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 Resource Guide -> Vertical Industries -> Bioinformatics

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A Jython plug-in for NeuroML

Jython Module is an open source Python plug-in that extends Neuron Markup Language (NeuroML). The module allows dynamic access to NeuroML modules and provides a command line for tasks such as executi... [Jan. 30, 2002]

AnatML

Anatomical Markup Language (AnatML) is an XML-based language for describing anatomy, in particular for modeling the human musculoskeletal system, and facilitating data exchange among contributing sc... [Jan. 9, 2002]

Apple/Genentech BLAST

Apple/Genentech Basic Local Alignment Search Tool (BLAST) is an open source, enhanced implementation of the standalone version of National Center for Biotechnology Information (NCBI) Basic Local Ali... [Feb. 25, 2002]

Bioinformatic Sequence Markup Language (BSML)

Bioinformatic Sequence Markup Language (BSML)is a public domain XML application for bioinformatic data originally developed by Visual Genomics, now merged with LabBook, under a grant from the Nation... [Jan. 28, 2002]

Biomolecular Interaction Network Database (BIND)

The license-free Biomolecular Interaction Network Database (BIND) database stores descriptions of molecular complexes and pathways and biomolecular interactions. At the BIND site, users can downlo... [Jan. 9, 2002]

BioXML.org

This site was created to be a center for development for open source biological DTDs. There is a BioXML Wiki page of documentation including an explanation of the BioXML Architecture and a BioXML Tut... [Jun. 4, 2001]

Chapter 1: Biology in the Computer Age

Biology in the Computer Age is a chapter excerpted from the O'Reilly & Associates book Developing Bioinformatics Computer Skills, by Cynthia Gibas and Per Jambeck. The chapter begins with a look back... [Jan. 24, 2002]

Chemical Markup Language 1.0 Reference with examples

Chemical Markup Language (CML) 1.0 Reference is an Extensible Stylesheet Language Transformations (XSLT) -based interactive reference for CML, an XML application for the management of chemical infor... [May. 20, 2001]

Fasta2XML

FASTA is a sequence data file format and tool for finding similar sequences developed by Pearson and Lipman and available at searching facilities such as European Molecular Biology Laboratory (EMBL)... [Jan. 28, 2002]

GAME DTD (Genome Annotation Markup Elements)

Genome Annotation Markup Elements (GAME) is a syntax for the exchange of genomic annotation. It will enable genome centres, m... [Jul. 25, 2000]

gb2xml : Genbank to XML conversion tool

gb2xml is a utility for converting between XML and Genetic Sequence Data Bank (GenBank) format. The Genbank to XML conversion tool is an form-based online format conversion helper based upon gb2xml.... [Jan. 10, 2002]

Genome Annotation Markup Elements (GAME)

Part of the new science of Bioinformatics (somewhere between Biology and Computer Science), Genome Annotation Markup Elements (GAME) is a syntax for the exchange of genomic annotation. It will enabl... [Jul. 25, 2000]

Integrated Resource of Protein Domains and Functional Sites (InterPro)

Integrated Resource of Protein Domains and Functional Sites (InterPro) is an XML databank incorporating information from the Protein Families Database (Pfam), Protein Fingerprint Database (PRINTS), ... [Jan. 28, 2002]

Integrated Taxonomic Information System (ITIS)

Integrated Taxonomic Information System (ITIS) is being constructed by a partnership teaming taxonomic specialists and organizations with governmental agencies of the United States, Canada and Mexic... [Jan. 27, 2002]

Integrated Taxonomic Information System (ITIS)

Integrated Taxonomic Information System (ITIS) is being constructed by a partnership teaming taxonomic specialists and organizations with governmental agencies of the United States, Canada and Mexic... [Feb. 7, 2002]

JUMBO 3.0-J XML-CML molecular browser and toolkit

Java Universal Markup Browser for Objects (Jumbo) is a Java-based molecular browser for Chemical Markup Language (CML) and XML documents. The Jumbo toolkit includes an independent CML editor, documen... [Feb. 7, 2002]

LabBook Genomic XML Viewer

LabBook Genomic XML Viewer is a version of LabBook Genomic XML Browser that is provided free to the scientific community. The viewer converts Genetic Sequence Data Bank (GenBank) files to XML to enab... [Jan. 24, 2002]

MacVector

MacVector is a sequence analysis program that runs natively on Mac OS X and also supports the Classic environment (Mac OS 8.6 or later). MacVector can be used for sequence editing and visualizatio... [Jan. 28, 2002]

