BioRuby: bioinformatics software for the Ruby programming language
نویسندگان
چکیده
SUMMARY The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. AVAILABILITY BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. CONTACT [email protected]
منابع مشابه
Comparative Analysis of Software Repository Metrics in BioPerl, BioJava and BioRuby
The open source programming languages, often with a biosuffix, i.e. BioPerl, BioJava, and BioRuby, have been widely used in bioinformatics and computational biology research. The computational tools written in these languages provide multiple functionalities as the languages make them flexible to create customized analysis and examination of biological data. In this paper, we investigate one of...
متن کاملmspire: mass spectrometry proteomics in Ruby
UNLABELLED Mass spectrometry-based proteomics stands to gain from additional analysis of its data, but its large, complex datasets make demands on speed and memory usage requiring special consideration from scripting languages. The software library 'mspire'-developed in the Ruby programming language-offers quick and memory-efficient readers for standard xml proteomics formats, converters for in...
متن کاملBiogem: an effective tool-based approach for scaling up open source software development in bioinformatics
SUMMARY Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up col...
متن کاملFSelector: a Ruby gem for feature selection
SUMMARY The FSelector package contains a comprehensive list of feature selection algorithms for supporting bioinformatics and machine learning research. FSelector primarily collects and implements the filter type of feature selection techniques, which are computationally efficient for mining large datasets. In particular, FSelector allows ensemble feature selection that takes advantage of multi...
متن کاملLibSBMLSim: a reference implementation of fully functional SBML simulator
MOTIVATION The Systems Biology Markup Language (SBML) is currently supported by >230 software tools, among which 160 support numerical integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within this field, there is still no language-neutral library that supports all features of SBML for simulating ODE models. Therefore, a demand exists for a s...
متن کامل