Efforts towards accessible and reliable bioinformatics

[1]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[2]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[3]  Sattanathan Subramanian,et al.  Pipelined data-flow delegated orchestration for data-intensive eScience workflows , 2013, Int. J. Web Inf. Syst..

[4]  Jill P. Mesirov,et al.  GenomeSpace: an environment for frictionless bioinformatics , 2013 .

[5]  Thomas Lengauer,et al.  Editorial. The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) , 1999, Bioinform..

[6]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[7]  Christian Burks,et al.  Molecular Biology Database List , 1999, Nucleic Acids Res..

[8]  H. Bernstein.  Recent changes to RasMol, recombining the variants. , 2000, Trends in biochemical sciences.

[9]  D. Lipman,et al.  National Center for Biotechnology Information , 2019, Springer Reference Medizin.

[10]  Rodger Staden,et al.  The current status and portability of our sequence handling software , 1986, Nucleic Acids Res..

[11]  Sylvain Gaillard,et al.  Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics , 2006, BMC Bioinformatics.

[12]  Rodrigo Lopez,et al.  The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI , 2015, Nucleic Acids Res..

[13]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[14]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[15]  S Henikoff,et al.  Sequence analysis by electronic mail server. , 1993, Trends in biochemical sciences.

[16]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[17]  Mark D. Wilkinson,et al.  BioMOBY: An Open Source Biological Web Services Proposal , 2002, Briefings Bioinform..

[18]  J. Eisen.  The Genetic Data Environment , 1997 .

[19]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[20]  Dieter Schmalstieg,et al.  StratomeX: Visual Analysis of Large‐Scale Heterogeneous Genomics Data for Cancer Subtype Characterization , 2012, Comput. Graph. Forum.

[21]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[22]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[23]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[24]  Carole A. Goble,et al.  The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud , 2013, Nucleic Acids Res..

[25]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[26]  Nicolas Le Novère,et al.  Identifiers.org and MIRIAM Registry: community resources to provide persistent identification , 2011, Nucleic Acids Res..

[27]  Etsuko N. Moriyama,et al.  Vector NTI, a balanced all-in-one sequence analysis suite , 2004, Briefings Bioinform..

[28]  R. Staden.  A strategy of DNA sequencing employing computer programs. , 1979, Nucleic acids research.

[29]  M Hucka,et al.  Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. , 2004, Systems biology.

[30]  Amedeo Napoli,et al.  BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery , 2010, Int. J. Metadata Semant. Ontologies.

[31]  Paulien Hogeweg,et al.  The Roots of Bioinformatics in Theoretical Biology , 2011, PLoS Comput. Biol..

[32]  Robert Schmieder,et al.  SEQanswers: an open access community for collaboratively decoding genomes , 2012, Bioinform..

[33]  Leighton Pritchard,et al.  GenomeDiagram: a python package for the visualization of large-scale genomic data , 2006, Bioinform..

[34]  Emmanuel Barillot,et al.  HuGeMap: a distributed and integrated Human Genome Map database , 1998, Nucleic Acids Res..

[35]  Carole A. Goble,et al.  myExperiment: a repository and social network for the sharing of bioinformatics workflows , 2010, Nucleic Acids Res..

[36]  Gary Benson,et al.  Editorial: Nucleic Acids Research annual Web Server Issue in 2015 , 2015, Nucleic Acids Res..

[37]  Vincent J. Henry,et al.  OMICtools: an informative directory for multi-omic data analysis , 2014, Database J. Biol. Databases Curation.

[38]  Gary D. Bader,et al.  Cytoscape Web: an interactive web-based network browser , 2010, Bioinform..

[39]  P. Argos,et al.  SRS: information retrieval system for molecular biology data banks. , 1996, Methods in enzymology.

[40]  Christopher J. Rawlings,et al.  Ondex Web: web-based visualization and exploration of heterogeneous biological networks , 2013, Bioinform..

