Releases: opencobra/cobratoolbox
COBRA 3.4 = thermodynamically consistent constraint-based modelling
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.
v3.33
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 git@github.com:opencobra/cobratoolbox.git cobratoolbox
v3.32: Merge pull request #1811 from opencobra/develop
v3.31: Merge pull request #1809 from opencobra/develop
v3.3
Merge pull request #1804 from opencobra/develop Develop
Additional features for host microbial community co-metabolism modelling
Merge pull request #1761 from opencobra/develop Develop
Compatibility with whole body modelling
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).
The COBRA Toolbox v3.0.6
Merge pull request #1477 from opencobra/develop Regular merge of develop
The COBRA Toolbox v3.0.5
Merge pull request #1456 from opencobra/develop Regular merge of develop
The COBRA Toolbox v3.0.4
Merge pull request #1414 from opencobra/develop Regular merge of develop