programming languages

Summary

Summary: Specific languages used to prepare computer programs.

Top Publications

  1. ncbi COPASI--a COmplex PAthway SImulator
    Stefan Hoops
    Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
    Bioinformatics 22:3067-74. 2006
  2. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
  3. pmc The BioPAX community standard for pathway data sharing
    Emek Demir
    Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Nat Biotechnol 28:935-42. 2010
  4. ncbi Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
    Henning Schmidt
    Fraunhofer Chalmers Research Centre for Industrial Mathematics, Chalmers Science Park, SE 41288 Göteborg, Sweden
    Bioinformatics 22:514-5. 2006
  5. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
  6. ncbi Libsequence: a C++ class library for evolutionary genetic analysis
    Kevin Thornton
    Committee on Genetics, University of Chicago, 1101 East 57th Street, Chicago, IL 66037, USA
    Bioinformatics 19:2325-7. 2003
  7. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
  8. ncbi ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
  9. pmc jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions
    Kenny Helsens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    J Proteome Res 10:5260-3. 2011
  10. pmc Biopython: freely available Python tools for computational molecular biology and bioinformatics
    Peter J A Cock
    Plant Pathology, SCRI, Invergowrie, Dundee, UK
    Bioinformatics 25:1422-3. 2009

Detail Information

Publications263 found, 100 shown here

  1. ncbi COPASI--a COmplex PAthway SImulator
    Stefan 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...
  2. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M 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...
  3. pmc The BioPAX community standard for pathway data sharing
    Emek 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...
  4. ncbi Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
    Henning 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...
  5. ncbi Java Treeview--extensible visualization of microarray data
    Alok 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...
  6. ncbi Libsequence: a C++ class library for evolutionary genetic analysis
    Kevin 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...
  7. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth 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...
  8. ncbi ROCR: visualizing classifier performance in R
    Tobias 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...
  9. pmc jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions
    Kenny 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 ...
  10. pmc Biopython: freely available Python tools for computational molecular biology and bioinformatics
    Peter J A Cock
    Plant Pathology, SCRI, Invergowrie, Dundee, UK
    Bioinformatics 25:1422-3. 2009
    ....
  11. ncbi jmzML, an open-source Java API for mzML, the PSI standard for MS data
    Richard 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...
  12. ncbi TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    W 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...
  13. pmc The Ensembl analysis pipeline
    Simon 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...
  14. pmc Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
    Dagmar 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...
  15. pmc JSBML: a flexible Java library for working with SBML
    Andreas 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...
  16. pmc LibSBML: an API library for SBML
    Benjamin 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...
  17. ncbi Efficient Monte Carlo modelling of individual tumour cell propagation for hypoxic head and neck cancer
    W Tuckwell
    School of Chemistry and Physics, University of Adelaide, South Australia, Australia
    Phys Med Biol 53:4489-507. 2008
    ....
  18. ncbi ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text
    Burr 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...
  19. ncbi Open source clustering software
    M 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...
  20. ncbi GenRGenS: software for generating random genomic sequences and structures
    Yann 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...
  21. pmc OpenMS - an open-source software framework for mass spectrometry
    Marc 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...
  22. ncbi Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
    Robert 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...
  23. ncbi Biskit--a software platform for structural bioinformatics
    Raik 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)...
  24. pmc Using biological pathway data with paxtools
    Emek 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. ..
  25. pmc Agile methods in biomedical software development: a multi-site experience report
    David 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...
  26. pmc Proof-of-concept design and development of an EN13606-based electronic health care record service
    Adolfo 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...
  27. ncbi The Bio* toolkits--a brief overview
    Harry 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...
  28. pmc Computing health quality measures using Informatics for Integrating Biology and the Bedside
    Jeffrey 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...
  29. ncbi AMIDE: a free software tool for multimodality medical image analysis
    Andreas 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...
  30. ncbi An application programming interface for CellNetAnalyzer
    Steffen 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...
  31. ncbi SBMLToolbox: an SBML toolbox for MATLAB users
    Sarah 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...
  32. pmc A programming language for composable DNA circuits
    Andrew 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...
  33. ncbi Bio2RDF: towards a mashup to build bioinformatics knowledge systems
    François 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...
  34. ncbi oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
    Remo 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..
  35. ncbi PRIDE: the proteomics identifications database
    Lennart 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...
  36. ncbi A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes
    P 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...
  37. pmc Dynamical modeling and multi-experiment fitting with PottersWheel
    Thomas 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...
  38. ncbi AstexViewer: a visualisation aid for structure-based drug design
    Michael 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...
  39. pmc SLIM: an alternative Web interface for MEDLINE/PubMed searches - a preliminary study
    Michael 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...
  40. ncbi PhyloWidget: web-based visualizations for the tree of life
    Gregory 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...
  41. pmc An iconic language for the graphical representation of medical concepts
    Jean 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...
  42. ncbi Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output
    Michael 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...
  43. ncbi GenomeDiagram: a python package for the visualization of large-scale genomic data
    Leighton 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...
  44. ncbi Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language
    Zoltan 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...
  45. pmc Structured representation of the pharmacodynamics section of the summary of product characteristics for antibiotics: application for automated extraction and visualization of their antimicrobial activity spectra
    Catherine 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...
  46. ncbi SED-ED, a workflow editor for computational biology experiments written in SED-ML
    Richard 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...
  47. ncbi A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimens
