Summary: Specific languages used to prepare computer programs.
Publications263 found, 100 shown here
- COPASI--a COmplex PAthway SImulatorStefan Hoops
Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
Bioinformatics 22:3067-74. 2006..Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods...
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsM Hucka
Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
Bioinformatics 19:524-31. 2003..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
- The BioPAX community standard for pathway data sharingEmek Demir
Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
Nat Biotechnol 28:935-42. 2010..This large amount of pathway data in a computable form will support visualization, analysis and biological discovery...
- Systems Biology Toolbox for MATLAB: a computational platform for research in systems biologyHenning Schmidt
Fraunhofer Chalmers Research Centre for Industrial Mathematics, Chalmers Science Park, SE 41288 Göteborg, Sweden
Bioinformatics 22:514-5. 2006..The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis...
- Java Treeview--extensible visualization of microarray dataAlok J Saldanha
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Bioinformatics 20:3246-8. 2004..An applet version is also available that can be used on any website with no special server-side setup...
- Libsequence: a C++ class library for evolutionary genetic analysisKevin Thornton
Committee on Genetics, University of Chicago, 1101 East 57th Street, Chicago, IL 66037, USA
Bioinformatics 19:2325-7. 2003..The object-oriented design of the library is intended to be extensible, allowing users to design custom classes for their own needs. In addition, routines are provided to process samples generated by a widely used coalescent simulation...
- GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genesElizabeth I Boyle
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Bioinformatics 20:3710-5. 2004..GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script...
- ROCR: visualizing classifier performance in RTobias Sing
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
Bioinformatics 21:3940-1. 2005..Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage...
- jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitionsKenny Helsens
Department of Medical Protein Research, VIB, Ghent, Belgium
J Proteome Res 10:5260-3. 2011..The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com . TraML files can also be converted online at http://iomics.ugent.be/jtraml ...
- Biopython: freely available Python tools for computational molecular biology and bioinformaticsPeter J A Cock
Plant Pathology, SCRI, Invergowrie, Dundee, UK
Bioinformatics 25:1422-3. 2009....
- jmzML, an open-source Java API for mzML, the PSI standard for MS dataRichard G Côté
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
Proteomics 10:1332-5. 2010..jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com...
- TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-findersW H Majoros
Bioinformatics Department, The Institute for Genomic Research, Rockville, MD 20850, USA
Bioinformatics 20:2878-9. 2004..Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes...
- The Ensembl analysis pipelineSimon C Potter
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Genome Res 14:934-41. 2004..Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis...
- Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup LanguageDagmar Waltemath
Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, D 18051 Rostock, Germany
BMC Syst Biol 5:198. 2011..The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools...
- JSBML: a flexible Java library for working with SBMLAndreas Dräger
Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
Bioinformatics 27:2167-8. 2011..JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend...
- LibSBML: an API library for SBMLBenjamin J Bornstein
NASA Jet Propulsion Laboratory, Biological Network Modeling Center, California Institute of Technology, Pasadena, CA, USA
Bioinformatics 24:880-1. 2008..Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software...
- Efficient Monte Carlo modelling of individual tumour cell propagation for hypoxic head and neck cancerW Tuckwell
School of Chemistry and Physics, University of Adelaide, South Australia, Australia
Phys Med Biol 53:4489-507. 2008....
- ABNER: an open source tool for automatically tagging genes, proteins and other entity names in textBurr Settles
Department of Computer Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin Madison Madison, WI 52706, USA
Bioinformatics 21:3191-2. 2005..It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora...
- Open source clustering softwareM J L de Hoon
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639 Japan
Bioinformatics 20:1453-4. 2004..In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C...
- GenRGenS: software for generating random genomic sequences and structuresYann Ponty
LRI, UMR CNRS 8623, Université Paris Sud 11 F91405 Orsay cedex, France
Bioinformatics 22:1534-5. 2006..GenRGenS also allows the user to combine several of these different models at the same time...
- OpenMS - an open-source software framework for mass spectrometryMarc Sturm
Center for Bioinformatics, Eberhard Karls University Tubingen, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 9:163. 2008..Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow...
- Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymesRobert Penchovsky
Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520 8103, USA
Nat Biotechnol 23:1424-33. 2005..This engineering approach provides a rapid and inexpensive way to create allosteric RNAs for constructing complex molecular circuits, nucleic acid detection systems and gene control elements...
- Biskit--a software platform for structural bioinformaticsRaik Grünberg
CRG, Systems Biology Program, Dr Aiguader 88, E 08003 Barcelona, Spain
Bioinformatics 23:769-70. 2007..Moreover, Biskit simplifies the parallelization of time consuming calculations via PVM (Parallel Virtual Machine)...
