GSoC 2020: Simulation of Systems Biology Models in Java

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...

Hi, We had our last meeting of the community bonding period last week on 26th May. As always, it was again great meeting the mentors. We discussed further on the issues of running the SBMLTestSuite tests and some other points with this. And, now the community bonding period has ended, and many new changes have been added to SBSCL. Here’s the summary of the work done in a week with the meeting: Continuing the discussion about the SBMLTestSuite tests from my last blog, we decided to compare the plots of the SBSCL simulator results with the pre-defined results and check the distances between them. For this, we decided to use the SBML Test Runner , a standalone desktop application with a GUI for controlling SBML-compatible applications and making them run test cases from the SBML Test Suite . I worked on this and made a wrapper for SBML Test Runner to run the tests using the SBSCL simulator. The documentation for how to work with SBML Test Runner has also been added to the INSTALL.md file ...