#2 First Hangout Meeting

Last Tuesday, I had my first Hangout meeting with my mentors. Here's the recap:

• We completed the student-mentor agreement for GSoC, 2019, which was to be mailed to the org admin.
• Meanwhile, the mentors had a bit of a hard time pronouncing my name, as one can imagine, with the strong H sounds in Indian names!
• My mentors helped me set up the OfflineValidatorTests class, which would be required to test the tests I write!
• The run configuration of the Java class was updated with the directory path to the test files, the range of the test codes, and the filter 'xml'.
• The program was executed successfully for the layout package, but when we tried to run it with the configuration for spatial, it faltered and ran checks for core. 
• The problem was figured out by my mentor and was fixed the very next day.
• In the end, it was decided that we'll be meeting every Tuesday evening (IST). I also resolved a couple of doubts regarding the tests and with that, we concluded our meeting.

For the remaining time in the community bonding period, I decided to go through the implementations of constraints from other packages and try to resolve any issues I encounter along the way.

Till next time,

Cheers!

Starting Google Summer of Code, 2019

Hi all!

I am Bhavye Jain, and I am glad to share that I was selected to participate in Google Summer of Code (GSoC) this year, with the organisation National Resource for Network Biology (NRNB)! Many thanks to my mentors Nicolas Rodriguez, Thomas M. Hamm and Dr. Andreas Dräger for the guidance during this journey!

My proposal for this year's GSoC was titled "Validation of Spatial System Biology Models in Java" and the project can be viewed here. I intend to use this blog to share my progress on the project. The official coding period starts from 27 May, 2019 and currently, the community bonding period is underway. I'll try to utilize this period by interacting with my mentors and discussing the workflow of the project.

The Organisation

The aim of the National Resource for Network Biology (NRNB) is 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 better understand biological systems and, in particular, how they fail in disease. You can learn more about it by visiting http://nrnb.org/

The Project

My project is based on the GitHub issue #120 and I will be working on this GitHub repository. 

SBML is a machine-readable representation format, based on XML, for representing biological models. SBML can encode models consisting of entities (species) acted upon by processes (reactions). JSBML (Java^TM SBML) is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. An extension of SBML, called spatial processes (spatial), supports for describing processes that involve a spatial component and describing the geometries involved.

In this project, the Java implementation of the spatial modeling package for SBML will be updated and a full validation function will be implemented for this package. A well-built, predefined system for offline validation of SBML files already exists, and this project will enhance its capabilities. 

I shall be working in a phased manner to write the various ConstraintDeclaration classes for the validation rules provided in the latest specification of the spatial package. The skeleton code for writing a ConstraintDeclaration is provided in the documentation of JSBML, and several helper functions are available for use while creating the new classes. The details of the implementation can be viewed in my project proposal. During the last phase of the project, I will try to add new rules manually, which have not been explicitly listed in the specification, but can be extrapolated from the textual description of the classes in spatial package.

My mentors say that if I complete my project early, I might get a chance to work on something even more interesting! Let's hope I get through with my work timely enough to get to that part!

Till next time,
Cheers! :D