BioRuby: bioinformatics software for the Ruby programming language

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: katayama@bioruby.org

• Publication year

  2010

• Venue

  Bioinform.

• Publication date

  2010-08-25

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btq475PMID 20739307PMCID 2951089
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• BioJava: an open-source framework for bioinformatics in 2012

  2012cited by this paper
• miRMaid: a unified programming interface for microRNA data resources

  2010cited by this paper
• TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services

  2010cited by this paper
• phyloXML: XML for evolutionary biology and comparative genomics

  2009cited by this paper
• Biopython: freely available Python tools for computational molecular biology and bioinformatics

  2009cited by this paper
• Ulla: a program for calculating environment-specific amino acid substitution tables

  2009cited by this paper
• The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

  2009cited by this paper
• BioJava: an open-source framework for bioinformatics

  2008cited by this paper
• mspire: mass spectrometry proteomics in Ruby

  2008cited by this paper
• BMC Bioinformatics BioMed Central Correspondence Extended Newick: it is time for a standard representation of

  2008cited by this paper
• KEGG for linking genomes to life and the environment

  2007cited by this paper
• Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

  2007cited by this paper
• Open source tools and toolkits for bioinformatics: significance, and where are we?

  2006cited by this paper
• The MPI Bioinformatics Toolkit for protein sequence analysis

  2006cited by this paper
• MAFFT version 5: improvement in accuracy of multiple sequence alignment

  2005cited by this paper
• Light-weight integration of molecular biological databases

  2004cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003cited by this paper
• The Bioperl toolkit: Perl modules for the life sciences.

  2002cited by this paper

• Molecular Clock Dating of Deep-Time Evolution Using Complex Mixture Models

  2026cites this paper
• Building an Intelligent Food Assurance System Based on DevOps: A Review

  2025cites this paper
• taxalogue: a toolkit to create comprehensive CO1 reference databases

  2023influential citation
• A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

  2022cites this paper
• Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils.

  2022cites this paper
• Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium

  2021cites this paper
• Critical assessment of coiled-coil predictions based on protein structure data

  2021cites this paper
• Evolutionary Trajectory of the Replication Mode of Bacterial Replicons

  2021cites this paper
• Vcflib and tools for processing the VCF variant call format

  2021cites this paper
• Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages

  2021cites this paper
• Mitogenome evolution in the Lacerta viridis complex (Lacertidae, Squamata) reveals phylogeny of diverging clades

  2021influential citation
• PDB‐tools web: A user‐friendly interface for the manipulation of PDB files

  2020cites this paper
• A haplotype-led approach to increase the precision of wheat breeding

  2020cites this paper
• A haplotype-led approach to increase the precision of wheat breeding

  2020cites this paper
• BioShell 3.0: Library for Processing Structural Biology Data

  2020cites this paper
• BioStructures.jl: read, write and manipulate macromolecular structures in Julia

  2020cites this paper
• Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in Rhizobiales

  2020cites this paper
• BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis.

  2020cites this paper
• Dating Alphaproteobacteria evolution with eukaryotic fossils

  2020cites this paper
• Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation

  2019cites this paper
• Precision Medicine Informatics: Principles, Prospects, and Challenges

  2019cites this paper
• RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

  2019cites this paper
• Emergence of DSS efforts in genomics: Past contributions and challenges

  2019cites this paper
• Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize

  2019cites this paper
• Systems Genetics for Evolutionary Studies.

  2019cites this paper
• Sharing Programming Resources Between Bio* Projects

  2019cites this paper
• Eliminating uncertainty in the process of knowledge acquisition from the large-scale genomic data

  2019cites this paper
• Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

  2019cites this paper
• TogoGenome/TogoStanza: modularized Semantic Web genome database

  2019cites this paper
• Phylogenomic analysis demonstrates a pattern of rare and long-lasting concerted evolution in prokaryotes

  2018cites this paper
• The transcriptional landscape of polyploid wheat

  2018cites this paper
• Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes

  2018cites this paper
• University of Birmingham The transcriptional landscape of polyploid wheat

  2018cites this paper
• MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates

  2018cites this paper
• Title Identification of imprinted genes subject to parent-of-originspecific expression in Arabidopsis thaliana seeds

  2018cites this paper
• Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive

  2017cites this paper
• BLASTphp: a PHP wrapper for NCBI BLAST API

  2017cites this paper
• Большие данные в биоинформатике

  2017cites this paper
• Big Data in Bioinformatics

  2017cites this paper
• Methods for analyzing next-generation sequencing data IX.Genome annotation, visualization, and registration to DDBJ

  2017cites this paper
• ProtozoaDB 2.0: A Trypanosoma Brucei Case Study

  2017cites this paper
• A Cluster of Fatal Tick-borne Encephalitis Virus Infection in Organ Transplant Setting.

