Ten Simple Rules for taking advantage of Git and GitHub

Yasset Perez-Riverol; Laurent Gatto; Rui Wang; Timo Sachsenberg; Julian Uszkoreit; Felipe da Veiga Leprevost; Christian Fufezan; Tobias Ternent; Stephen J. Eglen; Daniel S. Katz; Tom J. Pollard; Alexander Konovalov; Robert M. Flight; Kai Blin; Juan Antonio Vizcaíno

doi:10.1371/journal.pcbi.1004947

Ten Simple Rules for taking advantage of Git and GitHub

Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno

Research output: Contribution to journal › Article › peer-review

Abstract

A 'Ten Simple Rules' guide to Git and GitHub. We describe and provide examples on how to use these software to track projects, as users, teams and organizations. We document collaborative development using branching and forking, interaction between collaborators using issues and continuous integration and automation using, for example, Travis CI and codevoc. We also describe dissemination and social aspects of GitHub such as GitHub pages, following and watching repositories, and give advice on how to make code citable.

Original language	English
Article number	e1004947
Number of pages	11
Journal	PLoS Computational Biology
Volume	12
Issue number	7
DOIs	https://doi.org/10.1371/journal.pcbi.1004947 https://doi.org/10.1101/048744
Publication status	Published - 14 Jul 2016

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10.1371/journal.pcbi.1004947Licence: CC BY
10.1101/048744

Konovalov_2016_PLoSComputBiol_GitHub_CC
Copyright: © 2016 Perez-Riverol et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Final published version, 547 KBLicence: CC BY

http://biorxiv.org/content/early/2016/05/06/048744

CoDiMa: CoDiMa (CCP in the area of Computational Discrete Mathematics)
Linton, S. A. (PI) & Konovalov, O. (CoI)
EPSRC
1/03/15 → 29/02/20
Project: Standard

Olexandr Konovalov
- obk1st-andrews.acuk
Person: Academic

Cite this

Perez-Riverol, Y., Gatto, L., Wang, R., Sachsenberg, T., Uszkoreit, J., da Veiga Leprevost, F., Fufezan, C., Ternent, T., Eglen, S. J., Katz, D. S., Pollard, T. J., Konovalov, A., Flight, R. M., Blin, K., & Vizcaíno, J. A. (2016). Ten Simple Rules for taking advantage of Git and GitHub. PLoS Computational Biology, 12(7), Article e1004947. https://doi.org/10.1371/journal.pcbi.1004947, https://doi.org/10.1101/048744

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title = "Ten Simple Rules for taking advantage of Git and GitHub",

abstract = "A 'Ten Simple Rules' guide to Git and GitHub. We describe and provide examples on how to use these software to track projects, as users, teams and organizations. We document collaborative development using branching and forking, interaction between collaborators using issues and continuous integration and automation using, for example, Travis CI and codevoc. We also describe dissemination and social aspects of GitHub such as GitHub pages, following and watching repositories, and give advice on how to make code citable.",

author = "Yasset Perez-Riverol and Laurent Gatto and Rui Wang and Timo Sachsenberg and Julian Uszkoreit and {da Veiga Leprevost}, Felipe and Christian Fufezan and Tobias Ternent and Eglen, {Stephen J.} and Katz, {Daniel S.} and Pollard, {Tom J.} and Alexander Konovalov and Flight, {Robert M.} and Kai Blin and Vizca{\'i}no, {Juan Antonio}",

note = "This study was supported by Wellcome Trust [grant number WT101477MA] (http://www.wellcome.ac.uk/), BBSRC [grant numbers BB/K01997X/1, BB/I00095X/1, BB/L024225/1 and BB/L002817/1] (http://www.bbsrc.ac.uk/), BMBF grant de.NBI - German Network for Bioinformatics Infrastructure (FKZ031 A 534A) (https://www.denbi.de/), NIH grant numbers R01-GM-094231 and R01-EB-017205 (http://www.nih.gov/), EPSRC [reference EP/M022641/1] (https://www.epsrc.ac.uk), NSF grant number 1252893 (http://www.nsf.gov/), and Novo Nordisk Foundation (http://www.novonordiskfonden.dk/en).",

year = "2016",

month = jul,

day = "14",

doi = "10.1371/journal.pcbi.1004947",

language = "English",

volume = "12",

journal = "PLoS Computational Biology",

issn = "1553-734X",

publisher = "Public Library of Science",

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Perez-Riverol, Y, Gatto, L, Wang, R, Sachsenberg, T, Uszkoreit, J, da Veiga Leprevost, F, Fufezan, C, Ternent, T, Eglen, SJ, Katz, DS, Pollard, TJ, Konovalov, A, Flight, RM, Blin, K & Vizcaíno, JA 2016, 'Ten Simple Rules for taking advantage of Git and GitHub', PLoS Computational Biology, vol. 12, no. 7, e1004947. https://doi.org/10.1371/journal.pcbi.1004947, https://doi.org/10.1101/048744

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AU - Perez-Riverol, Yasset

AU - Gatto, Laurent

AU - Wang, Rui

AU - Sachsenberg, Timo

AU - Uszkoreit, Julian

AU - da Veiga Leprevost, Felipe

AU - Fufezan, Christian

AU - Ternent, Tobias

AU - Eglen, Stephen J.

AU - Katz, Daniel S.

AU - Pollard, Tom J.

AU - Konovalov, Alexander

AU - Flight, Robert M.

AU - Blin, Kai

AU - Vizcaíno, Juan Antonio

N1 - This study was supported by Wellcome Trust [grant number WT101477MA] (http://www.wellcome.ac.uk/), BBSRC [grant numbers BB/K01997X/1, BB/I00095X/1, BB/L024225/1 and BB/L002817/1] (http://www.bbsrc.ac.uk/), BMBF grant de.NBI - German Network for Bioinformatics Infrastructure (FKZ031 A 534A) (https://www.denbi.de/), NIH grant numbers R01-GM-094231 and R01-EB-017205 (http://www.nih.gov/), EPSRC [reference EP/M022641/1] (https://www.epsrc.ac.uk), NSF grant number 1252893 (http://www.nsf.gov/), and Novo Nordisk Foundation (http://www.novonordiskfonden.dk/en).

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AB - A 'Ten Simple Rules' guide to Git and GitHub. We describe and provide examples on how to use these software to track projects, as users, teams and organizations. We document collaborative development using branching and forking, interaction between collaborators using issues and continuous integration and automation using, for example, Travis CI and codevoc. We also describe dissemination and social aspects of GitHub such as GitHub pages, following and watching repositories, and give advice on how to make code citable.

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DO - 10.1371/journal.pcbi.1004947

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JO - PLoS Computational Biology

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Ten Simple Rules for taking advantage of Git and GitHub

Abstract

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CoDiMa: CoDiMa (CCP in the area of Computational Discrete Mathematics)

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Olexandr Konovalov

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