Coding Phase Week 1

“Physics is the universe’s operating system.”
                                                                        — Steven R Garman

Coding phase has started. This week I have assigned a task to use lmfit (https://jugit.fz-juelich.de/mlz/lmfit) c implementation to design a plugin which can be used as an optimizer and can be loaded by the class loader I have designed. I need to do some edit to get a working build from source in windows. I am looking forward to adding the class loader designed by me in the libroadrunner by changing the cmakelist and swig interface.

On my last meeting when we are talking about the optimizer I felt that I need to have a good knowledge of the nonlinear least squares problem to have a better understanding of the project. So, I will devote a separate time to gain some knowledge about optimizer which will be beneficial at the later stage of the project.

This week is going to be a bit hectic because I have lots of tasks to do. I am currently focusing on developing a general interface for the project. I have referred the rrplugin interface for it. Having a general interface is very important.

In the process of GSoC, I am learning lots of new things. At last, I think GSoC is all about gaining practical knowledge and contributing to the open source organization. Will update the progress in the next subsequent blogs. 

Comments

Post a Comment

Popular posts from this blog

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

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

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