| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| MONOSTABLE | 2016-08-25 | ||
| BISTABLE | 2016-08-25 | ||
| Readme.txt | 2016-08-27 | 2.6 kB | |
| CodeWorkFlow.pdf | 2016-08-25 | 16.6 kB | |
| Totals: 4 Items | 19.2 kB | 1 |
Read me.
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This code was developed by Dr. Luis U. Aguilera, it is part of the publication “A New Efficient Approach to Fit Stochastic Models on the Basis of High-throughput Experimental Data Using a Model of IRF7 Gene Expression as Case Study”, by Luis U. Aguilera, Christoph Zimmer and Ursula Kummer.
The packages available on this source code are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge. Please cite the original publication.
Description of the source code:
Here, we developed a method to fit stochastic simulations to experimental high-throughput data, meaning data that exhibits distributions. The method uses a comparison of the probability density functions that are computed based on Monte Carlo simulations and the experimental data. Multiple parameter values are iteratively evaluated using optimization routines. The method improves its performance by selecting parameters values after comparing the similitude between the deterministic stability of the system and the modes in the experimental data distribution. The programming strategy involved the binding of Copasi with Matlab to generate a fully automated source code.
Instructions to run:
- The code was tested and coded in Linux and Mac operative systems.
- To run it Matlab is needed as well as Copasi.
- To fit a monostable system go to MONOSTABLE folder.
- To fit a bistable system go to BISTABLE folder.
MONOSTABLE.
- Open MasterFunction.m and run it.
- This runs the method for the Model 1 given in the publication. Notice that the copasi files are needed, runScan and the folder with the synthetic data.
BISTABLE.
- Open function MasterFunctionGeneticAlgorithm.m
- To run it for a Random search select numberOfGenerations = 1.
- To run it for the Genetic Algorithm select numberOfGenerations >1.
- The provided copasi files are needed and runScan.
To have a better description of the method please see the following presentation:
https://www.youtube.com/watch?v=QborBxW6mnA&list=LL1wemS9gYM1ZG2FfiUf_A_Q&index=13
The following functions are used:
Yoder, N.: peakfinder. MATLAB Central File Exchange (2009)
Balkay, L.: FCS data reader. MATLAB Central File Exchange (2006)
In case of questions please contact me:
luisubald@gmail.com
