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Items: 1 to 20 of 178

1.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

2.

PDB file parser and structure class implemented in Python.

Hamelryck T, Manderick B.

Bioinformatics. 2003 Nov 22;19(17):2308-10.

PMID:
14630660
3.

Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.

Talevich E, Invergo BM, Cock PJ, Chapman BA.

BMC Bioinformatics. 2012 Aug 21;13:209. doi: 10.1186/1471-2105-13-209.

4.

BioRuby: bioinformatics software for the Ruby programming language.

Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T.

Bioinformatics. 2010 Oct 15;26(20):2617-9. doi: 10.1093/bioinformatics/btq475. Epub 2010 Aug 25.

5.

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.

Bioinformatics. 2012 Dec 1;28(23):3163-5. doi: 10.1093/bioinformatics/bts577. Epub 2012 Sep 27.

6.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.

Bioinformatics. 2015 Jan 15;31(2):268-70. doi: 10.1093/bioinformatics/btu630. Epub 2014 Sep 30.

7.

BioSmalltalk: a pure object system and library for bioinformatics.

Morales HF, Giovambattista G.

Bioinformatics. 2013 Sep 15;29(18):2355-6. doi: 10.1093/bioinformatics/btt398. Epub 2013 Jul 9.

PMID:
23842806
8.

BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.

9.

Ruffus: a lightweight Python library for computational pipelines.

Goodstadt L.

Bioinformatics. 2010 Nov 1;26(21):2778-9. doi: 10.1093/bioinformatics/btq524. Epub 2010 Sep 16.

PMID:
20847218
10.

A comparison of common programming languages used in bioinformatics.

Fourment M, Gillings MR.

BMC Bioinformatics. 2008 Feb 5;9:82. doi: 10.1186/1471-2105-9-82.

11.

OpenStructure: a flexible software framework for computational structural biology.

Biasini M, Mariani V, Haas J, Scheuber S, Schenk AD, Schwede T, Philippsen A.

Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481. Epub 2010 Aug 23.

12.

PathBuilder--open source software for annotating and developing pathway resources.

Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A.

Bioinformatics. 2009 Nov 1;25(21):2860-2. doi: 10.1093/bioinformatics/btp453. Epub 2009 Jul 23.

13.

BIAS: Bioinformatics Integrated Application Software.

Finak G, Godin N, Hallett M, Pepin F, Rajabi Z, Srivastava V, Tang Z.

Bioinformatics. 2005 Apr 15;21(8):1745-6. Epub 2004 Nov 30.

PMID:
15572471
14.

BioXSD: the common data-exchange format for everyday bioinformatics web services.

Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I.

Bioinformatics. 2010 Sep 15;26(18):i540-6. doi: 10.1093/bioinformatics/btq391.

15.

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.

16.

DendroPy: a Python library for phylogenetic computing.

Sukumaran J, Holder MT.

Bioinformatics. 2010 Jun 15;26(12):1569-71. doi: 10.1093/bioinformatics/btq228. Epub 2010 Apr 25.

PMID:
20421198
17.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

Prins P, Goto N, Yates A, Gautier L, Willis S, Fields C, Katayama T.

Methods Mol Biol. 2012;856:513-27. doi: 10.1007/978-1-61779-585-5_21.

PMID:
22399473
18.

BioServices: a common Python package to access biological Web Services programmatically.

Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J.

Bioinformatics. 2013 Dec 15;29(24):3241-2. doi: 10.1093/bioinformatics/btt547. Epub 2013 Sep 23.

19.

The Ensembl REST API: Ensembl Data for Any Language.

Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GR, Ruffier M, Taylor K, Vullo A, Flicek P.

Bioinformatics. 2015 Jan 1;31(1):143-5. doi: 10.1093/bioinformatics/btu613. Epub 2014 Sep 17.

20.

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P.

Bioinformatics. 2012 Apr 1;28(7):1035-7. doi: 10.1093/bioinformatics/bts080. Epub 2012 Feb 12.

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