Update old plugins to Work in the current system

 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 = 0.38510152986871105  +/- 0.06085623193470731

k2 = 0.17874831118735468  +/- 0.020173064234737123.

It is not exact, but the optimization process is so fast. 

The graph of the experiment is 


Currently, I am looking forward to optimizing the parameter by skipping some species. 

Comments

Post a Comment

Popular posts from this blog

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 Earlier these plugins were not working due to outdated wrapper and some minor bugs. 3) Updated Python wrapper for r...
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 pas...
Read more

Provided all Libroadrunner functions to plugins using RoadRunner C API

We are completely driven by self-interest. In the last week, I realized that building everything from scratch will be reinventing the wheel and at some point in time we have to reuse someone else written code in our program. So, I thought to use rrplugins in my code and worked on how to remove the dependency of LibRoadRunner. As of now, I decided to provide plugins all roadrunner functions through a C API which is already built. Now the main problems lie in removing roadrunner dependency from the plugin loader. For which will discuss a solution with mentors tomorrow early morning. This week I understand some basic concepts which I missed in my class. The detailed difference between dynamic and static linking. A brief concept is in this link  https://www.geeksforgeeks.org/difference-between-static-and-shared-libraries/ .  Also in this Wuhan Corona Virus pandemic time due to my university will conduct my end semester exams. So I will be not be working on this project fro...
Read more