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 to Assignment rule and also does not get the proper variable to which the value has to be assigned using JSBML.

  • So, after not getting the proper reason for issues, we decided to add further improvements to SBSCL.

  • We first decided to start adding support for FBC Version 3, but as SBSCL is dependent on JSBML, JSBML needs to be compatible with FBC V3, which is not yet done.

  • So, we finally decided to start working on adding the support for stochastic simulation in SBSCL.

  • For stochastic simulation support, I had worked on the FERN repository to make it useful in SBSCL.

  • I merged the FERN repository to SBSCL, maintaining the GitHub history, and as FERN required some of the classes of SBSCL, I updated FERN to use updated classes from SBSCL and calculate the values.

  • Merging FERN to SBSCL required to solve some merge conflicts and clean the code that has now been done.

  • The first model from the stochastic test suite ran quite well, satisfying the test suite results by finding mean and standard deviations after simulating 10,000 times.


These are the main work updates of the week. It was quite great when the first model from the stochastic test suite ran quite well, which confirmed that FERN developed many years before, still ran well after some updates. The updated code with the merged FERN repository can be found at the fern branch in my forked repository.


Regards!

Location: Deesa, Gujarat, India

Comments

Post a Comment

Popular posts from this blog

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 sim
Read more

GSoC Week 10

-
Image
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
Read more

GSoC Week 15

-
Image
  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
Read more