- Using biological pathway data with paxtoolsEmek Demir
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
PLoS Comput Biol 9:e1003194. 2013..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. ..
- Agile methods in biomedical software development: a multi-site experience reportDavid W Kane
SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA
BMC Bioinformatics 7:273. 2006..We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods...
- Proof-of-concept design and development of an EN13606-based electronic health care record serviceAdolfo Muñoz
Laboratorio de Bioingeniería y Telemedicina, Hospital Universitario Puerta de Hierro c San Martín de Porres 4, 28035 Madrid, Spain
J Am Med Inform Assoc 14:118-29. 2007..The authors present an Electronic Healthcare Record (EHR) server, designed and developed as a proof of concept of the revised prEN13606:2005 European standard concerning EHR communications...
- The Bio* toolkits--a brief overviewHarry Mangalam
tacg Informatics, Irvine, CA 92612, USA
Brief Bioinform 3:296-302. 2002..This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer...
- Computing health quality measures using Informatics for Integrating Biology and the BedsideJeffrey G Klann
Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA 02129, United States
J Med Internet Res 15:e75. 2013..Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)'s Query Health platform to move toward this goal...
- AMIDE: a free software tool for multimodality medical image analysisAndreas Markus Loening
Stanford University, Department of Radiology and the Bio X Program, 318 Campus Drive, East Wing, 1st Floor, Stanford, CA 94305 542, USA
Mol Imaging 2:131-7. 2003..AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License...
- An application programming interface for CellNetAnalyzerSteffen Klamt
Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse, Magdeburg, Germany
Biosystems 105:162-8. 2011..Lastly, two example applications demonstrate the use and versatile applicability of CNA's API. CNA is freely available for academic use and can be downloaded from http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html...
- SBMLToolbox: an SBML toolbox for MATLAB usersSarah M Keating
Science and Technology Research Institute, University of Hertfordshire Hatfield, UK
Bioinformatics 22:1275-7. 2006..SBMLToolbox supports all levels and versions of SBML...
- A programming language for composable DNA circuitsAndrew Phillips
Microsoft Research, Cambridge, UK
J R Soc Interface 6:S419-36. 2009..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...
- Bio2RDF: towards a mashup to build bioinformatics knowledge systemsFrançois Belleau
Centre de Recherche du CHUL, Universite Laval, 2705 Boulevard Laurier, Que, Canada G1V4G2
J Biomed Inform 41:706-16. 2008..The Bio2RDF repository can be queried at http://bio2rdf.org...
- oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R languageRemo Sanges
CBM Cluster in Biomedicine S c r l, Area Science Park, Basovizza SS 14, km 163, 5 34012 Trieste, Italy
Bioinformatics 23:3406-8. 2007..e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines. AVAILABILITY: http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html..
- PRIDE: the proteomics identifications databaseLennart Martens
Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
Proteomics 5:3537-45. 2005..The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation...
- A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changesP Baldi
Department of Information and Computer Science, University of California at Irvine, Irvine, CA 92697 3425, USA
Bioinformatics 17:509-19. 2001..Current methods are unsatisfactory due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data...
- Dynamical modeling and multi-experiment fitting with PottersWheelThomas Maiwald
Freiburg Center for Data Analysis and Modeling, Freiburg University, Freiburg, Germany
Bioinformatics 24:2037-43. 2008..It requires high-performance integration of ordinary differential equations and robust optimization...
- AstexViewer: a visualisation aid for structure-based drug designMichael J Hartshorn
Astex Technology Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB5 9QA, UK
J Comput Aided Mol Des 16:871-81. 2002..The software is being made freely available to the community and may be downloaded from http://www.astex-technology.com/AstexViewer...
- SLIM: an alternative Web interface for MEDLINE/PubMed searches - a preliminary studyMichael Muin
Office of High Performance Computing and Communications, National Library of Medicine, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
BMC Med Inform Decis Mak 5:37. 2005..Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded...
- PhyloWidget: web-based visualizations for the tree of lifeGregory E Jordan
EMBL EBI, Hinxton, Cambridge, CB10 1SD, UK and Peabody Museum of Natural History, Yale University, P O Box 208118, New Haven, CT 06520, USA
Bioinformatics 24:1641-2. 2008..It can be accessed online or downloaded as a standalone application. A simple URL-based API allows databases to easily link to and customize PhyloWidget for interactively viewing medium- to large-sized trees...
- An iconic language for the graphical representation of medical conceptsJean Baptiste Lamy
Laboratoire d Informatique Médicale et de Bioinformatique LIM and BIO, UFR SMBH, Universite Paris 13, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
BMC Med Inform Decis Mak 8:16. 2008..We propose a two-step approach for facilitating access to drug monographs. The first step, presented here, is the design of a graphical language, called VCM...
- Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer outputMichael Turewicz
Medizinisches Proteom Center, Ruhr Universitat Bochum, Bochum, Germany
Methods Mol Biol 696:179-203. 2011..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...
- GenomeDiagram: a python package for the visualization of large-scale genomic dataLeighton Pritchard
Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
Bioinformatics 22:616-7. 2006..The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems...
- Ruby-Helix: an implementation of helical image processing based on object-oriented scripting languageZoltan Metlagel
Department of Cell Biology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9039, USA
J Struct Biol 157:95-105. 2007..As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution...
- Structured representation of the pharmacodynamics section of the summary of product characteristics for antibiotics: application for automated extraction and visualization of their antimicrobial activity spectraCatherine Duclos
Laboratoire d Informatique Médicale et de Bioinformatique LIM and BIO, UFR de Santé, Médecine et Biologie Humaine, Paris 13, Bobigny Cedex, France
J Am Med Inform Assoc 11:285-93. 2004..The aim of this study was to construct automatically a knowledge base concerning the pharmacodynamic properties of antibiotics and a visualization tool...
- SED-ED, a workflow editor for computational biology experiments written in SED-MLRichard R Adams
SynthSys Edinburgh, University of Edinburgh, Edinburgh, UK
Bioinformatics 28:1180-1. 2012..SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format...
- A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimensAhmad H Namini
Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA, USA
Stud Health Technol Inform 107:1264-7. 2004..With the architecture currently in use by six member institutions, SPIN appears to be a viable, secure methodology to submit pathology information for query and specimen retrieval by investigators..
- An evaluation of ontology exchange languages for bioinformaticsR McEntire
SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA
Proc Int Conf Intell Syst Mol Biol 8:239-50. 2000....
- Units of measure in clinical information systemsG Schadow
Regenstrief Institute for Health Care and Indiana University, Indianapolis 46202 2859, USA
J Am Med Inform Assoc 6:151-62. 1999..The authors therefore developed a code for units that is much more complete and free from ambiguities...
- CellML: its future, present and pastCatherine M Lloyd
Bioengineering Institute, University of Auckland, Level 6, 70 Symonds Street, Auckland, New Zealand
Prog Biophys Mol Biol 85:433-50. 2004....
- Introducing DoT-U2--an XML-based knowledge supported checklist software for documentation of a newborn clinical screening examinationF Philipp
Department of Medical Informatics, University of Heidelberg, Im Neuenheimer Feld 400, D 69120 Heidelberg, Germany
Comput Methods Programs Biomed 77:115-20. 2005..We found that modular software development with platform independent Java and XML leads to highly flexible software which can be adapted to very different scenarios without knowing their requirements ahead of time...
- A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation methodAugustin Luna
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
BMC Bioinformatics 12:167. 2011..A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation...
- CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomesNikhat Zafar
School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110 USA
BMC Bioinformatics 3:12. 2002..A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining...
- Disseminating medical knowledge: the PROforma approachJ Fox
Imperial Cancer Research Fund, London, UK
Artif Intell Med 14:157-81. 1998..This paper provides a description of the language and associated software tools, and discusses its potential roles in, and implications for, medical knowledge publishing...
- Flexible informatics for linking experimental data to mathematical models via DataRailJulio Saez-Rodriguez
Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Bioinformatics 24:840-7. 2008....
- Bio::NEXUS: a Perl API for the NEXUS format for comparative biological dataThomas Hladish
Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
BMC Bioinformatics 8:191. 2007..However, due to its complexity, NEXUS is not well supported by software and is not easily accessible to bioinformatics users and developers...
- NCL: a C++ class library for interpreting data files in NEXUS formatPaul O Lewis
Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269 3043, USA
Bioinformatics 19:2330-1. 2003..The purpose of making the NCL available is to encourage the use of the NEXUS format by making it relatively easy for programmers to add the ability to interpret NEXUS files in newly developed software...
- SWIFT MODELLER: a Java based GUI for molecular modelingAbhinav Mathur
Department of Biotechnology, Birla Institute of Technology, Mesra, 835215 Jharkhand, India
J Mol Model 17:2601-7. 2011..SWIFT MODELLER lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with...
- XML technologies for the Omaha System: a data model, a Java tool and several case studies supporting home healthcarePierpaolo Vittorini
Department of Internal Medicine and Public Health, University of L Aquila, Via S Salvatore 1, 67010 L Aquila, Italy
Comput Methods Programs Biomed 93:297-312. 2009....
