Naohisa Goto edited this page Jun 14, 2016 · 1 revision


Nature 493, 664–668. A Y-like social chromosome causes alternative colony organization in fire ants. John Wang, Yannick Wurm, Mingkwan Nipitwattanaphon, Oksana Riba-Grognuz, Yu-Ching Huang, DeWayne Shoemaker, Laurent Keller


PLoS ONE 7(11): e45715. The Molecular Clockwork of the Fire Ant Solenopsis invicta. Krista K. Ingram, Alexander Kutowoi, Yannick Wurm, DeWayne Shoemaker, Rudolf Meier, Guy Bloch.


Nucleic Acids Res. 2011 Oct 12.

Polbase: a repository of biochemical, genetic and structural information about DNA polymerases.

Langhorst BW, Jack WE, Reha-Krantz L, Nichols NM.

''' Supporting software tools include: Ubuntu Linux, 10 Postgres, Memcache, Ruby, Rails, Sphinx and Thinking Sphinx, Apache and Phusion Passenger, UserVoice, Jquery, DataTables, Authlogic, Declarative Authorization, Nokogiri, Paperclip, Formtastic, Will Paginate, BioRuby and Delayed Job. '''

BMC Research Notes 2011 Sep 9; 4(1):338

diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data.

Hammesfahr B, Odronitz F, Hellkamp M, Kollmar M.

''' Ruby together with BioRuby [31] is also used for scripts that automatically retrieve data via the NCBI-API, reconstruct the phylogenetic tree of diArk's species, and analyse genome assembly files. '''

BMC Research Notes 2011 Sep 8; 4(1):331

Agile parallel bioinformatics workflow management using Pwrake.

Mishima H, Sasaki K, Tanaka M, Tatebe O, Yoshiura KI.

''' In particular, the BioRuby [44] library offers highly abstracted data processing methods for bioinformatics. '''

BMC Plant Biology 2011 Aug 12;11:113.

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

McKeown PC, Laouielle-Duprat S, Prins P, Wolff P, Schmid MW, Donoghue MT, Fort A, Duszynska D, Comte A, Lao NT, Wennblom TJ, Smant G, Köhler C, Grossniklaus U, Spillane C.

''' The GenFrag software is written in Ruby, and can be run on all platforms supported by Ruby, including Windows, OSX, Linux and the Java virtual machine. The restriction enzyme module is available as part of the Open Bioinformatics Foundation BioRuby toolkit [69] and includes all known restriction enzymes by name. Genomic information can be read in any BioRuby supported format, including FASTA. The web interface is written in Ruby on Rails, and SQLite is used for caching searches. '''

Bioinformatics July 29, 2011

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data

Ramirez-Gonzalez R, Caccamo M, Maclean D.

''' Each sequence object has many feature objects which are described as in GFF3 and parsed into the database using the BioRuby GFF3 class. '''

BMC Research Notes 2011 Jul 28; 4:265

Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio.

Hatje K, Keller O, Hammesfahr B, Pillmann H, Waack S, Kollmar M.

''' Internally, the sequence data is processed with the help of BioRuby [28]. '''

BMC Bioinformatics. 2011 Jun 30;12:270.

Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

Pillmann H, Hatje K, Odronitz F, Hammesfahr B, Kollmar M.

''' The nucleotide sequences of the exon candidates are translated into amino acid sequences using the BioRuby library [28]. '''

Genome Research 2011, 21: 1339-1348

The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming

Nygaard S, Zhang G, Schiøtt M, Li C, Wurm Y, Hu H, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJP, Wang J, and Boomsma JJ

''' The phylogenetic tree of the M16 Peptidase genes was constructed using Ruby/Bioruby (Aerts and Law 2009; Goto et al. 2010) scripts to organize the multiple alignment and tree construction. '''

Theor Appl Genet. 2011 May 18.

A genome-wide genetic map of NB-LRR disease resistance loci in potato.

Bakker E, Borm T, Prins P, van der Vossen E, Uenk G, Arens M, de Boer J, van Eck H, Muskens M, Vossen J, van der Linden G, van Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J, Goverse A.

