An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

BMC Bioinformatics

Volumn 11, Issue SUPPL. 12, 2010, Pages

  Gautier, Laurent ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

AGILE DEVELOPMENT; BIOLOGICAL ASSAYS; LANGUAGE TRANSLATORS; MULTIDISCIPLINARY PROJECTS; NEXT-GENERATION SEQUENCING; NUMERICAL PROCESSING; PYTHON INTERFACES; RESEARCH COMMUNITIES;

DATA HANDLING; HIGH LEVEL LANGUAGES; LIBRARIES; NUMERICAL METHODS;

TRANSLATION (LANGUAGES);

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; HIGH THROUGHPUT SCREENING; LIBRARY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT SCREENING ASSAYS; LIBRARIES, DIGITAL; PROGRAMMING LANGUAGES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 78650826806     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S12-S11     Document Type: Article

References (23)

1. Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
2. R Development Core Team R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing 2010, Vienna, Austria, 3-900051-07-0, R Development Core Team., http://www.R-project.org
3. Python. , http://www.python.org
4. A Gentle Introduction to Programming Using Python. , http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-189-a-gentle-introduction-to-programming-using-python-january-iap-2010/
5. Introduction to Programming using Python. , http://www.pasteur.fr/formation/infobio/python/
6. Prechelt L. An empirical comparison of seven programming languages. Computer 2002, 33.
7. Cock PJ, Antao T, Chang JT, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009, 25(11):1422-1423. 10.1093/bioinformatics/btp163, 2682512, 19304878.
8. Knight R, Maxwell P, Birmingham A, et al. PyCogent: a toolkit for making sense from sequence. Genome Biol 2007, 8:R171. 10.1186/gb-2007-8-8-r171, 2375001, 17708774.
9. pygr - Scalabable bioinformatics interfaces in Python. , http://code.google.com/p/pygr/
10. bx-python. , http://bitbucket.org/jamestaylor/bx-python/overview
11. Stajich JE, Block D, K KB, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611-1618. 10.1101/gr.361602, 187536, 12368254.
12. BioRuby - Open source bioinformatics library for Ruby. , http://bioruby.org
13. Holland RCG, Down T, Pocock M, et al. BioJava: an Open-Source Framework for Bioinformatics. Bioinformatics 2008, 2530884, 18689808.
14. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research
15. rpy2. , http://rpy2.sourceforge.net
16. Bobrow DG, Kahn K, Kiczales G, Masinter L, Stefik M, Zdybel F. CommonLoops: merging Lisp and object-oriented programming. SIGPLAN Not 1986, 21(11):17-29.
17. Clojure. , http://clojure.org
18. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:1. 10.1093/bioinformatics/btp616, 2796815, 19850757.
19. The Web framework for perfectionists with deadlines. , http://www.djangoproject.com
20. Plone CMS: Open Source Content Management. , http://www.plone.org
21. R project. , http://www.r-project.org
22. Bottle: Python Web Framework. , http://www.bottle.paws.de
23. Ubuntu. , http://www.ubuntu.org