BIODAS.ORG

BioDAS

Welcome To BioDAS.org. What can I do with DAS ? Contribute to this Wiki. A new version of DAS was recently released! See the Versions of DAS. Section below for more information. The Distributed Annotation System. DAS) defines a communication protocol used to exchange annotations. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. What can I do with DAS ? Interactive web-based genome viewer.

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ls●●●●@cshl.edu

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BioDAS | biodas.org Reviews

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Welcome To BioDAS.org. What can I do with DAS ? Contribute to this Wiki. A new version of DAS was recently released! See the Versions of DAS. Section below for more information. The Distributed Annotation System. DAS) defines a communication protocol used to exchange annotations. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. What can I do with DAS ? Interactive web-based genome viewer.

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BioDAS | biodas.org Reviews

https://biodas.org

Welcome To BioDAS.org. What can I do with DAS ? Contribute to this Wiki. A new version of DAS was recently released! See the Versions of DAS. Section below for more information. The Distributed Annotation System. DAS) defines a communication protocol used to exchange annotations. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. What can I do with DAS ? Interactive web-based genome viewer.

INTERNAL PAGES

biodas.org

1

DAS2 Protocol, Introduction

http://www.biodas.org/documents/das2/das2_protocol.html

Id: das2 protocol.html,v 1.26 2006/08/17 23:58:48 dalke Exp $. Genomic sequence and annotation. DAS is a protocol for sharing biological data. This version of the specification, DAS 2.0, describes features located on the genomic sequence. Future versions will add support for sharing annotations of protein sequences, expression data, 3D structures and ontologies. The genomic DAS interface is deliberately designed so there will be a large core shared with the protein sequence DAS. DAS 20 addresses some sho...

2

Distributed Annotation System

http://www.biodas.org/documents/spec-1.53.html

Distributed Sequence Annotation System (DAS). Lincoln D. Stein, Sean Eddy, Robin Dowell. This is a working document describing the rationale and protocol for a distributed sequence annotation system. See Changes. For recent changes to the spec. Extensions to the 1.0 specification introduced in version 1.5 are indicated in brown. These extensions should be backward compatible to clients and servers written for the 1.0 spec. Description of the System. To give a concrete example, the. The DAS consists of a.

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informatics.malariagen.net

A tour of some VCF Visualisation software | malariagen informatics

https://informatics.malariagen.net/2012/08/22/a-tour-of-some-vcf-visualisation-software

Bioinformatics, software engineering and computer science for MalariaGEN. Stay updated via RSS. Benchmarking HDF5 for storing and accessing large arrays of genotype data. Anopheles gambiae 1000 genomes project. Patterns of resistance by Joel Winston. Malaria Drug Resistance and Genomics Animation. Migrating from P. falciparum reference genome 3D7 version 2 to version 3. Load data from a VCF file into numpy arrays. A tour of some VCF Visualisation software. Jobs – Bioinformatics. System that allows launch...

supfam.cs.bris.ac.uk

SUPERFAMILY Web Services

http://supfam.cs.bris.ac.uk/SUPERFAMILY/web_services.html

All SUPERFAMILY assignments are made available through the Distributed Annotation System (DAS). The DAS. Is a communication protocol used to exchange biological sequence annotations. The DAS server offers the oppurtunity to stay up to date with the SUPERFAMILY assignments without downloading and installing database dumps. The SUPERFAMILY DAS server provides protein domain assignment details in XML format for use by DAS clients such as Ensembl. Genome browser) and DASTY. Using the SUPERFAMILY DAS server.

biojava.org

Dazzle

http://biojava.org/wiki/Dazzle

Javadoc API (4.2.1). Javadoc API (1.9.1). Dazzle is an easy to use server for the Distributed Annotation System ( DAS. It is implemented as a Java servlet, using the BioJava APIs. Dazzle is a modular system which uses small datasource plugins to provide access to a range of databases. Several general-purpose plugins. Are included in the package, and it it straightforward to develop new plugins. To connect to your own databases. Using subversion and built using ant:. Should be changed to. Note that the ab...

