Matlab code files to get average of 100,000 MCMC samplings with CHRR algorithm
1. Analysis.m
--> In this code, you can operate 2. OperateGIMME.m and 3. averageAfterSampling.m.
2. OperateGIMME.m
--> Using GIMME function, this code makes RNA-seq data integrated model.
3. averageAfterSampling.m
--> There are 2 functions in this code; mcmc and averageAfterSampling.
When you operate averageAfterSampling function in 1. Analysis.m, it will first run
mcmc that operate 100,000 MCMC samplings with CHRR algorithm changing condition
of model and bounds of reaction.
After that, it will make structure taking average of MCMC sampling and name of reactions.
A xlsx file with original sampling values and the values normalized with Biomass value will be saved.
Song, Y., Lee, J. S., Shin, J., Lee, G. M., Jin, S., Kang, S., ... & Cho, S. (2020). Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei. Proceedings of the National Academy of Sciences, 117(13), 7516-7523.