Constraint-based metabolic modeling has become an important computational method in biomedical research, to understand metabolism related disease mechanism, to predict potential new drug targets antimetabolites, and biomarkers of complex diseases, such as cancer. The rapid accumulation of genomic and proteomic data from large scale disease studies, such as the Cancer Genome Atlas (TCGA), provides an unprecedented opportunity for personalized metabolic modeling of large number of patient samples. The currently available metabolic modeling software, such as COBRA 3.0, requires substantial computing time conducting a metabolic modeling, which limits its applications in large scale genome-wide analysis.
The FastMM was designed to provide a easy-to-use and efficient toolbox for constraint meatolic modeling.
In FastMM, most of the time-cost functions of metabolic modeling are written by C. These functions including: flux variability analysis, genome-wide single gene knockout analysis, genome-wide double gene knockout analysis, genome-wide single metabolite knockout analysis, genome-wide double metabolite knockout analysis, and MCMC sampling.
The wrapper of FastMM was written by matlab/octave, and can be perferctly merged into COBRA 3.0 toolbox.
FastMM is 2~400 times faster than COBRA 3.0 in performing flux variability analysis and knockout analysis and returns consistent results. When applied to MCMC sampling, FastMM is also 10~15 times faster than COBRA 3.0.
Li, G., Dai, S., Han, F. et al. FastMM: an efficient toolbox for personalized constraint-based metabolic modeling. BMC Bioinformatics 21, 67 (2020). https://doi.org/10.1186/s12859-020-3410-4
The core programs of FastMM are independent, howerver, the matlab interface is dependent on the following software/toolbox:
1). Install MATLAB. MATLAB is the software environment for engineers and scientists. You can get detailed installation information by visiting http://www.mathworks.com/products/matlab/
2). Optional: Install Cobra toolbox in Matlab. Cobra toolbox is a matlab toolbox that used to implement metabolic modeling. Users can download and install this toolbox from: https://opencobra.github.io/cobratoolbox/
3). Optional(recommand): Install Gurobi optimizer MATLAB interface. Please download and install the latest Gurobi optimizer and set MATLAB interface. Users can download and install this toolbox from: https://www.gurobi.com/
4). Optional(recommand): Install Cplex optimizer MATLAB interface. Users can download the cplex from http://www-01.ibm.com/software/websphere/products/optimization/cplex-studio-community-edition/
To install FastMM, users just download FastMM and type the following command in matlab/Octave:
InstallAnd add the ./bin sub directory into your enriroment
Type the following command in matlab:
TestBasic use provide a regular one-command solution for efficient metabolic modeling. The user just configure the inputs in pars.txt and then type one commnand in matlab/Octave:
FastMMAll of the advanced functions of FastMM can be found in ./doc/FastMM_mannual.pdf