Microarray Markup Language (MAML)

This Document Type Definition (DTD) describes Microarray Markup Language (MAML), which is part of an effort to deal with the explosive growth in the amount of data produced by gene expression analys... [Dec. 18, 2000]

Molecular Dynamics Markup Language (MODL)

Molecular Dynamics Markup Language is used to help make sense of the huge amounts of data typical of chemical simulations. The language tags constructs such as atom, bond and molecule to mark up... [Jun. 12, 2000]

NeuroML

Neuron Markup Language (NeuroML) is an XML application for describing models of neurons and networks of neurons. This site provides links to the Java-based NeuroML Development Kit, documentation, the... [Jan. 24, 2002]

Parsing Protein Domains with Perl

In this article James Tisdall, author of the O'Reilly & Associates book Beginning Perl for Bioinformatics, shows biologists with or without programming experiece how to use Perl to apply the ... [Dec. 7, 2001]

Parsing Protein Domains with Perl

In this article James Tisdall, author of the O'Reilly & Associates book Beginning Perl for Bioinformatics, shows biologists with or without programming experiece how to use Perl to apply the ... [Nov. 15, 2002]

PML/LML Physical Model Language

Different approaches exist for modeling human tissues, mostly discrete and continuous physical models, e.g. respectively Mass-Spring Networks and Finite Element Method. Whatever approach is chosen, th...

Protein Information Resource International Protein Sequence Database (PIR-PSD)

The Protein Information Resource-International Protein Sequence Database (PIR-PSD) is a cross-referenced, annotated protein sequence databank developed by the nonprofit organization PIR-Internationa... [Jan. 23, 2002]

RiboML

Ribonucleic Acid Markup Language (RiboML) is an XML application for ribosomal science. The RiboML page provides a link to the RiboML Document Type Definition (DTD) and a sample RiboML document that ... [Jan. 14, 2002]

Savvy: Scalable Vector Graphics Plasmid Map

Savvy is online plasmid mapping software that accepts parameters from a form-based interface and renders a plasmid (a circular, double-stranded unit of DNA) via Scalable Vector Graphics (SVG). Sa... [Jan. 7, 2002]

StarDOM

StarDOM is a Python-based utility for converting STAR information into XML by creating a Document Object Model (DOM) representation of the Star data. Self-Defining Text Archival and Retrieval (STA... [Jan. 7, 2002]

Systems Biology Markup Language (SBML)

Systems Biology Markup Language (SBML) is an XML-based language for describing simulations in systems biology. The language is oriented towards representing biochemical networks common in research on... [Apr. 30, 2001]

Taxonomic Markup Language (TML)

Taxonomic Markup Language (TML) is an XML-based application for the classification of organisms in an ordered system, or taxonomy. The TML Document Type Definition (DTD) describes the structure of an... [Jan. 10, 2002]

The Dazzle server

The open source Dazzle servlet is a server framework for Distributed Sequence Annotation System (DAS) that works with servlet containers such as Tomcat. The Dazzle page includes links to a Dazzle s... [Jan. 29, 2002]

The Gene Expression Markup Language (GEML)

The Gene Expression Markup Language (GEML) is a file format for storing DNA microarray and gene expression data. GEML is an open-standard XML format which enables exchange of data between gene expre... [Apr. 12, 2000]

UQ Physics: xmds - the Extensible Multi-Dimensional Simulator

Extensible Multi-Dimensional Simulator (xmds) is a software package used in solving field integration problems in applications such as lattice simulations for study of the atom-molecular interaction ... [Feb. 7, 2002]

XEMBL Project Web Service

The XEMBL Web service, which makes European Molecular Biology Laboratory (EMBL) Nucleotide Sequence data from the EMBL/GenBank/DNA Data Bank of Japan (DDBJ) database available, is running on salce... [Oct. 31, 2001]

XOL Ontology Exchange Language

XML-Based Ontology Exchange Language (XOL) is a language for exchange of ontologies, created to facilitate the creation of shared ontologies (originally developed for use in bioinformatics). The ... [Dec. 22, 2000]

XSIL Extensible Scientific Interchange Language

The Extensible Scientific Interchange Language (XSIL) is a flexible, hierarchical, extensible, transport language for scientific data objects. This page posts links to the DTD, sample files and t... [Jun. 11, 2000]