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 t...

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...

Last week, I mainly worked on passing the current failing stochastic tests and ran Travis CI successfully. With this, we also started working on refactoring the SBMLinterpreter class, which has become quite a big class doing many things. Here is the quick summary of the updates from the weekly meeting with the work updates: In the meeting, we mainly discussed the failing stochastic tests. We decided to work on them and check whether the results were converging towards the pre-defined results on increasing the number of simulations or not. If they don't, then it was for sure that there is some issue in the implementation. So, I started working on that, and the small issue I found was that while comparing with the pre-defined results, the wrong column was considered from the pre-defined results, which made some tests fail. It is fixed now through this commit . After this, on further checking, we saw that some of the tests were like failing all the time regardless of the number of sim...

Hi, Continuing the work on the SBML L3V2 issues, this week was also focused mainly on solving the SBML L3V2 issues occurring while testing the SBML Test Suite models. Here’s a quick summary of the weekly work report with the meeting summary: In the last meeting, we mainly discussed the issues related to the SBML models with changing compartment size and on the implementation of the rateOf function.  Mentors suggested that the current implementation of rateOf (getting the values from the changeRate array of SBMLinterpreter class) does not seem a good way instead should calculate the derivatives in the rateOf method itself. It passes for the current models with rateOf as they are quite simple but may fail on complex models. We gave a lot of time of the week discussing the simulation of the SBML models with changing compartment size. We were not able to get the proper way how the SBML Test Suite calculated the results for these test cases. However this is not solved yet but you can gi...

Hi, This week was mainly focused on working to solve the issues of the SBML L3V2 encountered while simulating the SBML Test Suite using SBSCL. Out of 1809 tests from the SBML Test Suite (containing all the types and all the SBML levels and versions), about 57 SBML L3V2 tests fail. Here’s the complete summary of last week’s meeting with the work update during the week. In the meeting, mentors suggested making a pull request to the main SBSCL repository with all the information of work done till now, so they can review the work properly. As discussed, I made the PR #48 last Thursday. With this, the requested changes from the mentors have also been updated.  Mentors also suggested working on resolving the current SBML L3V2 issues this week rather than starting the work on support for FBC V3. We discussed adding the delay functionality to the rateOf function. I worked on adding this feature, and we had many discussions on this, but due to the problems in getting the delayed values of ...

Hi, As discussed in the last blog, I started working on my first milestone of adding support for the SBML L3V2 models to SBSCL. This blog contains a summary of the meeting with the new features I added and the issues I worked on and fixed this week to add SBML L3V2 support. So, let's quickly dive in summary: The main suggestion from the mentors in the meeting was that I should make GitHub issues for each of the new problems (similar problems in a single issue) I get and discuss them on GitHub. All new issues can be found at this link . We talked about issue #38 and found out that now that test case works fine (maybe I was making some mistake in the values earlier). Then, we discussed the issue that SBML L3V2 allows now for the reaction without reactants and products and currently got an issue for these models. But afterward, I found that there was only a warning that the model is without reactants and products. The issue was that rules were dependent on the kinetic laws and were i...

Hi, Last week, we had our first meeting after the coding period started on the 2nd of May. Again, excellent experience and discussed many new issues I encountered in the week. We mainly discussed the FBC (Flux Balance Constraints) issues where I paused in the last blog and the new problems I got in running the SBML Test Suite models. Here’s the  complete summary of the meeting with the weekly progress of work done: Continuing with the last blog, the first discussion we did was on resolving the FBC model issues. We found out that there was an issue in checking the namespace of the FBC model in JSBML. We opened a GitHub issue for the same in JSBML (issue #216 ). Currently, we resolved it by changing the method of getting namespace to getting the FBC package version until JSBML solves it [ Commit Link ]. The results of FluxBalanceAnalysis were somewhat scrambled up, which I made correct using a hashmap with key as reaction id and value as its flux. We decided to rename the CobraSolver...