(citation of BioRuby paper)

Bioinformatics (2011) 27 (7): 1013-1014. doi: 10.1093/bioinformatics/btr050

A Ruby API to query the Ensembl database for genomic features

Francesco Strozzi and Jan Aerts

''' In recent years, the Python and Ruby scripting languages have gained significant ground in the bioinformatics community (Aerts and Law, 2009; Cock et al., 2009; Goto et al., 2010, see e.g.), increasing the need for a programmable interface in these languages. In this article, we describe a second API to the Ensembl database, focusing on the Ruby programming community. ''' ''' The Ruby API to Ensembl is not part of the BioRuby project, but might be linked to it as a plugin in the future. '''

PNAS 2011 108(14), 5679-5684

The genome of the fire ant Solenopsis invicta

Wurm Y., Wang J., Riba-Grognuz O., Corona M., Nygaard S., Hunt B.G., Ingram K.K., Falquet L., Nipitwattanaphon M., Gotzek D., Dijkstra M.B., Oettler J., Comtesse F., Shih C.J., Wu W.J., Yang C.C., Thomas J., Beaudoing E., Pradervand S., Flegel V., Cook E.D., Fabbretti R., Stockinger H., Long L., Farmerie W.G., Oakey J., Boomsma J.J., Pamilo P., Yi S.V., Heinze J., Goodisman M.A., Farinelli L., Harshman K., Hulo N., Cerutti L., Xenarios I., Shoemaker D., Keller L.

''' Analyses were assisted by custom Ruby/Bioruby (68, 69), Perl (70), and R (71) scripts '''

Genes Cells. 2011 Jan;16(1):80-9.

Transcription factors CgUPC2A and CgUPC2B regulate ergosterol biosynthetic genes in Candida glabrata.

Nagi M, Nakayama H, Tanabe K, Bard M, Aoyama T, Okano M, Higashi S, Ueno K, Chibana H, Niimi M, Yamagoe S, Umeyama T, Kajiwara S, Ohno H, Miyazaki Y.

''' Synteny was analyzed using our scripts incorporated into Ruby ( and BioRuby ( The synteny around a targeted gene was analyzed by comparing chromosomal genes near the target gene with adjacent genes close to homologues corresponding to the target gene. '''


Gene. 2010 Dec 1;469(1-2):45-51. Epub 2010 Sep 15.

Reducing chimera formation during PCR amplification to ensure accurate genotyping.

Smyth RP, Schlub TE, Grimm A, Venturi V, Chopra A, Mallal S, Davenport MP, Mak J.

''' All sequencing analysis was performed using software custom written in BioRuby ( '''

BMC Bioinformatics. 2010 Jul 21;11:388.

A comparative study of conservation and variation scores.

Johansson F, Toh H.

(Caption of Table 3)

''' I: implemented for this study and available at '''

Nucl. Acids Res. (2010) 38 (suppl 2): W706-W711.

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services

Toshiaki Katayama*, Mitsuteru Nakao* and Toshihisa Takagi

''' The Open Bio* libraries (14), including BioPerl (15), BioRuby (, BioPython (16) and BioJava (17), provide parsers for major database entry and software output formats such as the BLAST report. ''' ''' Without this, the user will need to install a bioinformatics library such as BioPerl, BioPython, BioRuby or BioJava and to write a program to extract the desired information from the retrieved entries. ... To resolve this situation, we embedded BioPerl and BioRuby libraries in the TogoWS server. '''

FEBS Lett. 2010 Jul 15. [Epub ahead of print]

AMPK beta subunits display isoform specific affinities for carbohydrates.

Koay A, Woodcroft B, Petrie EJ, Yue H, Emanuelle S, Bieri M, Bailey MF, Hargreaves M, Park JT, Park KH, Ralph S, Neumann D, Stapleton D, Gooley PR.

''' Distance, parsimony and maximum likelihood tree making methods were then used to infer trees using PHYLIP PROTDIST, PROTPARS [21], and PhyML [22], respectively, automated using custom-built BioRuby scripts [23]. '''

BMC Biol. 2010 May 24;8(1):68. [Epub ahead of print]

Nutrient control of eukaryote cell growth: a systems biology study in yeast.

Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG.

''' All other methods were implemented in either Ruby using the BioRuby package [77], RSRuby [78], or R [75] using packages from Bioconductor [79]. '''

BMC Genomics. 2010 May 10;11(1):291. [Epub ahead of print]

Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.

Mao X, Olman V, Stuart R, Paulsen IT, Palenik B, Xu Y.

''' We implemented a script based on BioRuby ( to calculate the average fold-change of expression levels for each gene under two conditions if microarray data is available, otherwise we have collected genes from published papers, which were found to be differentially expressed (see Additional file 12). '''


Genome Res. 2009 Aug;19(8):1393-403. Epub 2009 May 14.