- Presenting XML-based medical discharge letters according to CDAH B Bludau
University of Heidelberg, Internal Medicine Dep II, Bergheimerstr 58, D 69115 Heidelberg, Germany, E mail
Methods Inf Med 42:552-6. 2003..The HL7 Clinical Document Architecture (CDA) is an important XML-based standard for the representation of clinical documents...
- Protein molecular function prediction by Bayesian phylogenomicsBarbara E Engelhardt
Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
PLoS Comput Biol 1:e45. 2005..The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors...
- PDBML: the representation of archival macromolecular structure data in XMLJohn Westbrook
Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey 610 Taylor Road, Piscataway, NJ 08854, USA
Bioinformatics 21:988-92. 2005..The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files...
- TOPP--the OpenMS proteomics pipelineOliver Kohlbacher
Simulation of Biological Systems, Eberhard Karls University Tübingen Sand 14, 72076 Tubingen, Germany
Bioinformatics 23:e191-7. 2007..In order to facilitate these studies, it would be desirable to have a flexible 'toolbox' of versatile and user-friendly applications allowing for rapid construction of computational workflows in proteomics...
- Consistent annotation of gene expression arraysBenoit Ballester
European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
BMC Genomics 11:294. 2010....
- The MGED Ontology: a resource for semantics-based description of microarray experimentsPatricia L Whetzel
Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA
Bioinformatics 22:866-73. 2006....
- The tissue microarray data exchange specification: a document type definition to validate and enhance XML dataDavid G Nohle
The Mid Region AIDS and Cancer Specimen Resource ACSR, Department of Pathology, The Ohio State University, Columbus, OH, USA
BMC Med Inform Decis Mak 5:12. 2005..Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness...
- Wildfire: distributed, Grid-enabled workflow construction and executionFrancis Tang
Information Science Research, Bioinformatics Institute, 30 Biopolis Street, 07 01, Matrix, 138671, Singapore
BMC Bioinformatics 6:69. 2005..The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers...
- Atlas - a data warehouse for integrative bioinformaticsSohrab P Shah
UBC Bioinformatics Centre, University of British Columbia, Vancouver, BC, Canada
BMC Bioinformatics 6:34. 2005..The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development...
- Nexplorer: phylogeny-based exploration of sequence family dataVivek Gopalan
Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Bioinformatics 22:120-1. 2006..Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics...
- Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformaticsChristoph Steinbeck
Cologne University Bioinformatics Center CUBIC, Germany
Curr Pharm Des 12:2111-20. 2006..This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software...
- CytometryML, an XML format based on DICOM and FCS for analytical cytology dataRobert C Leif
XML_Med, a Division of Newport Instruments, San Diego, California 92115, USA
Cytometry A 54:56-65. 2003..Because of the clinical utility of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies...
- Comparing computer-interpretable guideline models: a case-study approachMor Peleg
Stanford Medical Informatics, Stanford University School of Medicine, Stanford, California 94305 5479, USA
J Am Med Inform Assoc 10:52-68. 2003..We have studied similarities and differences between CIGs in order to identify issues that must be resolved before a consensus on a set of common components can be developed...
- Pedro: a configurable data entry tool for XMLKevin L Garwood
Department of Computer Science, University of Manchester, UK
Bioinformatics 20:2463-5. 2004..The software also has the ability to import records from tab delimited text files and features various validation routines...
- Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray dataPeter Li
Manchester Centre for Integrative Systems Biology and School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
BMC Bioinformatics 9:334. 2008..For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data...
- Towards programming languages for genetic engineering of living cellsMichael Pedersen
Microsoft Research Cambridge, Cambridge, UK
J R Soc Interface 6:S437-50. 2009..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 ..
- A physiome standards-based model publication paradigmDavid P Nickerson
Division of Bioengineering, National University of Singapore, Singapore 117574, Republic of Singapore
Philos Trans A Math Phys Eng Sci 367:1823-44. 2009..Here, we review the current state of the art and what needs to be done before such a model publication becomes commonplace...
- The Bioinformatics Template Library--generic components for biocomputingW R Pitt
School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK
Bioinformatics 17:729-37. 2001..AVAILABILITY: The BTL is available free of charge from our web site http://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html..
- The CRASSS plug-in for integrating annotation data with hierarchical clustering resultsEugen C Buehler
Applied Computer Science and Mathematics, Merck Research Laboratories, P O Box 2000 RY84 202, Rahway, NJ 07065 0900, USA
Bioinformatics 20:3266-9. 2004..The method is implemented as a Java plug-in for a commercial gene expression analysis program (GeneSpring)...