biodalliance.org

Adding data

http://www.biodalliance.org/adding.html

Dalliance is designed to make it easy to add your own data, or data from public collections. There are currently two different approaches for adding data: DAS is rich and flexible, but requires you to run your own server. Binary formats are less flexible, but easy to set up. We expect to support more file-based formats, including VCF and GFF, in the near future. Adding data via DAS. Dalliance is a Distributed Annotation System (DAS). While Java-ish people might like Dazzle. Adding indexed binary files.

ismb01.cbs.dtu.dk

ISMB 2001 Poster Abstracts: Databases, Information and Knowledge Management

http://ismb01.cbs.dtu.dk/DatabasesInformationKnowledgeManagement.html

Databases, Information and Knowledge Management. Use of Runs Statistics for Pattern Recognition in Genomic DNA Sequences. Biomine multiple database sequence analysis tool. Efficient virtual screening toll for early drug discovery. WebGen-Net: a workbench system for support of genetic network construction. ArrayExpress a Public Repository for Gene Expression Data at the European Bioinformatics Institute. Trawler: Fishing in the Biomedical Literaturome. A tissue classification system. Gene Ontology Ann...

blipkit.open-bio.org

Blip: Architecture

http://blipkit.open-bio.org/architecture.html

Blip: Biomedical Logic Programming. Blip is a data integration toolkit. It wraps a variety of file formats and data resources (called bioresources. Providing a unified query layer. This figure shows how a general purpose application (in this case Amigo-NG, a serval. Web application) queries data from a variety of sources. TODO: imagemap this png. TODO: fix diagram - prolog xml transform now used in place of XSL for SBML data. At the bottom of the diagram are the bioresources. Db, etc. Each of these d...

blipkit.open-bio.org

Blip: Serval

http://blipkit.open-bio.org/serval.html

Blip: Biomedical Logic Programming. Prolog as a server application language. To find out more. Serval is a logical-functional framework for developing web applications. It is generic and largely independent of the bio-specific modules. However, both serval and the bio-specific modules depend upon the same utility module, so I have decided just to bundle serval with blip for now. If you are interested in a distribution that is independent on Blip, contact the developer. However, Prolog's native I/O comman...

blipkit.open-bio.org

Blipkit: Biomedical LogIc Programming Knowledge Integration Kit

http://blipkit.open-bio.org/index.html

Blip: Biomedical Logic Programming. Blip is a collection of logic programming modules intended primarily for bioinformatics and biomedical applications, although it contains some modules which may be of more general interest. Blip is intended to be both an application library, and a deductive database/query system. Blip is written in SWI-Prolog. A fast, robust and scalable implementation of ISO Prolog. Blip is Free Software. Available, licensed under the LGPL. Blip, aka blipkit. Can be cited as. SWI-Prol...

blipkit.open-bio.org

Blip: Tutorial

http://blipkit.open-bio.org/tutorial.html

Blip: Biomedical Logic Programming. The blip command-line tool. Writing applications using blip. NOTE: this section is being replaced by the tutorial section in blipdoc. The blip command-line tool. Blip comes with a command line tool to allow simple non-programmatic access to a limited subset of the functionality of the full blip package. Run with the "-h" option for full instructions. Here are some examples. If you run blip without specifying a command you will be placed in prolog query mode. Blip has b...

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biodas.org

BioDAS

Welcome To BioDAS.org. What can I do with DAS ? Contribute to this Wiki. A new version of DAS was recently released! See the Versions of DAS. Section below for more information. The Distributed Annotation System. DAS) defines a communication protocol used to exchange annotations. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. What can I do with DAS ? Interactive web-based genome viewer.

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biodasman.wordpress.com

Biodasman's Blog | Biodas and related technical blog

Biodas and related technical blog. To skip running tests when packaging in maven. Personal Genomics/Deploying a DAS server for Dummies/6 Easy steps. Easy Deployment of DAS server for Personal Genotype data to the Amazon Cloud. Easy steps to have your personal genomic data available as a DAS source:. 1) Set up an Amazon Web Services Account (AWS) which is as easy as setting up a normal amazon shopping account on the web. 2) Download and unpack a war file from this url. 3) replace the person1.txt file ...

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