https://github.com/alexkalderimis/rubydas

DAS server for Ruby
https://github.com/alexkalderimis/rubydas

Last synced: 20 days ago
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DAS server for Ruby

• Host: GitHub
• URL: https://github.com/alexkalderimis/rubydas
• Owner: alexkalderimis
• Created: 2012-02-28T10:36:22.000Z (almost 13 years ago)
• Default Branch: master
• Last Pushed: 2012-03-13T14:54:29.000Z (almost 13 years ago)
• Last Synced: 2024-06-11T16:25:47.158Z (8 months ago)
• Language: Ruby
• Homepage:
• Size: 13.4 MB
• Stars: 3
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.markdown

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README

        
A gem to use the Distributed Annotation System with Ruby. 

# DAS

The [Distributed Annotation System](http://en.wikipedia.org/wiki/Distributed_Annotation_System) is a protocol developed to allow the distributed annotation of nucleotide and protein sequences. DAS servers are used to deliver reference sequences and/or annotations for those sequences. DAS clients can be used to remix the information from different sources and deliver a single representation of the information. Examples for DAS-clients are [ENSEMBL Genome Browser](http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32889611-32973805), [Spice](http://www.efamily.org.uk/software/dasclients/spice) and [Dalliance](http://biodalliance.org). 

Widely-used DAS-server-implementations are [myDAS](http://code.google.com/p/mydas/) – which is based on Java – and [ProServer](http://www.sanger.ac.uk/resources/software/proserver/) which is based on Perl. 

# RubyDAS

RubyDAS tries to provide a reference- and annotation-server with the DAS 1.6 standard based on Ruby. Reference-sequences and the annotations are stored in a database of choice using Datamapper. The dependencies of RubyDAS as of now are: 

* [BioRuby](http://bioruby.open-bio.org/)

* [Sinatra](http://www.sinatrarb.com/)

* [http://datamapper.org/](http://datamapper.org/)

## Features

* Read GFF3

* Read FASTA 

* DAS *sequences*-command

* DAS *sources*-command 

* DAS *features*-commands

## How-To

To test the current implementation just run server.rb and point your browser to localhost:4567/das/rubydas/sequence?segment=MAL5:1000,2000 localhost:4567/das/rubydas/types?segment=MAL5:1000,2000 or localhost:4567/das/rubydas/features?segment=MAL5:1000,2000

## To-Do

* Implement *entry_points*

* Implement *sources*

* Add further input-file-formats

* Test compatibility with DAS-clients

## Contact

If you are interested in joining the development of RubyDAS you can join the Google Group/mailinglist at https://groups.google.com/group/rubydas