GSoC Week 12

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 at this…

GSoC Week 11

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 simula…

GSoC Week 10

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 StochasticTestSui…

GSoC Week 9

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 them …

GSoC Week 8

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 al…

GSoC Week 7

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 give a lo…

GSoC Week 6

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 derivati…