The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Addition of XomicsToModel & thermoKernel code XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models by German Preciat, Agnieszka B. Wegrzyn, Ines Thiele, Thomas Hankemeierand Ronan M.T. Fleming
in support of the paper:
Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism by German Preciat1, Agnieszka B. Wegrzyn1, Edinson Lucumi Moreno1, Cornelius C.W. Willacey1, Jennifer Modamio2, Fatima L. Monteiro2, Diana El Assal2, Alissa Schurink1, Miguel A.P. Oliveira2, Zhi Zhang2, Ben Cousins3,4, Hulda S. Haraldsdóttir2, Siham Hachi2, Susanne Zach5, German Leparc5, Yin Tat Lee6, Bastian Hengerer5, Santosh Vempala4, Michael A. Saunders7, Amy Harms1, Enrico Glaab2, Jens C. Schwamborn2, Ines Thiele8, Thomas Hankemeier1† and Ronan M.T. Fleming1,2,8
1 Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Netherlands, 2 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg, 3 Department of Industrial Engineering and Operations Research, Data Science Institute, Columbia University, New York, NY, 4 School of Computer Science, Algorithms and Randomness Center, Georgia Institute of Technology, Atlanta, GA, USA, 5 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany, 6 Department of Computer Science and Engineering, University of Washington, USA, 7 Department of Management Science and Engineering, Stanford University, Stanford, 94305, CA, USA, 8 School of Medicine, University of Galway, University Rd, Galway, Ireland.
Please note that each release is not a git repository and therefore the updateCobraToolbox function will not work. If you want to use that function, so that you can get cobra toolbox updates then use a terminal command like: git clone [email protected]:opencobra/cobratoolbox.git cobratoolbox
Compatibility with whole body modelling, as described in: Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich & Ronan MT Fleming, Personalized whole-body models integrate metabolism, physiology, and the gut microbiome, Molecular Systems Biology (in press).