  2017cites this paper
• Evolution of duplicated non-coding RNAs in plants

  2017cites this paper
• Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces

  2017cites this paper
• MassBlast: A workflow to accelerate RNA-seq and DNA database analysis

  2017cites this paper
• Pipengine: an ultra light YAML-based pipeline execution engine

  2017cites this paper
• xmlBLASTparser V1.1 — A PHP BASED NCBI BLAST XML OUTPUT PARSER

  2017influential citation
• A Cluster of Fatal Tick-borne Encephalitis Virus Infection in Organ Transplant Setting

  2017cites this paper
• Uncovering hidden variation in polyploid wheat

  2017cites this paper
• Automated identification of reference genes based on RNA-seq data

  2017cites this paper
• The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials

  2016cites this paper
• How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications

  2016cites this paper
• Refined Pichia pastoris reference genome sequence.

  2016influential citation
• Next generation genomics tools for wheat improvement

  2016influential citation
• Visual programming for next-generation sequencing data analytics

  2016cites this paper
• SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species

  2016cites this paper
• An Introduction to Programming for Bioscientists: A Python-Based Primer

  2016cites this paper
• A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra

  2016cites this paper
• HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells

  2016cites this paper
• Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

  2016cites this paper
• Pulmonary Infection and Inflammation

  2016cites this paper
• Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo—Brazil)

  2016influential citation
• NCBI Mass Sequence Downloader-Large dataset downloading made easy

  2016cites this paper
• Automatic Workflow for the Identification of Constitutively-Expressed Genes Based on Mapped NGS Reads

  2016cites this paper
• The Machine that Builds Itself: How the Strengths of Lisp Family Languages Facilitate Building Complex and Flexible Bioinformatic Models

  2016cites this paper
• Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling

  2016cites this paper
• The need for more Lispers in bioinformatics

  2016cites this paper
• Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis.

  2016cites this paper
• Tools and data services registry: a community effort to document bioinformatics resources

  2015cites this paper
• ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome

  2015influential citation
• NCBI BLAST+ integrated into Galaxy

  2015cites this paper
• Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens.

  2015cites this paper
• GenOO: A Modern Perl Framework for High Throughput Sequencing analysis

  2015cites this paper
• PolyMarker: A fast polyploid primer design pipeline

  2015cites this paper
• Adapting simultaneous analysis phylogenomic techniques to study complex disease gene relationships

  2015cites this paper
• REdiii: a pipeline for automated structure solution.

  2015cites this paper
• Title Corresponding Author

  2015cites this paper
• MAFCO: A Compression Tool for MAF Files

  2015cites this paper
• High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome

  2015cites this paper
• Mapping a Type 1 FHB resistance on chromosome 4AS of Triticum macha and deployment in combination with two Type 2 resistances

  2015cites this paper
• Dynamically composing languages in a modular way: supporting C extensions for dynamic languages

  2015cites this paper
• The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences

  2015cites this paper
• GenOO: A programming framework for High Throughput Sequencing analysis

  2015cites this paper
• Long-Lasting Gene Conversion Shapes the Convergent Evolution of the Critical Methanogenesis Genes

  2015cites this paper
• JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

  2015cites this paper
• Rust-Bio: a fast and safe bioinformatics library

  2015cites this paper
• A Computational and Statistical Framework for Screening Novel Antimicrobial Peptides

  2015cites this paper
• Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs.

  2015cites this paper
• BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

  2015cites this paper
• RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.

  2015cites this paper
• Ant genomics (Hymenoptera: Formicidae): challenges to overcome and opportunities to seize

  2015cites this paper
• Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica

  2015cites this paper
• TransRate: reference-free quality assessment of de novo transcriptome assemblies

  2015cites this paper
• The Bioinformatics Open Source Conference (BOSC) 2013

  2015cites this paper
• Sequenceserver: a modern graphical user interface for custom BLAST databases

  2015cites this paper
• Efforts towards accessible and reliable bioinformatics

  2015cites this paper
• Sequence analysis PolyMarker : A fast polyploid primer design pipeline

  2015cites this paper
• PolyMarker: A fast polyploid primer design

  2015cites this paper
• Development of novel software tools and methods for investigating the significance of overlapping transcription factor genomic interactions

  2015cites this paper
• High-throughput open source computational methods for genetics and genomics

  2015influential citation