    Ahmad 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..
  48. ncbi An evaluation of ontology exchange languages for bioinformatics
    R McEntire
    SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA
    Proc Int Conf Intell Syst Mol Biol 8:239-50. 2000
    ....
  49. pmc Units of measure in clinical information systems
    G 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...
  50. ncbi CellML: its future, present and past
    Catherine M Lloyd
    Bioengineering Institute, University of Auckland, Level 6, 70 Symonds Street, Auckland, New Zealand
    Prog Biophys Mol Biol 85:433-50. 2004
    ....
  51. ncbi Introducing DoT-U2--an XML-based knowledge supported checklist software for documentation of a newborn clinical screening examination
    F 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...
  52. pmc A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
    Augustin 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...
  53. pmc CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes
    Nikhat 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...
  54. ncbi Disseminating medical knowledge: the PROforma approach
    J 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...
  55. pmc Flexible informatics for linking experimental data to mathematical models via DataRail
    Julio Saez-Rodriguez
    Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 24:840-7. 2008
    ....
  56. pmc Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data
    Thomas 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...
  57. ncbi NCL: a C++ class library for interpreting data files in NEXUS format
    Paul 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...
  58. ncbi SWIFT MODELLER: a Java based GUI for molecular modeling
    Abhinav 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...
  59. ncbi XML technologies for the Omaha System: a data model, a Java tool and several case studies supporting home healthcare
    Pierpaolo 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
    ....
  60. ncbi Presenting XML-based medical discharge letters according to CDA
    H 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...
  61. pmc Protein molecular function prediction by Bayesian phylogenomics
    Barbara 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...
  62. ncbi PDBML: the representation of archival macromolecular structure data in XML
    John 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...
  63. ncbi TOPP--the OpenMS proteomics pipeline
    Oliver 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...
  64. pmc Consistent annotation of gene expression arrays
    Benoit Ballester
    European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:294. 2010
    ....
  65. ncbi The MGED Ontology: a resource for semantics-based description of microarray experiments
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA
    Bioinformatics 22:866-73. 2006
    ....
  66. pmc The tissue microarray data exchange specification: a document type definition to validate and enhance XML data
    David 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...
  67. pmc Wildfire: distributed, Grid-enabled workflow construction and execution
    Francis 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...
  68. pmc Atlas - a data warehouse for integrative bioinformatics
    Sohrab 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...
  69. pmc Nexplorer: phylogeny-based exploration of sequence family data
    Vivek 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...
  70. ncbi Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics
    Christoph 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...
  71. ncbi CytometryML, an XML format based on DICOM and FCS for analytical cytology data
    Robert 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...
  72. pmc Comparing computer-interpretable guideline models: a case-study approach
    Mor 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...
  73. ncbi Pedro: a configurable data entry tool for XML
    Kevin 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...
  74. pmc Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data
    Peter 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...
  75. pmc Towards programming languages for genetic engineering of living cells
    Michael 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 ..
  76. ncbi A physiome standards-based model publication paradigm
    David 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...
  77. ncbi The Bioinformatics Template Library--generic components for biocomputing
    W 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..
  78. ncbi The CRASSS plug-in for integrating annotation data with hierarchical clustering results
    Eugen 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)...
  79. ncbi OBO to OWL: a protege OWL tab to read/save OBO ontologies
    Dilvan 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...
  80. ncbi Code generation: a strategy for neural network simulators
    Dan 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 )...
  81. ncbi 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...
  82. ncbi Microarray databases: standards and ontologies
    Christian 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...
  83. ncbi PhosphaBase: an ontology-driven database resource for protein phosphatases
    K 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...
  84. ncbi MOLE: a data management application based on a protein production data model
    Chris 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)...
  85. pmc Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser
    Judith 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...
  86. pmc HotSwap for bioinformatics: a STRAP tutorial
    Christoph 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...
  87. pmc BIOZON: a system for unification, management and analysis of heterogeneous biological data
    Aaron 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...
  88. ncbi Simultaneous modelling of metabolic, genetic and product-interaction networks
    N 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...
  89. ncbi SEView: a Java applet for browsing molecular sequence data
    T 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...
  90. pmc ParPEST: a pipeline for EST data analysis based on parallel computing
    Nunzio 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...
  91. ncbi The markup is the model: reasoning about systems biology models in the Semantic Web era
    Douglas 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...
  92. pmc ArrayQuest: a web resource for the analysis of DNA microarray data
    Gary 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...
  93. ncbi BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains
    Michael 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...
  94. pmc Base-By-Base: single nucleotide-level analysis of whole viral genome alignments
    Ryan 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...
  95. ncbi Intelligent client for integrating bioinformatics services
    Ismael 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...
  96. ncbi Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
    Lena 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...
  97. ncbi The role of informatics in the coordinated management of biological resources collections
    Paolo Romano
    Bioinformatics and Structural Proteomics, National Cancer Research Institute, Genoa, Italy
    Appl Bioinformatics 4:175-86. 2005
    ....
  98. pmc An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results
    Romesh 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...
  99. pmc RNAML: a standard syntax for exchanging RNA information
    Allison 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...
  100. ncbi PDB file parser and structure class implemented in Python
    Thomas 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...
  101. pmc A comparison of common programming languages used in bioinformatics
    Mathieu Fourment
    Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
    BMC Bioinformatics 9:82. 2008
    The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms...