[41]  Alex Bateman,et al.  Ten Simple Rules for Editing Wikipedia , 2010, PLoS Comput. Biol..

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

[43]  Jason P. Mulvenna,et al.  Bioclojure: a functional library for the manipulation of biological sequences , 2014, Bioinform..

[44]  Rodger Staden,et al.  Graphic methods to determine the function of nucleic acid sequences , 1984, Nucleic Acids Res..

[45]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[46]  Alessandro Vullo,et al.  Ensembl 2015 , 2014, Nucleic Acids Res..

[47]  Monica C Munoz-Torres,et al.  Web Apollo: a web-based genomic annotation editing platform , 2013, Genome Biology.

[48]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[49]  Emmanuel Barillot,et al.  DBcat: a catalog of biological databases , 1999, Nucleic Acids Res..

[50]  Kevin Thornton,et al.  libsequence: a C++ class library for evolutionary genetic analysis , 2003, Bioinform..

[51]  Mikko Koski,et al.  Chipster: user-friendly analysis software for microarray and other high-throughput data , 2011, BMC Genomics.

[52]  Gultekin Özsoyoglu,et al.  Pathways Database System: An Integrated System for Biological Pathways , 2003, Bioinform..

[53]  Hideaki Sugawara,et al.  Biological SOAP servers and web services provided by the public sequence data bank , 2003, Nucleic Acids Res..

[54]  Olivier Sallou,et al.  Sprints, Hackathons and Codefests as community gluons in computational biology , 2013 .

[55]  Geir Kjetil Sandve,et al.  Identifying elemental genomic track types and representing them uniformly , 2011, BMC Bioinformatics.

[56]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[57]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[58]  Burkhard Rost,et al.  FreeContact: fast and free software for protein contact prediction from residue co-evolution , 2014, BMC Bioinformatics.

[59]  Avner Schlessinger,et al.  PredictProtein—an open resource for online prediction of protein structural and functional features , 2014, Nucleic Acids Res..

[60]  Paul T. Spellman,et al.  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.

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

[62]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[63]  G. Cameron,et al.  The EMBL data library. , 1988, Nucleic acids research.

[64]  Martin Vingron,et al.  The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources , 2004, Bioinform..

[65]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[66]  Gary D Bader,et al.  BMC Biology BioMed Central , 2007 .

[67]  Christian M. Zmasek,et al.  phyloXML: XML for evolutionary biology and comparative genomics , 2009, BMC Bioinformatics.

[68]  Don Gilbert,et al.  Bioinformatics software resources. , 2004, Briefings in bioinformatics.

[69]  Scott McMillan,et al.  The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers , 2005, Nucleic Acids Res..

[70]  Arek Kasprzyk,et al.  BioMart: driving a paradigm change in biological data management , 2011, Database J. Biol. Databases Curation.

[71]  Thomas L. Madden,et al.  BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..

[72]  Jon C. Ison,et al.  Using registries to integrate bioinformatics tools and services into workbench environments , 2016, International Journal on Software Tools for Technology Transfer.

[73]  Yves Moreau,et al.  ISMB/ECCB 2015 , 2015, Bioinform..

[74]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[75]  Andreas D. Baxevanis,et al.  The Molecular Biology Database Collection: an online compilation of relevant database resources , 2000, Nucleic Acids Res..

[76]  Tomas Vitvar,et al.  SAWSDL: Semantic Annotations for WSDL and XML Schema , 2007, IEEE Internet Computing.

[77]  Rolf Apweiler,et al.  The European Bioinformatics Institute’s data resources 2014 , 2013, Nucleic Acids Res..

[78]  Kathryn F. Beal,et al.  The Staden package, 1998. , 2000, Methods in molecular biology.

[79]  Angel Herráez,et al.  Biomolecules in the computer: Jmol to the rescue , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[80]  Chris F. Taylor,et al.  The MGED Ontology: a resource for semantics-based description of microarray experiments , 2006, Bioinform..