- OBO to OWL: a protege OWL tab to read/save OBO ontologiesDilvan A Moreira
Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA 94002, USA
Bioinformatics 23:1868-70. 2007..It uses the OBO to OWL mapping provided by the National Center for Biomedical Ontologies (NCBO) (a joint effort of OBO developers and OWL experts) and offers options to ease the task of saving/reading files in both formats...
- Code generation: a strategy for neural network simulatorsDan F M Goodman
Laboratoire Psychologie de la Perception, CNRS, Universite Paris Descartes, Paris, France
Neuroinformatics 8:183-96. 2010..The technique is quite general and could be applied to any simulation package. We demonstrate it with the 'Brian' simulator ( http://www.briansimulator.org )...
- XML: a lingua franca for science?E Barillot
G I S Infobiogen, Villejuif, France
Trends Biotechnol 18:331-3. 2000..Finally, they discuss real-life applications that have been developed using XML, with a focus on biology...
- Microarray databases: standards and ontologiesChristian J Stoeckert
Center for Bioinformatics and Department of Genetics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, Pennsylvania 19104 6021, USA
Nat Genet 32:469-73. 2002..The adoption of common standards and ontologies for the management and sharing of microarray data is essential and will provide immediate benefit to the research community...
- PhosphaBase: an ontology-driven database resource for protein phosphatasesK J Wolstencroft
School of Biological Sciences, University of Manchester, Manchester, United Kingdom
Proteins 58:290-4. 2005..The overall ontology-driven architecture provides a robust structure with distinct advantages for sustainability and provides the potential for the development of diagnostic tools, as well as a data repository...
- MOLE: a data management application based on a protein production data modelChris Morris
Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, United Kingdom
Proteins 58:285-9. 2005..To achieve this, MOLE is based on the data model for protein production devised at the European Bioinformatics Institute (Pajon A, et al., Proteins in press)...
- Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browserJudith E Stenger
The Duke Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
BMC Bioinformatics 6:95. 2005..We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis...
- HotSwap for bioinformatics: a STRAP tutorialChristoph Gille
Institute for Biochemistry, Charite University Hospital, Humboldt University, Berlin, Germany
BMC Bioinformatics 7:64. 2006..Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique...
- BIOZON: a system for unification, management and analysis of heterogeneous biological dataAaron Birkland
Department of Computer Science, Cornell University, Ithaca, NY, USA
BMC Bioinformatics 7:70. 2006..Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability...
- Simultaneous modelling of metabolic, genetic and product-interaction networksN S Juty
Medicines Research Centre, GlaxoSmithKline Pharmaceuticals, UK
Brief Bioinform 2:223-32. 2001..In silico investigations may now be performed using the mathematical simulation workbench, DBsolve, which incorporates the facility to introduce data directly from XML...
- SEView: a Java applet for browsing molecular sequence dataT Junier
Swiss Institute for Experimental Cancer Research ISREC, Epalinges s Lausanne, Switzerland
In Silico Biol 1:13-20. 1998..Independence from the source data's format is achieved through a description language and ad hoc translators, which make the system versatile and flexible...
- ParPEST: a pipeline for EST data analysis based on parallel computingNunzio D'Agostino
Department of Structural and Functional Biology, University Federico II, 80134 Naples, Italy
BMC Bioinformatics 6:S9. 2005..Therefore, suitable and efficient bioinformatic approaches are necessary to organize data related information content for further investigations...
- The markup is the model: reasoning about systems biology models in the Semantic Web eraDouglas B Kell
School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
J Theor Biol 252:538-43. 2008..Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization...
- ArrayQuest: a web resource for the analysis of DNA microarray dataGary L Argraves
Array Genetics, Inc, 59 Great Quarter Road, Newtown, CT 06482, USA
BMC Bioinformatics 6:287. 2005..Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools...
- BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domainsMichael L Blinov
Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Bioinformatics 20:3289-91. 2004..Models that can be generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies of signal transduction...
- Base-By-Base: single nucleotide-level analysis of whole viral genome alignmentsRyan Brodie
Biochemistry and Microbiology, University of Victoria, B, C, V8W 3P6 Canada
BMC Bioinformatics 5:96. 2004..For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools...
- Intelligent client for integrating bioinformatics servicesIsmael Navas-Delgado
Integrated Bioinformatics GNV5 at the University of Málaga, National Institute for Bioinformatics INB, Malaga, Spain
Bioinformatics 22:106-11. 2006..However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem...
- Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAXLena Strömbäck
Department of Computer and Information Science, Linkopings Universitet, S 581 83 Linkoping, Sweden
Bioinformatics 21:4401-7. 2005..Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed...
