“Everything worthwhile and intelligent has already been thought. One can only try to think it over again.”  ----By Goethe

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1. Isotopomer Correction for TBDMS-amino acids based GC-MS data (a convenient Excel table for isotopomer analysis: you only need to paste the raw GC-MS data for unique m/z in yellow column, and the green column will be the isotopomer data after correction of natural abundance.) This method is not precise if total labeling enrichments are too high (>90%) or too low (<10%).

Alternatively, you can use an excellent isotopomer correction software developed by (Wahl et al., 2004). Based on this software, we built the isotopomer corrections for diverese derivatized metabolites. You can download the zip file MSTooL (contains MATLAB files and then run the command "MSCorr"). Note: to run this software, you have to use MATLAB version 2012 or older. We include isotopomer analysis templates for both free metabolites and amino acids (derivatized by TMS and TBDMS). The MS correction protocol and tips can be downloaded.   You may use the file "TBDMS_V9" for isotopmer corrections of TBDMS based amino acids. If you use the downloaded software, you can cite the paper below.   

References: Wahl, S.A., Dauner, M., & Wiechert, W. New tools for mass isotopomer data evaluation in 13C flux analysis: mass isotope correction, data consistency checking, and precursor relationships. Biotechnology and Bioengineering. 85, 259-268 (2004).

2. 13C-metabolic flux analysis (MATLAB codes: programs must be run using MATLAB version 2012 with "Equation to Matrix").   

We have developed a 13C-MFA platform WUflux with user manual (He et al., BMC Bioinformatics, 2017)

The updated WUflux can be download  website. 

Program for Cyanobacterial photoheterotrophic metabolism (By Lian He). Main file    Function file

Program for Cyanobacterial mixotrophic metabolism (By Lian He). Main file    Function file

3. Carbone Fate Map for isotopomer tracing (We will continuously expand this map)

Below are two collaborative modeling projects that are managing by other research group. 

4. MicrobesFlux (Generate a metabolic model from genome database). Professor Yixin Chen, Professor Xueyang Feng and Dr. You Xu built and managed this platform. 

5. Machine learning platform for flux predictions: http://mflux.org/index.html  (Professor Forrest Bao at ISU is managing this platform.)

6. Algae-Bacteria Simulink MATLAB Codes 

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