User:Vincent Rouilly/Part Registry DAS server

Distributed Annotation System (DAS) resources

 * biodas.org website
 * Current specifications (v1.53)
 * DAS compliant software tools:
 * Servers:
 * LDAS (Light DAS)
 * Clients:
 * Web services:
 * Web services:

Prerequisites

 * Software installations:
 * BioPython
 * local Blast
 * BioPerl
 * MySQL database + BioSQL SQL script
 * Apache server
 * LDAS server
 * latest FASTA dump from Part Registry

Step 1

 * BioPython processing
 * Load FASTA part file
 * Clean-up FASTA part file by removing all parts with no sequences (Blast doesn't handle them)
 * For each part:
 * Blast part against the rest of the parts, looking for perfect match.
 * Annotate part with perfect matches in order to store assembly information
 * Store part in BioSQL database

Local server (personal use only)

 * General services:
 * dsn:http://127.0.0.1/cgi-bin/das/dsn
 * DAS server on 'miniregistry':
 * entry_points:http://127.0.0.1/cgi-bin/das/miniregistry/entry_points
 * types: http://127.0.0.1/cgi-bin/das/miniregistry/types
 * DNA reference server:
 * full BBa_B0015 DNA sequence: http://127.0.0.1/cgi-bin/das/miniregistry/dna?BBa_B0015
 * '''BBa_B0015 DNA sequence from [100bp-110bp]: http://127.0.0.1/cgi-bin/das/miniregistry/dna?segment=BBa_B0015:100,110
 * Assembly info:
 * sub-components: http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBa_B0015;category=structural
 * super-components: http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBa_B0015;category=supercomponent
 * Annotation info:
 * All features for BBa_B0015: http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBa_B0015