- The role of informatics in the coordinated management of biological resources collectionsPaolo Romano
Bioinformatics and Structural Proteomics, National Cancer Research Institute, Genoa, Italy
Appl Bioinformatics 4:175-86. 2005....
- An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry resultsRomesh Stanislaus
Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, South Carolina, USA
BMC Bioinformatics 5:9. 2004..This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data...
- RNAML: a standard syntax for exchanging RNA informationAllison Waugh
Stanford Medical Informatics, Stanford University Medical Center, California 94305, USA
RNA 8:707-17. 2002..In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation...
- PDB file parser and structure class implemented in PythonThomas Hamelryck
Department of Cellular and Molecular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie and Computational Modeling Lab, Department of Computer Science, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
Bioinformatics 19:2308-10. 2003..g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors...
- A comparison of common programming languages used in bioinformaticsMathieu Fourment
Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
BMC Bioinformatics 9:82. 2008The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms...
- Archiving the Vietnam Era Twin Studies of Aging (VETSA): New Uses for Old DataCAROL ELAINE FRANZ; Fiscal Year: 2013..facilitates the creation of internet accessible social science data through the application of powerful programming languages such as electronic mark-up language (XML) in a format compliant with international archiving standards...
- Lineage bias and clonal expansion of hematopoietic stem cell differentiationRong Lu; Fiscal Year: 2013..Irving L. Weissman at Stanford University. I am proficient with several programming languages including C/C++, R, Matlab, and Python, and I can independently design and carry out the advanced ..
- The Neuroscience of Our SensesLOUISA A STARK; Fiscal Year: 2013..of the GSLC team's synergistic expertise in science, education, interactive media, visualization, programming languages, and evaluation, building on our 16 years of experience in producing highly successful online curriculum ..
- GPU-enhanced Neuroscience Software ToolsJohn Melonakos; Fiscal Year: 2013..major problems in using MATLAB to conduct neuroscience research: 1) MATLAB is slow when compared to other programming languages such as C/C++, and 2) MATLAB visualizations are unable to handle large amounts of data or to render 3D ..
- GPU-based Computational Advancements for Neuroscience MATLAB ProgramsJohn Melonakos; Fiscal Year: 2010..major problems in using MATLAB to conduct neuroscience research: 1) MATLAB is slow when compared to other programming languages such as C/C++, and 2) MATLAB visualizations are unable to handle large amounts of data or to render 3D ..
- Development of a Software Pipeline for Sequence DataToby Bloom; Fiscal Year: 2012..Those new pipelines will be able to incorporate analysis algorithms implemented in a variety of programming languages, and will be able to use available compute resources to run as much as possible in parallel, thus reducing ..
- COMPUTER-BASED RESPIRATORY SUPPORT CONSULTANTDANIEL LINDSTROM; Fiscal Year: 1993..Systems will bring techniques from the field of knowledge-based systems and the use of object-oriented programming languages to this project...
- INDIANAPOLIS PATHOLOGY INFORMATICS NETWORKPaul Dexter; Fiscal Year: 2005..We will base our described distributed system on those operating systems, database systems, programming languages , and software (open-source as available) that will facilitate low-cost and secure national implementation...
- Open File Format and Public Domain Tools for Neural DataKIRK KORVER; Fiscal Year: 2003..the development of public-domain, open-source software tools for: importing/exporting the data in various programming languages and between a variety of analysis environments; editing, splicing, annotating and reviewing experiment ..
- TAS::75 0849::TAS Topic 260: RapidStat: A Hybrid of Spreadsheets and Graphical LaDR MARC ABRAMS; Fiscal Year: 2013..RapidStat product to make it easy to link together statistical computation engines written in R and other programming languages and statistical environments with easy-to-use Graphical User Interfaces (GUIs)...
- An Open and Scalable Stochastic Simulation Library for BiologyMARK STALZER; Fiscal Year: 2009..biomedical simulation: the lack of a standard library for stochastic simulation usable from a variety of programming languages and able to capitalize on various hardware acceleration options...
- RapidStat: A Hybrid of Spreadsheets and Graphical Language to Expedite User InterDR MARC ABRAMS; Fiscal Year: 2011..or a scripting language, to create simple user interfaces (UIs) to calculation engines written in various programming languages. The requirement includes realizing the approach in a high level programming language and a software ..
- Improving Guideline Development and ImplementationRichard N Shiffman; Fiscal Year: 2010..In addition, the proposed activities focus on systems that will preferentially impact children - a particularly vulnerable population. ..
- Graphical models for linkage disequilibrium in genetic mappingAlun Thomas; Fiscal Year: 2010..For this aim of the project we intend to apply the methods developed to dense genotype assays obtained for distantly related breast cancer cases in extended Utah pedigrees. ..
