Project-ModelPolisher: GSoC 2019

Greetings! As mentioned in the previous blog my targets for this week included: Test containerization completely. Add updates to README about containerization. Solve the  issue  of restructuring ModelPolisher. Open PR for the above tasks. Figure out and test queries for getting annotations from ADB. Complete integration of AnnotateDB . I was able to complete most of these tasks, here are the details: CONTAINERISATION:  The ModelPolisher is successfully containerized, and is available here currently. ModelPolisher has been divided into three containers/services, namely - BiGGDB, ADB, Java. The first two services host the respective databases with Postgres as base images, the third service with OpenJDK-11 as the base, is used to run ModelPolisher jar in a container. The containerization of ModelPolisher has been successfully tested by me. The ModelPolisher can now be run simply in two steps: Run `docker-compose up` Polish models using `docker-compose run...

The last meeting was held on Friday, 5th July. Unfortunately, I was not able to join the meeting due to a family emergency. I would like to thank Thomas for updating me with the discussions in the meeting. Discussion in the meeting (5 July) :  The core of AnnotateDB  is finished and is available as Docker containers. Probably, ModelPolisher will use the database by querying annotatedb as postgres database. AnnotateDB may be used in the future for BiGGID  resolution, and to annotate elements in models. Release versions of ModelPolisher maybe distributed on docker-hub in future. TestCode for current code of BiGGID resolution: Can set up a small DB instance, and fill it with the subset of data necessary from BiGG to query against, i.e. feed the data into the database in the test setup code (BeforeClass), test your code, remove them again in the tear-down phase (AfterClass). Some script creating the database might be necessary here. We can use a small model con...

Greetings! This blog details work done from 1st to 5th July, and issues to be addressed in next meeting. Progress this Week The issues in focus were: ModelPolisher updated to openjdk-11. Containerisation:  I tried to build a container for ModelPolisher which contains ModelPolisher jar, openjdk-11, postgreSQL, BiGG db(restored in potgreSQL). I was earlier trying to build docker image using docker-file, but I came across docker-commit, in which I made all the required changes in a ubuntu base image and committed the image to form a new one. This completely worked, this was a quick way but not good for shipping images. It will also cause the image's size to be very large and making a change in image would be much problematic in future. After trying these possibilities, I plan to write a docker-file to containerise docker by this weekend. Also. note that the image will be interactive and user will be able to give inputs and get outputs by mounting volume to the container...

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...