论文信息 - Programming languages and the biological sciences

Programming languages and the biological sciences

This paper presents an overview of the scripting, markup, and general purpose programming languages used for scientific research and discovery in the biological sciences. This material may be useful for inclusion in a programming languages class and as a starting point for undergraduate interdisciplinary research and programming projects.

James W. McGuffee

[1] Jeffrey Chang,et al. Biopython: Python tools for computational biology , 2000, SIGB.

[2] Satoru Miyano,et al. Open source clustering software , 2004 .

[3] Michael Travers,et al. BioLingua: a programmable knowledge environment for biologists , 2005, Bioinform..

[4] S Miyano,et al. Open source clustering software. , 2004, Bioinformatics.

[5] Matthew R. Pocock,et al. BioJava: open source components for bioinformatics , 2000, SIGB.

[6] Riccardo Dondi,et al. A library of efficient bioinformatics algorithms. , 2003, Applied bioinformatics.

[7] Darren T. Lim. A Ruby in the rough: using VHLLs in bioinformatics , 2006 .

[8] Michiel J. L. de Hoon,et al. Bioinformatics and Computational Biology with Biopython , 2003 .

[9] Ewan Birney,et al. The Bioperl project: motivation and usage , 2000, SIGB.

[10] Judith D. Cohn. XML and genomic data , 2000, SIGB.

[11] Emmanuel Barillot,et al. XML, bioinformatics and data integration , 2001, Bioinform..

[12] Jacques Cohen,et al. Bioinformatics—an introduction for computer scientists , 2004, CSUR.

[13] Brent Baas. Ruby in the CS curriculum , 2002 .

[14] Minoru Kanehisa,et al. BioRuby: Open-Source Bioinformatics Library , 2003 .

[15] Matthew R. Pocock,et al. The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.