Summary: Specific languages used to prepare computer programs.
- Klann J, Murphy S. Computing health quality measures using Informatics for Integrating Biology and the Bedside. J Med Internet Res. 2013;15:e75 pubmed publisher..It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers. ..
- Demir E, Babur O, Rodchenkov I, Aksoy B, Fukuda K, Gross B, et al. Using biological pathway data with paxtools. PLoS Comput Biol. 2013;9:e1003194 pubmed publisher..Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools. ..
- van Iersel M, Villéger A, Czauderna T, Boyd S, Bergmann F, Luna A, et al. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics. 2012;28:2016-21 pubmed..Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. email@example.com. ..
- Gkoutos G, Schofield P, Hoehndorf R. The Units Ontology: a tool for integrating units of measurement in science. Database (Oxford). 2012;2012:bas033 pubmed publisher..Here, we present the Units Ontology (UO), an ontology currently being used in many scientific resources for the standardized description of units of measurements. ..
- Rognes T. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinformatics. 2011;12:221 pubmed publisher..The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance. ..
- Ebrahim A, Lerman J, Palsson B, Hyduke D. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol. 2013;7:74 pubmed publisher..COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. http://opencobra.sourceforge.net/ ..
- Luna A, Karac E, Sunshine M, Chang L, Nussinov R, Aladjem M, et al. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics. 2011;12:167 pubmed publisher..The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim. ..
- Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;12:77 pubmed publisher..It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation. ..
- Lamy J, Duclos C, Bar Hen A, Ouvrard P, Venot A. An iconic language for the graphical representation of medical concepts. BMC Med Inform Decis Mak. 2008;8:16 pubmed publisher..It could also be used for broader applications, including the design of interfaces for consulting other types of medical document or medical data, or, very simply, to enrich medical texts. ..
- Côté R, Reisinger F, Martens L. jmzML, an open-source Java API for mzML, the PSI standard for MS data. Proteomics. 2010;10:1332-5 pubmed publisher..jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com. ..
- Phillips A, Cardelli L. A programming language for composable DNA circuits. J R Soc Interface. 2009;6 Suppl 4:S419-36 pubmed publisher..The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing. ..
- Nickerson D, Buist M. A physiome standards-based model publication paradigm. Philos Trans A Math Phys Eng Sci. 2009;367:1823-44 pubmed publisher..Here, we review the current state of the art and what needs to be done before such a model publication becomes commonplace. ..
- Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, et al. Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics. 2008;24:1100-1 pubmed..Rintact provides a programmatic interface to the IntAct repository and allows the use of the analytic methods provided by R and Bioconductor. Rintact is freely available at http://bioconductor.org ..
- Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto J, et al. OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol. 2010;4:45 pubmed publisher..Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models. ..
- Prince J, Marcotte E. mspire: mass spectrometry proteomics in Ruby. Bioinformatics. 2008;24:2796-7 pubmed publisher..Freely available at http://mspire.rubyforge.org. Additional data models, usage information, and methods available at http://bioinformatics.icmb.utexas.edu/mspire ..
- Vera G, Jansen R, Suppi R. R/parallel--speeding up bioinformatics analysis with R. BMC Bioinformatics. 2008;9:390 pubmed publisher..Future work is focused on extending the envelope of R/parallel by interconnecting and aggregating the power of several computers, both existing office computers and computing clusters. ..
- Maiwald T, Timmer J. Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics. 2008;24:2037-43 pubmed publisher..The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes. Supplementary data are available at Bioinformatics online. ..
- Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, et al. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS. 2008;12:115-21 pubmed publisher..GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org). ..
- Cooling M, Hunter P, Crampin E. Modelling biological modularity with CellML. IET Syst Biol. 2008;2:73-9 pubmed publisher..Finally, the authors discuss the dilemmas associated with modelling protein-to-protein interactions, and the vision for using future CellML enhancements to resolve potential duplications when combining independently developed models. ..
- Aitken S, Chen Y, Bard J. OBO Explorer: an editor for Open Biomedical Ontologies in OWL. Bioinformatics. 2008;24:443-4 pubmed..We present an ontology editor that allows end users to work directly with this OWL representation of OBO format ontologies. http://www.aiai.ed.ac.uk/project/cobra-ct. ..
- Goodman D. Code generation: a strategy for neural network simulators. Neuroinformatics. 2010;8:183-96 pubmed publisher..The technique is quite general and could be applied to any simulation package. We demonstrate it with the 'Brian' simulator ( http://www.briansimulator.org ). ..
- Jacobsen A, Krogh A, Kauppinen S, Lindow M. miRMaid: a unified programming interface for microRNA data resources. BMC Bioinformatics. 2010;11:29 pubmed publisher..Furthermore, miRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources. ..
- Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics. 2008;24:876-7 pubmed..Last version of BiNoM distributed under the LGPL licence together with documentation, source code and API are available at http://bioinfo.curie.fr/projects/binom ..
