[1] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410 http://dx.doi.org/10.1016/S0022-2836(05)?80360-2.
|
[2] | Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402 doi:10.1093/nar/25.17.3389.
|
[3] | Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680 doi:10.1093/nar/22.22.4673.
|
[4] | Vandewalle P (2012) Code sharing is associated with research impact in image processing. IEEE Computing in Science & Engineering 14: 42–47 http://rr.epfl.ch/37/.
|
[5] | Morin A, Urban J, Sliz P (2012) A quick guide to software licensing for the scientist-programmer. PLoS Comput Biol 8(7): e1002598 doi:10.1371/journal.pcbi.1002598.
|
[6] | Cock P (2011) Opening up NCBI BLAST? Available: http://blastedbio.blogspot.co.uk/2011/08?/opening-up-ncbi-blast.html Accessed 27 October 2012.
|
[7] | Wren JD (2008) URL decay in MEDLINE—a 4-year follow-up study. Bioinformatics 24(11): 1381–1385 doi:10.1093/bioinformatics/btn127.
|
[8] | Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, et al. (2011) Ten simple rules for getting help from online scientific communities. PLoS Comput Biol 7(9): e1002202 doi:10.1371/journal.pcbi.1002202.
|
[9] | Sofware Carpentry (2012) http://software-carpentry.org/ Accessed 27 October 2012.
|
[10] | Aruliah DA, Titus Brown C, Chue Hong NP, Davis M, Guy RT, et al.. (2012) Best practices for scientific computing. eprint arXiv:1210.0530. Available: http://arxiv.org/abs/1210.0530. Accessed 27 October 2012.
|
[11] | Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2012) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12(10): 1611–1618 doi:10.1101/gr.361602.
|
[12] | Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11): 1422–1423 Epub 20 Mar 2009. doi:10.1093/bioinformatics/btp163. doi: 10.1093/bioinformatics/btp163
|
[13] | Prli? A, Yates A, Bliven SE, Rose PW, Jacobsen J, et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 28(20): 2693–2695 Epub 9 Aug 2012. doi:10.1093/bioinformatics/bts494. doi: 10.1093/bioinformatics/bts494
|
[14] | Goto N, Prins P, Nakao M, Bonnal R, Aerts J, et al. (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics 26(20): 2617–2619 doi:10.1093/bioinformatics/btq475.
|
[15] | Barnes N (2012) The science code manifesto. Available: http://sciencecodemanifesto.org/. Accessed 15 October 2012.
|
[16] | Merali Zeeya (2010) Computational science: …error…why scientific programming does not compute. Nature 467: 775–777 doi:10.1038/467775a.
|
[17] | Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, et al. (2012) A toolbox for developing bioinformatics software. Brief Bioinform 13(2): 244–257 Epub 29 Jul 2011. doi:10.1093/bib/bbr035. doi: 10.1093/bib/bbr035
|
[18] | The Apache Software Foundation. The Apache way. Available: http://incubator.apache.org/learn/theapa?cheway.html. Accessed 17 October 2012.
|
[19] | Gardler R (2010) Community development at the Apache Software Foundation. Ross Gardler's keynote from BOSC 2010. Available: http://www.slideshare.net/bosc2010/gardl?er-bosc2010-communitydevelopmentattheasf. Accessed 27 October 2012.
|
[20] | Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, et al. (2012) Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics 28(7): 1035–1037 Epub 12 Feb 2012. doi:10.1093/bioinformatics/bts080. doi: 10.1093/bioinformatics/bts080
|
[21] | Raymond ES (1999) The cathedral & the bazaar. O'Reilly. ISBN 1-56592-724-9.
|
[22] | Kane DW, Hohman MM, Cerami EG, McCormick MW, Kuhlmman KF, et al. (2006) Agile methods in biomedical software development: a multi-site experience report. BMC Bioinformatics 7: 273 doi:10.1186/1471-2105-7-273.
|
[23] | Vicens Q, Bourne PE (2007) Ten simple rules for a successful collaboration. PLoS Comput Biol 3(3): e44 doi:10.1371/journal.pcbi.0030044.
|
[24] | Bourne PE, Chalupa LM (2006) Ten simple rules for getting grants. PLoS Comput Biol 2(2):e12 doi:10.1371/journal.pcbi.0020012.
|