How to cite

When citing the COBRA Toolbox, it is important to cite the original paper where an algorithm was first reported, as well as its implementation in the COBRA Toolbox. This is important, because the objective of the COBRA Toolbox is to amalgamate and integrate the functionality of a wide range of COBRA algorithms and this will be undermined if contributors of new algorithms do not get their fair share of citations. The following is one example how to approach this within the methods section of a paper (not the supplemental material please):

To generate a context-specific model the FASTCORE algorithm [1], implemented in The COBRA Toolbox v3.0 [2], was employed.

[1] = Vlassis N, Pacheco MP, Sauter T (2014) Fast Reconstruction of Compact Context-Specific Metabolic Network Models. PLoS Comput Biol 10(1): e1003424.

[2] Laurent Heirendt & Sylvain Arreckx, Thomas Pfau, Sebastian N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdottir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdottir, Chiam Yu Ng, German Preciat, Alise Zagare, Siu H.J. Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto Noronha, Aarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Inigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Miguel A.P. Oliveira, Phan T. Vuong, Lemmer P. El Assal, Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Francisco J. Aragon Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard Ø. Palsson, Ines Thiele, Ronan M.T. Fleming, Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0, Nature Protocols, volume 14, pages 639–702, 2019 doi.org/10.1038/s41596-018-0098-2.

It is important if you are submitting a paper that depends on the COBRA toolbox to mention a specific release version, and ideally also the git sha-1 hash code that identifies the current commit to make sure that reviewers are using the correct version.

Example citation:

COBRA Toolbox v3.5 ( commit ffd220aa7996b03d5546a7d24d9f8c626749d169 ) was used for all analyses.

You can find the release number on the Releases page, and the commit SHA-1 hash with the command:

git rev-parse HEAD