Research Grants57

  1. Archiving the Vietnam Era Twin Studies of Aging (VETSA): New Uses for Old Data
    CAROL 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...
  2. Lineage bias and clonal expansion of hematopoietic stem cell differentiation
    Rong 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 ..
  3. The Neuroscience of Our Senses
    LOUISA 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 ..
  4. GPU-enhanced Neuroscience Software Tools
    John 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 ..
  5. GPU-based Computational Advancements for Neuroscience MATLAB Programs
    John 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 ..
  6. Development of a Software Pipeline for Sequence Data
    Toby 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 ..
  7. COMPUTER-BASED RESPIRATORY SUPPORT CONSULTANT
    DANIEL 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...
  8. INDIANAPOLIS PATHOLOGY INFORMATICS NETWORK
    Paul 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...
  9. Open File Format and Public Domain Tools for Neural Data
    KIRK 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 ..
  10. TAS::75 0849::TAS Topic 260: RapidStat: A Hybrid of Spreadsheets and Graphical La
    DR 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)...
  11. An Open and Scalable Stochastic Simulation Library for Biology
    MARK 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...
  12. RapidStat: A Hybrid of Spreadsheets and Graphical Language to Expedite User Inter
    DR 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 ..
  13. Improving Guideline Development and Implementation
    Richard N Shiffman; Fiscal Year: 2010
    ..In addition, the proposed activities focus on systems that will preferentially impact children - a particularly vulnerable population. ..
  14. Graphical models for linkage disequilibrium in genetic mapping
    Alun 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. ..
  15. ASSOCIATION BETWEEN PHENOTYPES AND DISEQUALIBRIATE LOCI
    Alun 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. ..
  16. Interoperation of Genome Databases and Tools
    Kei 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. ..
  17. A Genetic Association Research Statistical Framework
    Ross 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. ..
  18. COMPUTATIONAL ANALYSIS OF HUMAN 'AT-RISK' DNA MOTIFS
    JUDITH 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. ..
  19. Cancer Center Microarray Bioinformatics Facility
    W 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. ..
  20. Mediated Integration of Neuroscience Resources
    Luis Marenco; Fiscal Year: 2008
    ..abstract_text> ..
  21. HIGH THROUGHPUT ANNOTATION OF GENOMIC DNA SEQUENCE
    Christian 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. ..
  22. MUSCLE FUNCTION AFTER TENDON TRANSFER SURGERY
    Scott 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. ..
  23. MRI-Compatible Diffuse Optical Tomography System
    ANDREAS HIELSCHER; Fiscal Year: 2005
    ..This comparison will quantify the advantages and disadvantages of these different optical imaging modalities. ..
  24. VOCABULARY MANAGEMENT FOR CLINICAL RESEARCH DATABASES
    Cynthia Brandt; Fiscal Year: 2005
    ....
  25. Growth and Colonization of the Intestine by E. coli
    Tyrrell Conway; Fiscal Year: 2008
    ..These studies may help explain differences in human susceptibility to infection by E. coli pathogens. [unreadable] [unreadable]..
  26. Frontiers of NMR in Molecular Biology VIII
    James Prestegard; Fiscal Year: 2003
    ..Discussion of more practical aspects will be promoted by the organization of afternoon workshops having a less formal structure. ..
  27. Assisting Systematic Review Preparation Using Automated Document Classification
    Aaron 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. ..
  28. Mechanisms and significance of cublin-mediated HDL uptake
    WILLIAM 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. ..
