical research is increasingly dependent on knowledge of biological networks of multiple types and scales, including gene, protein and drug interactions, cell-cell and cell-host communication, and vast social networks. Our technologies enable researchers to assemble and analyze these networks and to use them to understand better biological systems and, in particular, how they fail in disease. You can learn more about it by visiting http://nrnb.org/.


About the Project - SBSCL

My GSoC project is based on issue #141, and the repository is currently present at this link.

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. This library is based on the JSBML project and can be used on every operating system for which a Java Virtual Machine is available. Please note that this project does not contain any user interface, neither a command-line interface nor a graphical user interface. This project has been developed as a pure programming library. To support the MIASE effort, it understands SED-ML files. Its abstract type and interface hierarchy facilitate the implementation of further community standards, such as CellML.

In this project, I will be working on to update SBSCL to support the SBML Version 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, the BioModels as well as the BiGG Models database, and updating the documentation for the SBSCL repository. The complete details about my project can be found in my project proposal.



For any discussions, please contact me here:

E-Mail: hemilmodi54321@gmail.com

    hpanchiwala@cs.iitr.ac.in


Regards!

Location: Ahmedabad, Gujarat, India

Comments

Post a Comment

Popular posts from this blog

GSoC Week 10

-
Image
This week I mainly worked on adding the support of the stochastic simulation to SBSCL. And, it is excellent that the simulation is giving great results with most tests passing. This addition of stochastic simulation has improved SBSCL supporting most of the simulation types now, which makes it a fully-featured simulation library. Now, here’s the summary of the work done this week with the topics discussed in the meeting: Mentors suggested writing the work done overview of the week before some hours of the meeting so that they can go through and provide their views in the meeting properly. We then mainly discussed the stochastic simulation implementation (using FERN) and the runtime due to simulating many times to get the mean and standard deviation. We decided to test all the models from the stochastic test suite and update the result format according to the test suite results. I worked on this mainly, and now the output format of the result is updated. The new test file StochasticTest
Read more

GSoC Week 11

-
Last week, I mainly worked on passing the current failing stochastic tests and ran Travis CI successfully. With this, we also started working on refactoring the SBMLinterpreter class, which has become quite a big class doing many things. Here is the quick summary of the updates from the weekly meeting with the work updates: In the meeting, we mainly discussed the failing stochastic tests. We decided to work on them and check whether the results were converging towards the pre-defined results on increasing the number of simulations or not. If they don't, then it was for sure that there is some issue in the implementation. So, I started working on that, and the small issue I found was that while comparing with the pre-defined results, the wrong column was considered from the pre-defined results, which made some tests fail. It is fixed now through this commit . After this, on further checking, we saw that some of the tests were like failing all the time regardless of the number of sim
Read more