GSoC 2020: Simulation of Systems Biology Models in Java

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...

This week I mainly worked on adding the support of the stochastic simulation to SBSCL. And, it is excellent that the simulation is giving great results with most tests passing. This addition of stochastic simulation has improved SBSCL supporting most of the simulation types now, which makes it a fully-featured simulation library. Now, here’s the summary of the work done this week with the topics discussed in the meeting: Mentors suggested writing the work done overview of the week before some hours of the meeting so that they can go through and provide their views in the meeting properly. We then mainly discussed the stochastic simulation implementation (using FERN) and the runtime due to simulating many times to get the mean and standard deviation. We decided to test all the models from the stochastic test suite and update the result format according to the test suite results. I worked on this mainly, and now the output format of the result is updated. The new test file StochasticTest...

This week I mainly worked on the remaining issues of the SBML Test Suite, which I described in my last blog with starting work on support for the stochastic simulations in SBSCL. Here’s a quick summary of the last week’s meeting with the updates of the work done: One of my mentors suggested refactoring the master branch to the main branch. But it has not yet been done as doing this causes some issues in GitHub pages. Complete updates can be found at issue #52 created for this purpose. We discussed issues related to the models having events with delays and saw that things were going fine, so the only way to find the issue was to debug the code. Similar was the problem with converting the Algebraic rule to Assignment rule. After not getting a proper reason, we mailed the developer, Alexander Dörr, who implemented the events with a delay in SBSCL. We have not received his response yet, so we decided to get on this issue later. Also, AlgebraicRuleConverter has some problem in converting t...

Last week, I successfully passed the first evaluations and was extremely happy to get the mail saying, ‘Congratulations! You have passed the first evaluation’. A big thanks to the mentors, especially Andreas and Matthias, for helping me throughout just from the beginning. Now, coming to the work done last week with the updates from the weekly meeting. There was an issue in GLPKSolver that its instance was not deleted after its usage, which gave a memory allocation error. This was an issue with the SCPSolver library, which we are using as a linear programming interface to solve FBC models. I resolved the error currently by making a temporary copy of the GLPKSolver in SBSCL with deleting the instance of GlpkSolver after its usage, which solved the issue. I also mailed Dr. Hannes Planatscher, the developer of SCPSolver, to resolve this issue in SCPSolver. He confirmed to solve this in the coming months till that we decided to keep the temporary class as a workaround for SBSCL. This issue ...

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...