- ASSOCIATION BETWEEN PHENOTYPES AND DISEQUALIBRIATE LOCIAlun Thomas; Fiscal Year: 2006..This proposal is to extend graphical modeling methods already developed by the investigators for haploid data to diploid data, larger genomic regions, admixed populations and family data. ..
- Interoperation of Genome Databases and ToolsKei Hoi Cheung; Fiscal Year: 2005..We will extend our approach to other types of genomic data such as microarray data, which both laboratories and others will soon be generating in large quantities. ..
- A Genetic Association Research Statistical FrameworkRoss Lazarus; Fiscal Year: 2008..Developed in the context of airways disease, the software will be immediately and directly applicable to genetic research in other common, complex disorders. ..
- COMPUTATIONAL ANALYSIS OF HUMAN 'AT-RISK' DNA MOTIFSJUDITH STENGER; Fiscal Year: 2003..3) To set up an interactive on-line database and program server so that the scientific community can use the information and apply it to drive experimental research. ..
- Cancer Center Microarray Bioinformatics FacilityW Argraves; Fiscal Year: 2006..Finally, the resource facility will create an internet-accessible database of gene expression profile information collected by HCC investigators to make this data available to the scientific community at large. ..
- Mediated Integration of Neuroscience ResourcesLuis Marenco; Fiscal Year: 2008..abstract_text> ..
- HIGH THROUGHPUT ANNOTATION OF GENOMIC DNA SEQUENCEChristian Stoeckert; Fiscal Year: 2003..To respond to the public community, queries to the web interface will be incorporated and bulk files provided in response to users of the allgenes.org site. Planned is the inclusion of on-demand annotation of new contigs. ..
- MUSCLE FUNCTION AFTER TENDON TRANSFER SURGERYScott Delp; Fiscal Year: 2002..Aim 4 will examine how postoperative function of the rectus femoris influences knee motion during gait. The success of this work will result in better, more predictable treatment outcomes. ..
- MRI-Compatible Diffuse Optical Tomography SystemANDREAS HIELSCHER; Fiscal Year: 2005..This comparison will quantify the advantages and disadvantages of these different optical imaging modalities. ..
- VOCABULARY MANAGEMENT FOR CLINICAL RESEARCH DATABASESCynthia Brandt; Fiscal Year: 2005....
- Growth and Colonization of the Intestine by E. coliTyrrell Conway; Fiscal Year: 2008..These studies may help explain differences in human susceptibility to infection by E. coli pathogens. [unreadable] [unreadable]..
- Frontiers of NMR in Molecular Biology VIIIJames Prestegard; Fiscal Year: 2003..Discussion of more practical aspects will be promoted by the organization of afternoon workshops having a less formal structure. ..
- Assisting Systematic Review Preparation Using Automated Document ClassificationAaron Cohen; Fiscal Year: 2009..Since up-to-date systematic reviews are essential for establishing widespread high quality practice standards and guidelines, the overall public health will benefit from this work. ..
- Mechanisms and significance of cublin-mediated HDL uptakeWILLIAM ARGRAVES; Fiscal Year: 2009..Together, these studies will provide new insights into the function of cubilin in maternal-embryonic.lipoprotein transport, embryonic development and adult kidney function. ..
- Tool to Integrate Genomic and Proteomic Data of AgingZOE LACROIX; Fiscal Year: 2002..Aim 2: Enhance the access to information related to age-related diseases, disorders and disabilities through the exploration of multiple data sources. ..
- Cross-species gene finding and annotationLior Pachter; Fiscal Year: 2004..The computational complexity of the problem is greatly reduced by the use of something we call an approximate alignment. ..
- CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological SequencesWeizhong Li; Fiscal Year: 2010..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
- Protein Functional Site Characterization and AnalysisPhilip E Bourne; Fiscal Year: 2010..The results of this effort will be disseminated through the Protein Data Bank which is used by over 10,000 scientists every day. ..
- SYSTEMATIC COMBINATION OF ANATOMY AND NOMENCLATUREJonathan Silverstein; Fiscal Year: 2004....
- OPTICAL TOMOGRAPHY FOR THE DIAGNOSIS OF JOINT DISEASESANDREAS HIELSCHER; Fiscal Year: 2007..The ultimate goal of this proposal is to lay the groundwork for a clinical viable joint imager that can be used in a phase II clinical trial in i subsequent studies. ..
- NMR INVESTIGATIONS OF CELL SURFACE OLIGOSACCHARIDESJames Prestegard; Fiscal Year: 2008..Abnormal function of both systems relate to current health concerns. ..
