Week 6

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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.
Issues to Address in upcoming meeting:
  • Removal of 'objective' from SBML if 'listOfObjective' not present: I was not able to find 'objective' in xml mentioned in issue. Need to discuss the issue with an example with the mentors. 
  • Test cases to check the mapping regarding issue #39, #41: Issue faced was that I was not able to figure out how to get instance of BiGG database in the test class.
  • AnnotatedDB: Discuss with mentors about where to exactly include mappings from AnnotatedDB.
    Also, integration of AnnotatedDB will be the most important issue I will try to solve in the upcoming week.

    Thank You!

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