- Bauer S, Grossmann S, Vingron M, Robinson P. Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics. 2008;24:1650-1 pubmed publisher..charite.de/ontologizer. Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool. ..
- Li P, Castrillo J, Velarde G, Wassink I, Soiland Reyes S, Owen S, et al. Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data. BMC Bioinformatics. 2008;9:334 pubmed publisher..For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data...
- Bassi S. A primer on python for life science researchers. PLoS Comput Biol. 2007;3:e199 pubmed
- Saez Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos L, Millard B, Lauffenburger D, et al. Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics. 2008;24:840-7 pubmed publisher..DataRail is distributed under the GNU General Public License and available at http://code.google.com/p/sbpipeline/ ..
- Bornstein B, Keating S, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinformatics. 2008;24:880-1 pubmed publisher..LibSBML 3 was released in August 2007. Source code, binaries and documentation are freely available under LGPL open-source terms from http://sbml.org/software/libsbml. ..
- Holland R, Down T, Pocock M, Prlic A, Huen D, James K, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008;24:2096-7 pubmed publisher..biojava.org). BioJava requires Java 1.5 or higher. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists. ..
- Cock P, Antao T, Chang J, Chapman B, Cox C, DALKE A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422-3 pubmed publisher..Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license. ..
- Pedersen M, Phillips A. Towards programming languages for genetic engineering of living cells. J R Soc Interface. 2009;6 Suppl 4:S437-50 pubmed publisher..ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesized and put to work ..
- Fourment M, Gillings M. A comparison of common programming languages used in bioinformatics. BMC Bioinformatics. 2008;9:82 pubmed publisherThe performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms...
- Garny A, Nickerson D, Cooper J, Weber Dos Santos R, Miller A, McKeever S, et al. CellML and associated tools and techniques. Philos Trans A Math Phys Eng Sci. 2008;366:3017-43 pubmed publisher..We also address possible future directions including the need for additional mark-up languages. ..
- Demir E, Cary M, Paley S, Fukuda K, Lemer C, Vastrik I, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010;28:935-42 pubmed publisher..This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. ..
- Beard D, Britten R, Cooling M, Garny A, Halstead M, Hunter P, et al. CellML metadata standards, associated tools and repositories. Philos Trans A Math Phys Eng Sci. 2009;367:1845-67 pubmed publisher..This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website. ..
- Dematté L, Priami C, Romanel A. The Beta Workbench: a computational tool to study the dynamics of biological systems. Brief Bioinform. 2008;9:437-49 pubmed publisher..Finally, we provide a comparison with related approaches and some hints for future extensions. ..
- Aerts J, Law A. An introduction to scripting in Ruby for biologists. BMC Bioinformatics. 2009;10:221 pubmed publisher..We hope this will provide such researchers an idea of how powerful a tool Ruby can be for their data management tasks and encourage them to learn more about it. ..
- Kell D, Mendes P. The markup is the model: reasoning about systems biology models in the Semantic Web era. J Theor Biol. 2008;252:538-43 pubmed
- Asai Y, Suzuki Y, Kido Y, Oka H, Heien E, Nakanishi M, et al. Specifications of insilicoML 1.0: a multilevel biophysical model description language. J Physiol Sci. 2008;58:447-58 pubmed publisher..ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery. ..
- Ballester B, Johnson N, Proctor G, Flicek P. Consistent annotation of gene expression arrays. BMC Genomics. 2010;11:294 pubmed publisher..Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles. ..
- Sukumaran J, Holder M. DendroPy: a Python library for phylogenetic computing. Bioinformatics. 2010;26:1569-71 pubmed publisher..python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy). ..
- Belleau F, Nolin M, Tourigny N, Rigault P, Morissette J. Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008;41:706-16 pubmed publisher..The Bio2RDF repository can be queried at http://bio2rdf.org. ..
- Jordan G, Piel W. PhyloWidget: web-based visualizations for the tree of life. Bioinformatics. 2008;24:1641-2 pubmed publisher..A simple URL-based API allows databases to easily link to and customize PhyloWidget for interactively viewing medium- to large-sized trees. PhyloWidget is available for online use or download at http://www.phylowidget.org/. ..
- Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, et al. OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics. 2008;9:163 pubmed publisher..This has already been demonstrated in several studies. OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de. ..
- Jeong E, Nagasaki M, Saito A, Miyano S. Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol. 2007;7:623-38 pubmed..In order to demonstrate the potential of CSO-based pathway modeling, visualization, and simulation, we present an HFPNe model for the ASEL and ASER regulatory networks in Caenorhabditis elegans. ..
- Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010;26:2617-9 pubmed publisher..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/. firstname.lastname@example.org ..
- Römpp A, Schramm T, Hester A, Klinkert I, Both J, Heeren R, et al. imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging. Methods Mol Biol. 2011;696:205-24 pubmed publisher..All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org . ..
- Turewicz M, Deutsch E. Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output. Methods Mol Biol. 2011;696:179-203 pubmed publisher..In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML. ..