Week 1: Build and Understand


Yesterday marked the ending of the first week of the coding period. At the start, I was quite overwhelmed with the codebase as for the first time I was working with software using mostly in-house libraries, and as I am not familiar with bio-informatics so I could not intuitively understand the purpose of various functions, which posed one of the biggest problems.

Following is the summary of proceedings in the first week:

Learning PostgreSQL and JDBC: As ModelPolisher is written in Java and for ModelPolishing it uses the BiGG Database, thus it is mandatory for one to have a good understanding of PostgreSQL Queries and Java Database Connectivity. This was one of the first tasks I completed this week.Meeting:Discussion on Code: As I was having trouble understanding the purpose of various functions, I asked my mentor, Thomas, for his help. Thomas arranged a meeting on 29 May, the following were discussed:Data-flow in ModelPolisher codebase and purpose of various functions in Bi…

Community Bonding Ends!


Yesterday, the community bonding period was completed. I feel excited and overwhelmed as I enter the coding period, though I am sure GSoC 2019 will prove to be a great opportunity in learning various technologies and contributing towards my first open-source project.

During the community bonding period, I had two meetings with the mentors, specifically in 17th and 26th May. The first meeting proceeded with our personal introductions and a small discussion about how and why the project was initially developed. This GSoC project will not only improve the ModelPolisher but provide inter-cultural work experience to the student and the mentors.

Also, the following guidelines will be followed in this project:
Use of GitHub Project tool for maintaining project workflow abstractly.Open a branch develop from current master.All the features and bug fixes will be added to this develop branch.After completion of a group of bug fixes or features, develop can be merged in master. In the …

Getting Started

Hello readers!
I am a CSE student at Indian Institute of Technology, Roorkee. I have recently been selected as a student in GSoC 2019 under the open source organization National Resource for Network Biology (NRNB). I will be working on the project - "Extending ModelPolisher to a universal annotation tool". I am really thankful to Google and NRNB for accepting my proposal and especially to my mentors Jun.-Prof. Dr Andreas Dräger, Dr Matthias König, Thomas Jakob Zajac who also helped me prepare the proposal. I look forward to learning extensively this summers. This blog series is dedicated to sharing my progress in the project throughout the GSoC period. As I will be working on ModelPolisher tool, here is a brief introduction of ModelPolisher and my project:
ModelPolisher is a tool which accesses BiGG Models Knowledgebase to annotate and autocomplete SBML models. My project aims towards extending ModelPolisher annotation capabilities for models lacking BiGG IDs, producing separat…