Domain shuffling and the evolution of vertebrates.

Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N, Wada H.

''' Some scripts for parsing the data and for making pairwise domain matrixes were written using Ruby ( and BioRuby ( '''

BMC Evol Biol. 2009 Aug 11;9:197.

Cyanobacterial contribution to the genomes of the plastid-lacking protists.

Maruyama S, Matsuzaki M, Misawa K, Nozaki H.

''' A genome-wide phylogenetic program was made with several bench-made BioRuby scripts (Additional file 1), referring to the previously reported phylogenomic pipeline used in the macronuclear genome analysis of Tetrahymena thermophila [63]. '''

Database (Oxford). 2009;2009:bap009. Epub 2009 Aug 4.

Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs.

Wissler L, Dattolo E, Moore AD, Reusch TB, Olsen JL, Migliaccio M, Bornberg-Bauer E, Procaccini G.

''' Our application operates under an Apache web server on a DEBIAN Linux system and integrates a MySQL database, Apache's Lucene search engine library, the BioRuby library, the statistical language R and NCBI BLAST. '''

Bioinformatics. 2009 Jun 15;25(12):1559-60. Epub 2009 Apr 8.

BIPA: a database for protein-nucleic acid interaction in 3D structures.

Lee S, Blundell TL.

''' The database was created in the MySQL ( database management system, and its web interface was developed using the Ruby on Rails (http://www.rubyonrails. org/) web framework and the BioRuby ( library. '''

Carbohydr Res. 2009 May 12;344(7):881-7. Epub 2009 Mar 9.

Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.

Hashimoto K, Tokimatsu T, Kawano S, Yoshizawa AC, Okuda S, Goto S, Kanehisa M.

''' Various computational operations were performed with the BioRuby library version 1.1 for the Ruby language (http:// '''

Amyloid. 2009 Mar;16(1):1-8.

AL-Base: a visual platform analysis tool for the study of amyloidogenic immunoglobulin light chain sequences.

Bodi K, Prokaeva T, Spencer B, Eberhard M, Connors LH, Seldin DC.

''' Ruby on Rails ties the back-end database to the front-end website, and simplifies the process of adding new features and functionality. Many features of the database make use of the BioRuby library ( '''

Bioinformatics. 2009 Apr 1;25(7):958-9. Epub 2009 Feb 13.

CGAS: comparative genomic analysis server.

Itoh M, Watanabe H.

''' The CGAS is a web server with the Ruby on Rails framework with JavaScript. The interface within the dot plot viewer and the annotation viewer was implemented using Google Maps API version 2. Interpretation of biological data and interactive entry fetching from public database were achieved by the BioRuby library ( and the TogoWS system. The documentation of CGAS is provided at '''

PLoS One. 2009;4(1):e4219. Epub 2009 Jan 19.

Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.

Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T.

''' This analysis pipeline was constructed by utilizing BioRuby [39], BioPerl [40], and MySQL. '''

Gene. 2009 Jul 15;441(1-2):100-10. Epub 2008 Dec 24.

Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes.

Hirakawa M, Nishihara H, Kanehisa M, Okada N.

''' ... Besides the above-mentioned tool, the computations in the present work were conducted using Ruby scripts employing BioRuby ( 3. Results. 3.1. Exploration of AmnSINE1s from genomes of broad Amniota species. ... '''


Mol Biol Evol. 2008 Jun;25(6):1167-79. Epub 2008 Mar 20.

A cryptic algal group unveiled: a plastid biosynthesis pathway in the oyster parasite Perkinsus marinus.

Matsuzaki M, Kuroiwa H, Kuroiwa T, Kita K, Nozaki H.

''' Iterations were performed using the newly developed Ruby script, facilitated by the BioRuby library ( (Goto et al. 2003). '''

J Lipid Res. 2008 Jan;49(1):183-91. Epub 2007 Oct 7.

The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes.

Hashimoto K, Yoshizawa AC, Okuda S, Kuma K, Goto S, Kanehisa M.

''' ... Then, using the distance, a hierarchical cluster was calculated with the complete linkage method of the R program package for statistical computing version 1.7.1 (27) and with the BioRuby library version 1.0 ( ... '''

Pac Symp Biocomput. 2008:580-91.

Enabling integrative genomic analysis of high-impact human diseases through text mining.

Dudley J, Butte AJ.

