Project-ModelPolisher: GSoC 2019

Greetings! This blog contains work done in week 4 and 5. It can be noticed that till week 3 I had completed most of the work in the background, updating Matlab Parser was still left, but neither had I pushed my code, nor did I check my code with ample test cases. Not directly working with the codebase is easy, but once the concept is understood and is clear, it is really desirable to check it by adding to the actual codebase and very importantly get suggestions from the mentors. Week 4 was hectic and was spent on adding all the work to the codebase and solving the Matlab parser issue. Here is a short detail about each issue and its solutions, solved in evaluation 1: Extend ModelPolisher annotation capability ( #39 , #41 ) : Issue: Add feature in ModelPolisher to add annotations to species, reactions, and geneProducts which do not have Bigg Ids. Solution: For species, reactions, geneProducts already some annotations, we can map the annotation URIs to their BiggIds.  Det...

Greetings! As I have not posted the blog for week 2, thus this blog will contain all the progress made in the project during week 2 and 3 both. In the first week, I had majorly completed learning Postgresql and JDBC which prove to be of very much use in these two weeks. Also, there were major discussions regarding change of focus for this project, as proposed by Matthias Koenig, which I will cover here. The milestone for the evaluation one focuses on extending the ModelPolisher annotation capabilities for models and elements of models which do not have proper BiGG Id( issue #39 ). It's obvious that we need some data from that element to map it to its BiGG Id. It was finalized to use the data present in the form of annotation in the ModelPolisher and map it down to BiGGId of the particular data (to the best of my current knowledge, that was the only way of getting the BiGG Id). For example, the annotations may contain one or more references like  http://identifiers.org/cheb...

Greetings! 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 ...