[81]  Sattanathan Subramanian,et al.  Direct data transfer between SOAP web services in orchestration , 2012, IIWAS '12.

[82]  Emmanuel Barillot,et al.  DBcat: a catalog of 500 biological databases , 2000, Nucleic Acids Res..

[83]  Ulf Leser,et al.  A proposal for a standard CORBA interface for genome maps , 1999, Bioinform..

[84]  R. Staden.  Sequence data handling by computer. , 1977, Nucleic acids research.

[85]  R. Staden.  Further procedures for sequence analysis by computer. , 1978, Nucleic acids research.

[86]  Aleksandra Pawlik,et al.  BioJS: an open source standard for biological visualisation – its status in 2014 , 2014, F1000Research.

[87]  Christopher J. Rawlings,et al.  Graph-based analysis and visualization of experimental results with ONDEX , 2006, Bioinform..

[88]  Enrico Pontelli,et al.  Initial Implementation of a Comparative Data Analysis Ontology , 2009, Evolutionary bioinformatics online.

[89]  László Kaján,et al.  Cloud Prediction of Protein Structure and Function with PredictProtein for Debian , 2013, BioMed research international.

[90]  Jiren Wang,et al.  Soap-HT-BLAST: high throughput BLAST based on Web services , 2003, Bioinform..

[91]  Enis Afgan,et al.  Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy , 2012, Current protocols in bioinformatics.

[92]  T. Oinn,et al.  Soaplab - a unified Sesame door to analysis tools , 2003 .

[93]  Calton Pu,et al.  Design and application of PDBlib, a C++ macromolecular class library , 1994, Comput. Appl. Biosci..

[94]  Tirso Pons,et al.  Homology modeling, model and software evaluation: three related resources , 1998, Bioinform..

[95]  Lennart Martens,et al.  Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. , 2007, Molecular & cellular proteomics : MCP.

[96]  Teresa K. Attwood,et al.  Concepts, historical milestones and the central place of bioinformatics in modern biology: a European perspective. , 2011 .

[97]  Yukako Tohsato,et al.  Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data , 2014, Bioinform..

[98]  K. Bretonnel Cohen,et al.  BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains , 2014, J. Biomed. Semant..

[99]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[100]  Hilmar Lapp,et al.  NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata , 2012, Systematic biology.

[101]  S. Tabassum.  Editorial , 1968, Euroasian journal of hepato-gastroenterology.

[102]  Gabor T. Marth,et al.  Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web , 2013, Bioinform..

[103]  Brian E. Granger,et al.  IPython: A System for Interactive Scientific Computing , 2007, Computing in Science & Engineering.

[104]  Reinhard Dölz.  Hierarchical Access System for Sequence Libraries in Europe (HASSLE): a tool to access sequence databases remotely , 1994, Comput. Appl. Biosci..

[105]  Haruki Nakamura,et al.  PDBML: the representation of archival macromolecular structure data in XML , 2005, Bioinform..

[106]  Maria Jesus Martin,et al.  BioJS: an open source JavaScript framework for biological data visualization , 2013, Bioinform..

[107]  Finn Drabløs,et al.  MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis , 2012, BMC Bioinformatics.

[108]  Robert Herzog,et al.  WWW2GCG, a web interface to the GCG biological sequences analysis software , 1996, Comput. Graph..

[109]  Tin Wee Tan,et al.  Towards BioDBcore: a community-defined information specification for biological databases , 2010, Database J. Biol. Databases Curation.

[110]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[111]  Ross A. Overbeek,et al.  The genetic data environment an expandable GUI for multiple sequence analysis , 1994, Comput. Appl. Biosci..

[112]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[113]  G D Schuler,et al.  A workbench for multiple alignment construction and analysis , 1991, Proteins.

[114]  Robert B. Russell,et al.  Topic Pages: PLoS Computational Biology Meets Wikipedia , 2012, PLoS Comput. Biol..

[115]  G. B. Petersen,et al.  HOMED: a homologous sequence editor , 1987, Comput. Appl. Biosci..