- Eighth International Conference on Systems Biology (ICSB 2007)Michael Hucka; Fiscal Year: 2007..The conference proceedings will be distributed to attendees in printed form and as a CD-ROM. [unreadable] [unreadable] [unreadable]..
- The Role of Megalin in Craniofacial DevelopmentWILLIAM ARGRAVES; Fiscal Year: 2006..The proposed experimentation is expected to lead to new insights into the mechanism by which Shh signaling controls craniofacial development. ..
- BioMediator: Biologic Data Integration& Analysis SystemPeter Tarczy Hornoch; Fiscal Year: 2005..abstract_text> ..
- Microarray Scanner and Accessories for MUSCWILLIAM ARGRAVES; Fiscal Year: 2006..Specifically, funds are requested for purchasing an Affymetrix GeneChip Scanner 3000 Upgrade and a Fluidics Station 450 Upgrade. [unreadable] [unreadable] [unreadable]..
- BIOINFORMATICS CENTER FOR INNATE IMMUNITY PGARoss Lazarus; Fiscal Year: 2004..abstract_text> ..
- Tools & Data Resources in Support of Structural GenomicsPHILIP BOURNE; Fiscal Year: 2006..The proposed public resource will complement the private software and data resulting from the individual structural genomics centers as they undertake competitive high throughput structure determination. ..
- Southeast Collaboratory for High-Field Biomolecular NMRJames Prestegard; Fiscal Year: 2006..Target areas for future expansion include carbohydrates and metallo-proteins. ..
- Sun Microsystems Sun Fire 6800 Server SupercomputerJUDITH STENGER; Fiscal Year: 2003..This HPC will provide the database storage capacity and querying speed plus the computational processing capability needed to analyze our clinical, genotypic, and bioinformatics data. ..
- A Comprehensive Test Suite for SBMLMichael Hucka; Fiscal Year: 2007..This is something that is crucial for users to have confidence in SBML as a standard model representation format for simulation and analysis in biomedical research. [unreadable] [unreadable] [unreadable] [unreadable]..
- Small Animal Tomography System for Green Fluorescent Protein ImagingANDREAS HIELSCHER; Fiscal Year: 2007..For example, the imaging system could help visualize tumor location and growth. If successfully implemented the new imaging system will provide new insights into how various diseases, such as cancer, spread and affect the body. ..
- Visual Data Extraction and Conversion Programming ToolHui Hsien Chou; Fiscal Year: 2005..Therefore, this tool will provide great enabling power to biomedical scientists to help them make rapid advances in biomedical research and medicine. ..
- Plasmodium Genome DatabaseChristian Stoeckert; Fiscal Year: 2008..The overall goal of this project is to develop and maintain a database that expedites biological discovery, including the identification of drug targets and vaccine antigens useful in the fight against malaria. ..
- SBML Forum Meeting October 2004Michael Hucka; Fiscal Year: 2004..The forum proceedings will be distributed to attendees and will be made available on the meeting's web site. ..
- ISMB 2005 Conf. Support for Students & Young ScientistsPHILIP BOURNE; Fiscal Year: 2005..This proposal seeks to assist them at this critical but resource-limited stage in their careers. ..
- BALANCING SURVIVAL AND OTOTOXICITY IN CISPLATIN THERAPYYuelin Li; Fiscal Year: 2003....
- Biomechanics and Correction of Crouch GaitScott L Delp; Fiscal Year: 2010..abstract_text> ..
- Software Maintenance for Biomolecular ComplexesChandrajit L Bajaj; Fiscal Year: 2010..3. Continued documentation and web based dissemination of all the components (libraries and tools) of our MVP. (http://ccvweb.csres.utexas.edu/software/). ..
- A New Approach to Rapid Protein-Protein DockingChandrajit Bajaj; Fiscal Year: 2008..abstract_text> ..
- Simulation-Based Treatment Planning for Gait DisordersScott Delp; Fiscal Year: 2007..unreadable] [unreadable]..
- KCD BASED SYSTEM FOR MEGAVOLTAGE PORTAL IMAGINGSanjiv Samant; Fiscal Year: 2002..This could facilitate the rapid introduction of conformal therapy into clinical practice by allowing for improved identification of anatomical structures compared to current imaging modalities. ..
- Hierarchical Methods for Large BioMolecular ComplexesChandrajit L Bajaj; Fiscal Year: 2010..AIM 4: To implement, test, package and freely distribute our structural feature determination and fast search/fitting techniques. ..
- Re-engineering the MEGA software packageSudhir Kumar; Fiscal Year: 2009..These core software enhancements will contribute to the longevity of MEGA for use in molecular evolution, bioinformatics, functional genomics, computational biology, and basic biomedicine applications. ..