Second Evalutaion

Its's hard enough to find an error in your code when you're looking for it; it's even harder when you've ASSUMED your code is ERROR-FREE.

                                                                                                               - Steve McConnell
 I have successfully passed the second evaluation with a good remark as well from my mentor :). It feels proud when a mentor gives a strong positive remark on the ongoing project. 
For the second Evaluation, I was asked to provide a screencast of all build (with all the code that I have committed since the second evaluation). I used two very nice open-source software (Google Summer of Code creates a deep space inside developers for using Open source software). I used OBS studio ( If you want to use it refer to this https://www.howtogeek.com/183231/how-to-record-your-desktop-and-create-a-screencast-on-windows/  tutorial) to do screencast and used Handbrake for bit editing. Both are open-source software. GSoC teaches you to value open-source software and use it and also contribute to it.
This week I will mainly focus toward building swig wrapper of the whole code and give the final touch to cmake files. This week my classes will start as well so it will be very hectic this last month of GSoC. Hope it helps me to reach the next level of my capabilities. Since now participating in GSoC was a great experience and I learned a lot of things in this phase.


Comments

Post a Comment

Popular posts from this blog

Monte Carlo Bootstrap

Image
 The main work of Monte Carlo is to " Get some confidence   estimates".   The Monte Carlo plugin is used to obtain estimates of the confidence limits for a model’s parameters. This is in the context where experimental data exists and a parameter minimization method, such as Levenberg-Marquardt or Nelder-Mead has already been used in order to find a parameter minimum. The Monte Carlo algorithm is used subsequently at this minimum and will give an estimate of parameter confidence limits corresponding to the variance in the original experimental data. The plugin has properties such as the size of the Monte Carlo population, minimization algorithm to use (e.g. Nelder-Mead or Levenberg-Marquardt), and on output, confidence limits for each involved parameter. With some past updates, Monte Carlo is not working mainly due to the modifications in rrplugins and change of python version from 2.x to 3.x. I have modified the wrapper to let it work. Majorly the problem was with the passing
Read more

Update old plugins to Work in the current system

Image
 I have updated all the plugins ( https://github.com/sys-bio/rrplugins/tree/master/plugins/released ) working in the old system. Mostly they are not working because of the wrapper. When we pass a python string to C through CPython we need to it the format ctypes.c_char_p(String.encode('utf-8')) where String is the "string" we need to pass. Currently, the optimizer is not working if we need to fit the data by skipping any species. It is the first bad design I have seen in rrplugins. Now I am trying to port all the plugins from the old system to the new system.  One of the optimization example where I have to fit rate K1 and K2 based on species S1, S2, and S3 is:  Model: antimony_str = """ J1: S1 -> S2; k1*S1 J2: S2 -> S3; k2*S2    S1 = 1; S2 = 0; S3 = 0;  k1 = 0; k2 = 0;  """ The exact fitted value is k1 =0.45 and k2=0.15.  My output comes out to be  ChiSquare =  1.6501935363049038 Reduced ChiSquare =  0.017555250386222382 k1
Read more

End of GSoC 2.0

    My second innings of Google Summer of Code comes to an end. I have learned a lot of things. There is still some work left which I will complete after my exams. The link to my summer internship report is https://gist.github.com/debashish05/e1ec288a81d77e0fe61cbf336d147109 . I have learned a lot of things from my mentors and develop an inclination towards research. Works Done during this period: 1) RRPlugins have been integrated with Libroadrunner. So we don't require a separate build for rrplugins. Earlier this task was achieved in my last year project. But the problem is the change in roadrunner will force the plugins to need to rebuild, which is not the case now. 2) Build time will reduce since the plugins and roadrunner are not interdependent. Updated all the plugins (https://github.com/sys-bio/rrplugins/tree/master/plugins/released), in the current system. Earlier these plugins were not working due to outdated wrapper and some minor bugs. 3) Updated Python wrapper for rrplug
Read more