[116]  Michael Y. Galperin,et al.  The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection , 2014, Nucleic Acids Res..

[117]  V. Marx.  Biology: The big challenges of big data , 2013, Nature.

[118]  Toshihisa Takagi,et al.  The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data , 2014, Nucleic Acids Res..

[119]  Emily S. Charlson,et al.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications , 2011, Nature Biotechnology.

[120]  Toshihisa Takagi,et al.  TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services , 2010, Nucleic Acids Res..

[121]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[122]  Patricia Rodriguez-Tomé,et al.  The European Bioinformatics Institute (EBI) databases , 1994, Nucleic Acids Res..

[123]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[124]  Tim Berners-Lee,et al.  The World-Wide Web , 1994, CACM.

[125]  Galt P. Barber,et al.  BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..

[126]  Ronny Lorenz,et al.  The Vienna RNA Websuite , 2008, Nucleic Acids Res..

[127]  Marta Bleda,et al.  Genome Maps, a new generation genome browser , 2013, Nucleic Acids Res..

[128]  Other Contributors Are Indicated Where They Contribute.  The Free Software Foundation , 2017 .

[129]  Rainer Fuchs,et al.  CLUSTAL V: improved software for multiple sequence alignment , 1992, Comput. Appl. Biosci..

[130]  Sameer Velankar,et al.  SOAP-based services provided by the European Bioinformatics Institute , 2005, Nucleic Acids Res..

[131]  Mark Johnson,et al.  NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..

[132]  Ulf Leser,et al.  EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation , 1999, German Conference on Bioinformatics.

[133]  Brent S. Pedersen,et al.  BioStar: An Online Question & Answer Resource for the Bioinformatics Community , 2011, PLoS Comput. Biol..

[134]  Gordon Gremme,et al.  AnnotationSketch: a genome annotation drawing library , 2009, Bioinform..

[135]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[136]  Patricia Rodriguez-Tomé,et al.  Mapplet: a CORBA-based genome map viewer , 1998, Bioinform..

[137]  Tiziana Margaria,et al.  Semantics-based composition of EMBOSS services , 2011, J. Biomed. Semant..

[138]  Greg Brown,et al.  A performance and energy comparison of FPGAs, GPUs, and multicores for sliding-window applications , 2012, FPGA '12.

[139]  R D Appel,et al.  A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. , 1994, Trends in biochemical sciences.

[140]  Mark A. Williams,et al.  The Bioinformatics Template Library—generic Components for Biocomputing , 2001 .

[141]  Dan M. Bolser,et al.  The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis , 2011, Nucleic Acids Res..

[142]  Hideaki Sugawara,et al.  Web API for biology with a workflow navigation system , 2009, Nucleic Acids Res..

[143]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[144]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[145]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[146]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[147]  Anton Nekrutenko,et al.  Galaxy CloudMan: delivering cloud compute clusters , 2010, BMC Bioinformatics.

[148]  Gary D Bader,et al.  PSICQUIC and PSISCORE: accessing and scoring molecular interactions , 2011, Nature Methods.

[149]  Christian Blouin,et al.  libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny , 2005, BMC Bioinformatics.

[150]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[151]  Hilmar Lapp,et al.  The Bioinformatics Open Source Conference (BOSC) 2013 , 2015, Bioinform..

[152]  Kjell Petersen,et al.  Analysis of Gene‐Expression Data Using J‐Express , 2008, Current protocols in bioinformatics.

[153]  Rodrigo Lopez,et al.  The EMBL-EBI bioinformatics web and programmatic tools framework , 2015, Nucleic Acids Res..

[154]  Natalya F. Noy,et al.  BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse , 2009 .

[155]  R Staden,et al.  The staden sequence analysis package , 1996, Molecular biotechnology.

[156]  David L. Wild,et al.  Protein analyst - a distributed object environment for protein sequence and structure analysis , 1999, Bioinform..

