Ten Simple Rules for Taking Advantage of Git and GitHub

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).

[1]  Knut Reinert,et al.  OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.

[2]  Sophia Ananiadou,et al.  Europe PMC: a full-text literature database for the life sciences and platform for innovation , 2014, Nucleic Acids Res..

[3]  Vasyl Pihur,et al.  MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data , 2013, Source Code for Biology and Medicine.

[4]  Martin Eisenacher,et al.  PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets , 2015, Molecular & Cellular Proteomics.

[5]  Valmir C. Barbosa,et al.  On best practices in the development of bioinformatics software , 2014, Front. Genet..

[6]  Credit where credit is overdue , 2009, Nature Biotechnology.

[7]  Paul T. Groth,et al.  Ten Simple Rules for the Care and Feeding of Scientific Data , 2014, PLoS Comput. Biol..

[8]  William Stafford Noble.  A Quick Guide to Organizing Computational Biology Projects , 2009, PLoS Comput. Biol..

[9]  Alexander Konovalov,et al.  Software Carpentry: Programming with R , 2017 .

[10]  Kathryn S. Lilley,et al.  MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation , 2012, Bioinform..

[11]  David L. Donoho,et al.  WaveLab and Reproducible Research , 1995 .

[12]  Alexander G. Fletcher,et al.  Ten Simple Rules for Effective Computational Research , 2014, PLoS Comput. Biol..

[13]  Mauno Vihinen,et al.  No more hidden solutions in bioinformatics , 2015, Nature.

[14]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[15]  Yasset Perez-Riverol,et al.  Making proteomics data accessible and reusable: Current state of proteomics databases and repositories , 2015, Proteomics.

[16]  Thomas Jackson,et al.  A data repository and analysis framework for spontaneous neural activity recordings in developing retina , 2013, bioRxiv.

[17]  John D. Blischak,et al.  A Quick Introduction to Version Control with Git and GitHub , 2016, PLoS Comput. Biol..

[18]  James D. Herbsleb,et al.  Social coding in GitHub: transparency and collaboration in an open software repository , 2012, CSCW.

[19]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[20]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[21]  Karthik Ram,et al.  Git can facilitate greater reproducibility and increased transparency in science , 2013, Source Code for Biology and Medicine.

[22]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[23]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..