GSoC 2020: Simulation of Systems Biology Models in Java

  Last blog with the work updates of GSoC 2020 after nearly completing the great project with great people💖 (it was just awesome). Will be surely sharing my complete experience of GSoC in another blog. So, coming to the final updates made to SBSCL last week with the meeting updates, here are the points: As discussed in the last blog, I updated the complete documentation of the library using maven and also updated the website ( https://draeger-lab.github.io/SBSCL/ ). Also, updated the README by adding the description from the new features and other minor fixes. Made a pull request (PR #57 ) with all the documentation updates. Last week, we could not have a proper meeting due to internship tests at my university, and I had just met one mentor for 20 minutes talk. He suggested me to add some guidelines for using the library with the diagrams showing the workflow of the library. So, I added the UserGuidelines.md explaining how to simulate different models using SBSCL. I also added the s

Last week, I mainly worked on formatting SBSCL and making some small updates. We also merged the formatting PR to the main repository. Here’s the quick review of the weekly meeting with the updates made: In the meeting, we decided to merge the existing PR (with stochastic simulation updates) after updating the SBMLTestSuiteTest and StochasticTestSuiteTest to identify tests automatically and also add a check to verify that the file is valid sbml or not. This was updated to the repository adding a method isValidSBML() to check whether the file was valid SBML and also the functionality of detecting the .xml files from the directory given. After this update and some requested changes by mentors, the PR #54 was merged to the main repository with complete support of stochastic simulation. We then decided to update the formatting of SBSCL and add config files for IntelliJ and Eclipse so that developers can use any for formatting the library. The work for this was done in the sbscl-formatt

Getting into the last phase of Google Summer of Code 2020, I mainly worked last week on updating the stochastic simulations support to make use of the present SBSCL classes and refactored different things. The summary of the work done with the meeting updates are: Mentors suggested merging the refactor-interpreter branch to the fern branch as reviewing PR takes more time, and there is not enough time left and also, after this two more PRs (with formatting and documenting updates) needs to be made. This is now done and also the PR is quite ready to merge now with many updates made this week. BiGG models tests were completely ignored before from the Travis build which has now been fixed with some minor fixes also in FluxBalanceAnalysis that now simulates all the BiGG models successfully. Also, I added the reference results from cobrapy and compared the SBSCL results with them, and all the tests passed successfully that confirmed that SBSCL works excellent with the SBML models with fbc

Another great week and exciting news that I passed the second evaluations successfully😊. Again extreme thanks to the mentors ready to help and guide me at any moment. Last week, I mainly worked on refactoring the classes and enabling the feature of seeing processed results in realtime rather than waiting for complete simulation. Here’s the summary of the work done with updates from the weekly meeting: We discussed on the newly added class EquationSystem , which now has all the initializations from the SBMLinterpreter only left with the processing things. This now separates the things from SBMLinterpreter, which now makes it look more transparent and better than before. One of the mentors suggested refactoring various variables, comments, and methods in EquationSystem class more explanatory and proper as they didn’t seem to go better, which has now been updated. We also decided to make a PR with all the stochastic simulation updates ( fern branch in forked repo), and it is now open a