Skip to content

Releases: opencobra/cobratoolbox

COBRA 3.4 = thermodynamically consistent constraint-based modelling

19 Dec 19:45
33f4db5
Compare
Choose a tag to compare

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

23 Sep 11:06
68d9461
Compare
Choose a tag to compare

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

v3.32: Merge pull request #1811 from opencobra/develop

23 Sep 10:43
8e09472
Compare
Choose a tag to compare

v3.31: Merge pull request #1809 from opencobra/develop

23 Sep 10:37
2acd2f7
Compare
Choose a tag to compare

v3.3

23 Sep 09:23
d57a6d3
Compare
Choose a tag to compare
Merge pull request #1804 from opencobra/develop

Develop

Additional features for host microbial community co-metabolism modelling

27 Apr 22:09
6c1ba69
Compare
Choose a tag to compare
Merge pull request #1761 from opencobra/develop

Develop

Compatibility with whole body modelling

30 Mar 10:38
9251835
Compare
Choose a tag to compare

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

24 May 13:04
efb2c06
Compare
Choose a tag to compare
Merge pull request #1477 from opencobra/develop

Regular merge of develop

The COBRA Toolbox v3.0.5

02 Apr 20:03
2ed83d1
Compare
Choose a tag to compare
Merge pull request #1456 from opencobra/develop

Regular merge of develop

The COBRA Toolbox v3.0.4

15 Jan 07:35
f3fe20d
Compare
Choose a tag to compare
Merge pull request #1414 from opencobra/develop

Regular merge of develop