[157]  Andreas Prlic,et al.  BioJava: an open-source framework for bioinformatics in 2012 , 2012, Bioinform..

[158]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[159]  Geoffrey J. Barton,et al.  Java bioinformatics analysis web services for multiple sequence alignment—JABAWS:MSA , 2011, Bioinform..

[160]  Patricia Rodriguez-Tomé.  The BioCatalog , 1998, Bioinform..

[161]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[162]  Barend Mons,et al.  Open PHACTS: semantic interoperability for drug discovery. , 2012, Drug discovery today.

[163]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[164]  Maureen J Donlin,et al.  Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.

[165]  Johannes Goll,et al.  A new reference implementation of the PSICQUIC web service , 2013, Nucleic Acids Res..

[166]  Steve Pettifer,et al.  WIWS: a protein structure bioinformatics Web service collection , 2010, Nucleic Acids Res..

[167]  Mark D. Wilkinson,et al.  The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation , 2011 .

[168]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[169]  D Gilbert.  Free software in molecular biology for Macintosh and MS Windows computers. , 2000, Methods in molecular biology.

[170]  Ronald J. Vetter,et al.  Mosaic and the World Wide Web , 1994, Computer.

[171]  Dawn Field,et al.  Open software for biologists: from famine to feast , 2006, Nature Biotechnology.

[172]  Rodrigo Lopez,et al.  Analysis Tool Web Services from the EMBL-EBI , 2013, Nucleic Acids Res..

[173]  Thure Etzold,et al.  SRS - an indexing and retrieval tool for flat file data libraries , 1993, Comput. Appl. Biosci..

[174]  M. Andreessen.  MCSA Mosaic Technical Summary , 1993 .

[175]  Olivier Sallou,et al.  Community-driven development for computational biology at Sprints, Hackathons and Codefests , 2014, BMC Bioinformatics.

[176]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[177]  Vassilios Ioannidis,et al.  ExPASy: SIB bioinformatics resource portal , 2012, Nucleic Acids Res..

[178]  D. Womble,et al.  GCG: The Wisconsin Package of sequence analysis programs. , 2000, Methods in molecular biology.

[179]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[180]  Rodger Staden,et al.  An improved sequence handling package that runs on the Apple Macintosh , 1990, Comput. Appl. Biosci..

[181]  Rodrigo Lopez,et al.  A new bioinformatics analysis tools framework at EMBL–EBI , 2010, Nucleic Acids Res..

[182]  Domenica D'Elia,et al.  The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community , 2009, BMC Bioinformatics.

[183]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[184]  Pawel Sztromwasser,et al.  Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows , 2011, J. Integr. Bioinform..

[185]  Gordon Gremme,et al.  GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[186]  Jonathan Crabtree,et al.  Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG , 2014, Bioinform..

[187]  J A Eisen,et al.  The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. , 1997, Methods in molecular biology.

[188]  Carole A. Goble,et al.  Community-driven computational biology with Debian Linux , 2010, BMC Bioinformatics.

[189]  Rodrigo Lopez,et al.  Public services from the European Bioinformatics Institute , 2003, Briefings Bioinform..

[190]  Surendra Kumar,et al.  AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses , 2009, BMC Bioinformatics.

[191]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[192]  Steve Pettifer,et al.  Utopia documents: linking scholarly literature with research data , 2010, Bioinform..

[193]  Allan Kuchinsky,et al.  Exploring Biological Networks with Cytoscape Software , 2008, Current protocols in bioinformatics.

[194]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[195]  Paweł Sztromwasser.  Throughput and robustness of bioinformatics pipelines for genome-scale data analysis , 2014 .

[196]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.

[197]  Jan Krüger,et al.  Playing with pesticides. , 1998, BMC Bioinformatics.

[198]  Daniel MacLean,et al.  Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics , 2012, Bioinform..

[199]  R A Harper.  EMBnet: an institute without walls. , 1996, Trends in biochemical sciences.