''' For the 1,231 GEO DataSets (GDS) experiments associated with a PUBMED identifier, we downloaded the corresponding MEDLINE record and extracted the MeSH using the BioRuby toolkit ( The extracted MeSH terms were stored in a relational database along with the associated GDS identifier, resulting in 20,654 distinct mappings. '''


J Antimicrob Chemother. 2007 Dec;60(6):1264-72. Epub 2007 Oct 2.

The Candida glabrata putative sterol transporter gene CgAUS1 protects cells against azoles in the presence of serum.

Nakayama H, Tanabe K, Bard M, Hodgson W, Wu S, Takemori D, Aoyama T, Kumaraswami NS, Metzler L, Takano Y, Chibana H, Niimi M.

''' ... multiple/pairwise sequence alignment program. 22 The synteny and transcriptional factors were analysed using our scripts implemented in Ruby (http://www.ruby-lang. org/) and BioRuby ( The synteny around a ... '''

Gene. 2007 Oct 15;401(1-2):172-80. Epub 2007 Aug 1.

Analysis of invariant sequences in 266 complete genomes.

Goto N, Kurokawa K, Yasunaga T.

''' We used BioRuby ( to summarize the results of InterProScan. 2.4. '''

BMC Bioinformatics. 2007 Mar 13;8:88.

Regulation of metabolic networks by small molecule metabolites.

Gutteridge A, Kanehisa M, Goto S.

''' Power law fitting and confidence limit evaluation is performed using the igraph package[39] for the R statistical computing platform. Other analysis is performed using Ruby and the BioRuby[40], RSRuby[41] and Tioga[42] packages. '''

Nucleic Acids Res. 2007 Jan;35(Database issue):D546-9. Epub 2006 Nov 16.

CutDB: a proteolytic event database.

Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A.

''' The information processing to transfer data into MySQL was performed using BioRuby. '''

Genome Inform. 2007;19:50-60.

Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

Kawashima S, Kawashima T, Putnam NH, Rokhsar DS, Wada H, Kanehisa M.

''' Outputs of hmmpfam are parsed by scripts written in Ruby programming language [29] with BioRuby library [22]. '''


BMC Genomics. 2006 Nov 29;7:300.

Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase).

Odronitz F, Kollmar M.

''' The automation scripts for parsing BLAST [14] and HMMER [15] output are written in Ruby [16] making use of the BioRuby library [17]. Sequences are scanned for domains using the Pfam_fs release 19.0 database [18] containing 8183 hidden markov models. '''

(Caption of Figure 1)

''' FASTA files containing sequence alignments are imported and exported using Ruby [16] scripts. The import function uses the BioRuby [17] library. Other databases are referenced via their IDs, which are used to generate hyperlinks to records on their web sites. Automated processes are started by a delegation server, which receives instructions from the database on insert or update of records. The automated processes write information into the database using Active Record. The frontend is generated using the Ruby on Rails [10] web application framework. '''

Genome Inform. 2006;17(1):173-83.

The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes.

Hashimoto K, Yoshizawa AC, Saito K, Yamada T, Kanehisa M.

''' The clustering analysis was performed with the R program package for statistical computing ver.1.7.1 [24, 36] and with the BioRuby library ver.1.0 [34]. '''


Bioinformatics. 2005 Apr 1;21(7):912-21. Epub 2004 Oct 27.

Fast and accurate database homology search using upper bounds of local alignment scores.

Itoh M, Goto S, Akutsu T, Kanehisa M.

''' To test the efficiency of our method under the condition that the whole set of protein sequences of similar species is known, we implemented a simple program by combining BLAST and SSEARCH programs using the BioRuby ( The BioRuby is a suite of open software tools for bioinformatics written in the Ruby programming language. '''


Mol Biol Evol. 2004 Oct;21(10):1813-9. Epub 2004 Jul 7.

Chloroplast phylogeny indicates that bryophytes are monophyletic.

Nishiyama T, Wolf PG, Kugita M, Sinclair RB, Sugita M, Sugiura C, Wakasugi T, Yamada K, Yoshinaga K, Yamaguchi K, Ueda K, Hasebe M.

''' Coding sequences were extracted from the annotated sequences using bioruby ( '''

Bioinformatics. 2004 Jan 1;20(1):51-7.

Light-weight integration of molecular biological databases.

Philippi S.

''' This implementation is exclusively based on freely available open source components like the PostgreSQL database management system and the BioRuby project. '''


''' These databases are freely available as flatfiles and thus converted into an XML format in the first processing step. The converters built for these purposes are partially based on the BioRuby open source project (BioRuby, 2003, '''