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Items: 14

1.

The Bioperl toolkit: Perl modules for the life sciences.

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E.

Genome Res. 2002 Oct;12(10):1611-8.

2.

Workflow based framework for life science informatics.

Tiwari A, Sekhar AK.

Comput Biol Chem. 2007 Oct;31(5-6):305-19. Epub 2007 Aug 19. Review.

PMID:
17931570
3.

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group.

Mooney SD, Baenziger PH.

Brief Bioinform. 2008 Jan;9(1):69-74. Epub 2007 Dec 5. Review.

PMID:
18057072
4.

A library of efficient bioinformatics algorithms.

Della Vedova G, Dondi R.

Appl Bioinformatics. 2003;2(2):117-21. Review.

PMID:
15130828
5.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Review.

PMID:
18238804
6.

Evolution of web services in bioinformatics.

Neerincx PB, Leunissen JA.

Brief Bioinform. 2005 Jun;6(2):178-88. Review.

PMID:
15975226
7.

Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL.

Curr Pharm Des. 2006;12(17):2111-20. Review.

8.

The Ensembl core software libraries.

Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E.

Genome Res. 2004 May;14(5):929-33. Review.

9.

Data clustering in life sciences.

Zhao Y, Karypis G.

Mol Biotechnol. 2005 Sep;31(1):55-80. Review.

PMID:
16118415
10.

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM.

Nucleic Acids Res. 2010 Apr;38(6):1767-71. doi: 10.1093/nar/gkp1137. Epub 2009 Dec 16. Review.

11.

A vision for collaborative training infrastructure for bioinformatics.

Williams JJ, Teal TK.

Ann N Y Acad Sci. 2017 Jan;1387(1):54-60. doi: 10.1111/nyas.13207. Epub 2016 Sep 7. Review.

PMID:
27603332
12.

Open source libraries and frameworks for biological data visualisation: a guide for developers.

Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics. 2015 Apr;15(8):1356-74. doi: 10.1002/pmic.201400377. Epub 2015 Feb 5. Review.

13.

Data integration in biological research: an overview.

Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV.

J Biol Res (Thessalon). 2015 Sep 2;22(1):9. doi: 10.1186/s40709-015-0032-5. eCollection 2015 Dec. Review.

14.

Catalyzing Inquiry at the Interface of Computing and Biology.

National Research Council (US) Committee on Frontiers at the Interface of Computing and Biology; Wooley JC, Lin HS, editors.

Washington (DC): National Academies Press (US); 2005.

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