[200]  Jason E. Stewart,et al.  Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.

[201]  Steve Pettifer,et al.  An active registry for bioinformatics web services , 2009, Bioinform..

[202]  Rodrigo Lopez,et al.  Public web-based services from the European Bioinformatics Institute , 2004, Nucleic Acids Res..

[203]  G. Schuler,et al.  Entrez: molecular biology database and retrieval system. , 1996, Methods in enzymology.

[204]  Inge Jonassen,et al.  J-Express: exploring gene expression data using Java , 2001, Bioinform..

[205]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[206]  Robert D. Finn,et al.  Rfam: Wikipedia, clans and the “decimal” release , 2010, Nucleic Acids Res..

[207]  Rutger A. Vos,et al.  BIO::Phylo-phyloinformatic analysis using perl , 2011, BMC Bioinformatics.

[208]  Fumikazu Konishi,et al.  The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies , 2013, J. Biomed. Semant..

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

[210]  Hagen Blankenburg,et al.  Integrating biological data – the Distributed Annotation System , 2008, BMC Bioinformatics.

[211]  Robert Buels,et al.  JBrowse: A Next-Generation Genome Browser , 2014 .

[212]  Paul Kavanagh,et al.  The Open Source Definition , 2004 .

[213]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[214]  Michelle D. Brazas,et al.  A decade of web server updates at the bioinformatics links directory: 2003–2012 , 2012, Nucleic Acids Res..

[215]  Matthias Schwab,et al.  Making scientific computations reproducible , 2000, Comput. Sci. Eng..

[216]  Renzo Kottmann,et al.  A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). , 2008, Omics : a journal of integrative biology.

[217]  Carole A. Goble,et al.  Taverna: a tool for building and running workflows of services , 2006, Nucleic Acids Res..

[218]  Pjotr Prins,et al.  BioRuby: bioinformatics software for the Ruby programming language , 2010, Bioinform..

[219]  Finn Drabløs,et al.  The Genomic HyperBrowser: an analysis web server for genome-scale data , 2013, Nucleic Acids Res..

[220]  Pierre Tufféry,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .

[221]  E. L. Cabot,et al.  Simultaneous editing of multiple nucleic acid and protein sequences with ESEE , 1989, Comput. Appl. Biosci..

[222]  Atsuko Yamaguchi,et al.  TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model , 2014, Nucleic Acids Res..

[223]  W. Taylor.  A flexible method to align large numbers of biological sequences , 2005, Journal of Molecular Evolution.

[224]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[225]  Tim J. P. Hubbard,et al.  Dalliance: interactive genome viewing on the web , 2011, Bioinform..

[226]  O Ritter,et al.  X-HUSAR, an X-based graphical interface for the analysis of genomic sequences. , 1995, Computer methods and programs in biomedicine.

[227]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[228]  R Staden,et al.  An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. , 1982, Nucleic acids research.

[229]  D. Haussler,et al.  Assembly of the working draft of the human genome with GigAssembler. , 2001, Genome research.

[230]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[231]  Dieter Schmalstieg,et al.  Caleydo: connecting pathways and gene expression , 2009, Bioinform..

[232]  J. Tate,et al.  The RNA WikiProject: community annotation of RNA families. , 2008, RNA.

[233]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[234]  Carole A. Goble,et al.  The myGrid ontology: bioinformatics service discovery , 2007, Int. J. Bioinform. Res. Appl..

[235]  Rodrigo Lopez,et al.  Web services at the European Bioinformatics Institute-2009 , 2009, Nucleic Acids Res..

[236]  Michael Y. Galperin,et al.  The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection , 2013, Nucleic Acids Res..

[237]  M Parker.  Biological data access through Gopher. , 1993, Trends in biochemical sciences.

[238]  Steve Pettifer,et al.  BioXSD: the common data-exchange format for everyday bioinformatics web services , 2010, Bioinform..

[239]  D D Womble.  Web-based interfaces for the GCG sequence analysis programs. , 2000, Methods in molecular biology.