  29. Tool to Integrate Genomic and Proteomic Data of Aging
    ZOE 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. ..
  30. Cross-species gene finding and annotation
    Lior Pachter; Fiscal Year: 2004
    ..The computational complexity of the problem is greatly reduced by the use of something we call an approximate alignment. ..
  31. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong 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. ..
  32. Protein Functional Site Characterization and Analysis
    Philip 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. ..
  33. SYSTEMATIC COMBINATION OF ANATOMY AND NOMENCLATURE
    Jonathan Silverstein; Fiscal Year: 2004
    ....
  34. OPTICAL TOMOGRAPHY FOR THE DIAGNOSIS OF JOINT DISEASES
    ANDREAS 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. ..
  35. NMR INVESTIGATIONS OF CELL SURFACE OLIGOSACCHARIDES
    James Prestegard; Fiscal Year: 2008
    ..Abnormal function of both systems relate to current health concerns. ..
  36. 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]..
  37. The Role of Megalin in Craniofacial Development
    WILLIAM ARGRAVES; Fiscal Year: 2006
    ..The proposed experimentation is expected to lead to new insights into the mechanism by which Shh signaling controls craniofacial development. ..
  38. BioMediator: Biologic Data Integration& Analysis System
    Peter Tarczy Hornoch; Fiscal Year: 2005
    ..abstract_text> ..
  39. Microarray Scanner and Accessories for MUSC
    WILLIAM 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]..
  40. BIOINFORMATICS CENTER FOR INNATE IMMUNITY PGA
    Ross Lazarus; Fiscal Year: 2004
    ..abstract_text> ..
  41. Tools & Data Resources in Support of Structural Genomics
    PHILIP 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. ..
  42. Southeast Collaboratory for High-Field Biomolecular NMR
    James Prestegard; Fiscal Year: 2006
    ..Target areas for future expansion include carbohydrates and metallo-proteins. ..
  43. Sun Microsystems Sun Fire 6800 Server Supercomputer
    JUDITH 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. ..
  44. A Comprehensive Test Suite for SBML
    Michael 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]..
  45. Small Animal Tomography System for Green Fluorescent Protein Imaging
    ANDREAS 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. ..
  46. Visual Data Extraction and Conversion Programming Tool
    Hui 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. ..
  47. Plasmodium Genome Database
    Christian 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. ..
  48. SBML Forum Meeting October 2004
    Michael Hucka; Fiscal Year: 2004
    ..The forum proceedings will be distributed to attendees and will be made available on the meeting's web site. ..
  49. ISMB 2005 Conf. Support for Students & Young Scientists
    PHILIP BOURNE; Fiscal Year: 2005
    ..This proposal seeks to assist them at this critical but resource-limited stage in their careers. ..
  50. BALANCING SURVIVAL AND OTOTOXICITY IN CISPLATIN THERAPY
    Yuelin Li; Fiscal Year: 2003
    ....
  51. Biomechanics and Correction of Crouch Gait
    Scott L Delp; Fiscal Year: 2010
    ..abstract_text> ..
  52. Software Maintenance for Biomolecular Complexes
    Chandrajit 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/). ..
  53. A New Approach to Rapid Protein-Protein Docking
    Chandrajit Bajaj; Fiscal Year: 2008
    ..abstract_text> ..
  54. Simulation-Based Treatment Planning for Gait Disorders
    Scott Delp; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  55. KCD BASED SYSTEM FOR MEGAVOLTAGE PORTAL IMAGING
    Sanjiv 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. ..
  56. Hierarchical Methods for Large BioMolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..AIM 4: To implement, test, package and freely distribute our structural feature determination and fast search/fitting techniques. ..
  57. Re-engineering the MEGA software package
    Sudhir 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. ..