Literature DB >> 12230038

The Bio* toolkits--a brief overview.

Harry Mangalam1.   

Abstract

Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.

Mesh：

Year:  2002        PMID： 12230038     DOI： 10.1093/bib/3.3.296

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  24 in total

1.  Sockeye: a 3D environment for comparative genomics.

Authors:  Stephen B Montgomery; Tamara Astakhova; Mikhail Bilenky; Ewan Birney; Tony Fu; Maik Hassel; Craig Melsopp; Marcin Rak; A Gordon Robertson; Monica Sleumer; Asim S Siddiqui; Steven J M Jones
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

2.  One hundred years of high-throughput Drosophila research.

Authors:  Mathias Beller; Brian Oliver
Journal:  Chromosome Res       Date:  2006       Impact factor: 5.239

3.  Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data.

Authors:  Thomas Hladish; Vivek Gopalan; Chengzhi Liang; Weigang Qiu; Peter Yang; Arlin Stoltzfus
Journal:  BMC Bioinformatics       Date:  2007-06-08       Impact factor: 3.169

4.  StrBioLib: a Java library for development of custom computational structural biology applications.

Authors:  John-Marc Chandonia
Journal:  Bioinformatics       Date:  2007-05-30       Impact factor: 6.937

5.  A comparison of common programming languages used in bioinformatics.

Authors:  Mathieu Fourment; Michael R Gillings
Journal:  BMC Bioinformatics       Date:  2008-02-05       Impact factor: 3.169

6.  A quick guide for developing effective bioinformatics programming skills.

Authors:  Joel T Dudley; Atul J Butte
Journal:  PLoS Comput Biol       Date:  2009-12-24       Impact factor: 4.475

7.  Community-driven computational biology with Debian Linux.

Authors:  Steffen Möller; Hajo Nils Krabbenhöft; Andreas Tille; David Paleino; Alan Williams; Katy Wolstencroft; Carole Goble; Richard Holland; Dominique Belhachemi; Charles Plessy
Journal:  BMC Bioinformatics       Date:  2010-12-21       Impact factor: 3.169

8.  Batch Blast Extractor: an automated blastx parser application.

Authors:  Mehdi Pirooznia; Edward J Perkins; Youping Deng
Journal:  BMC Genomics       Date:  2008-09-16       Impact factor: 3.969

9.  On single and multiple models of protein families for the detection of remote sequence relationships.

Authors:  James A Casbon; Mansoor A S Saqi
Journal:  BMC Bioinformatics       Date:  2006-01-31       Impact factor: 3.169

10.  VarDetect: a nucleotide sequence variation exploratory tool.

Authors:  Chumpol Ngamphiw; Supasak Kulawonganunchai; Anunchai Assawamakin; Ekachai Jenwitheesuk; Sissades Tongsima
Journal:  BMC Bioinformatics       Date:  2008-12-12       Impact factor: 3.169
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