[240]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[241]  Michael Y. Galperin,et al.  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..

[242]  Rodrigo Lopez,et al.  Web Services at the European Bioinformatics Institute , 2007, Nucleic Acids Res..

[243]  Yves Moreau,et al.  ECCB 2014: The 13th European Conference on Computational Biology , 2014, Bioinform..

[244]  Hernán F. Morales,et al.  BioSmalltalk: a pure object system and library for bioinformatics , 2013, Bioinform..

[245]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[246]  G. K. Sandve,et al.  The Genomic HyperBrowser: inferential genomics at the sequence level , 2010, Genome Biology.

[247]  Carole A. Goble,et al.  BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..

[248]  Andreas Prlic,et al.  Sequence analysis , 2003 .

[249]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[250]  S. Schuster,et al.  Model of Tryptophan Metabolism, Readily Scalable Using Tissue-specific Gene Expression Data* , 2013, The Journal of Biological Chemistry.

[251]  Benjamin T. Porebski,et al.  Interactive visualization tools for the structural biologist , 2013, Journal of applied crystallography.

[252]  Akira R. Kinjo,et al.  The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium* , 2010, J. Biomed. Semant..

[253]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[254]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[255]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[256]  Oliver Hofmann,et al.  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level , 2010, Bioinform..

[257]  Peter Murray-Rust,et al.  Development of chemical markup language (CML) as a system for handling complex chemical content , 2001 .

[258]  Rodger Staden,et al.  An X windows and UNIX implementation of our sequence analysis package , 1991, Comput. Appl. Biosci..

[259]  Di Tommaso Paolo,et al.  A novel tool for highly scalable computational pipelines , 2014 .

[260]  Jill P Mesirov,et al.  Accessible Reproducible Research , 2010, Science.

[261]  Jian Hu,et al.  Design and implementation of a CORBA-based genome mapping system prototype , 1998, Bioinform..

[262]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[263]  H. Mangalam,et al.  The Bio* toolkits--a brief overview. , 2002, Briefings in bioinformatics.

[264]  John Chilton,et al.  Portable workflow and tool descriptions with the CWL , 2015 .

[265]  Terri K. Attwood,et al.  The EMBRACE web service collection , 2010, Nucleic Acids Res..

[266]  Burkhard Rost,et al.  The PredictProtein server , 2003, Nucleic Acids Res..

[267]  Katerina Michalickova,et al.  BIR Pipeline for Preparation of Phylogenomic Data , 2015, Evolutionary bioinformatics online.

[268]  Pietro Liò,et al.  The BioMart community portal: an innovative alternative to large, centralized data repositories , 2015, Nucleic Acids Res..

[269]  Patrick Lambrix,et al.  Workshop on laboratory protocol standards for the Molecular Methods Database. , 2013, New biotechnology.

[270]  Robert D. Finn,et al.  Integrating sequence and structural biology with DAS , 2007, BMC Bioinformatics.

[271]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[272]  Sattanathan Subramanian,et al.  Optimizing the Data-Traffic of Centrally Coordinated Scientific Workflow Systems , 2010, 2010 IEEE International Conference on Web Services.

[273]  Kim Rutherford,et al.  Artemis: sequence visualization and annotation , 2000, Bioinform..

[274]  Robert D. Finn,et al.  Making your database available through Wikipedia: the pros and cons , 2011, Nucleic Acids Res..

[275]  Knut Reinert,et al.  SeqAn An efficient, generic C++ library for sequence analysis , 2008, BMC Bioinformatics.

[276]  Steve Pettifer,et al.  EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats , 2013, Bioinform..

[277]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[278]  Minoru Kanehisa,et al.  KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System , 2003 .

[279]  Vladimir Makarenkov,et al.  Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations , 2012, PloS one.

[280]  Reinhard Dölz.  The EMBnet Project-European Molecular Biology Network , 1992, Comput. Networks ISDN Syst..