3d-em das

Workflows over Grid-based Web servicesGeneral framework and a practical case in structural biology

3D-EM DAS3D-EM DAS

http://biocomp.cnb.uam.es/das/http://biocomp.cnb.uam.es:9000/das/

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Extending DAS to 3D-EM and Molecular Fitting


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What’s DAS ?

Distributed Annotation System

• Distributed Annotation System- Entity feature relationships.

• Distributed Annotation System-Made of distant, independent data sources.

• Distributed Annotation System- Client/Server paradigm- One Client and many Servers

www.biodas.org : “(…)The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view.”


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Geographic Annotation System


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Is DAS a Web Service ?

REST-like Web ServiceRepresentational State Transfer

Described by Roy Fielding in his PhD thesis.http://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm

Properties:• A resource is anything that has an identity.• Every resource has a URI.• A URI is “opaque” - exposes no details of implementation.•All Interactions are stateless.• Data and metadata formats are documented.• Data is available in multiple formats.• Representations include links to other resources.• Use available standards and technology.• Simple architecture.


• Genomic / Protein DAS

• Structural DAS (SPICE)

• 3D-EM DAS• Servers

• 3DEM, Reference server• 3DEM_Fitting, Fitting results server• 3DEM_EMDB, Annotation server

• Client•PeppeR

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Genomic / Proteomic DAS

• Uses a DAS protocol to query remote data sources about what sequences and annotations they know about a particular biology entity (gene, protein).

• Distributed :- Servers

One Reference server:Entry-points = Identifier + start / end points

Many Annotation servers:Features, relative to an entry-point

- ClientsWeb-based: Ensembl Genome Browser (http://www.ensembl.org/)Flash-based: Dasty (http://www.ebi.ac.uk/das-srv/uniprot/dasty/)

• Dowell RD, Jokerst RM, Day A, Eddy ST, Stein L. (2001). The Distributed Annotation System. BMC Bioinformatics 2:7.• Olason PI. (2005). Integrating protein annotation resources through theDistributed Annotation System. Nucleic Acids Res. 33: W468-W470.


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ClientClient

HTML query

Annotation ServersAnnotation Servers

Reference ServersReference Servers

XML responses


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DAS specification: Commands

dsn returns the list of data sources that are available from the server

entry-points returns the list of entry points available from the server

sequence returns the sequence (nucleotides or amino acids) corresponding to the requested segment

types returns the annotation types available from the server

features returns all the known annotations relative for the requested segment

Feature-by-idcomponentsupercomponentlinkstylesheet


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DAS specification: Query format

server_prefix/source/command

/dsn

/3DEM/3DEM

/3DEM_EMDB/3DEM_EMDB

/3DEM_Fitting/3DEM_Fitting/3DEM_Fitting

/entry_points/volmap

/types/features

/entry_points/types/features

http://biocomp.cnb.uam.es:9000/das

http://biocomp.cnb.uam.es:9000/dashttp://biocomp.cnb.uam.es:9000/das

http://biocomp.cnb.uam.es:9000/dashttp://biocomp.cnb.uam.es:9000/das

http://biocomp.cnb.uam.es:9000/dashttp://biocomp.cnb.uam.es:9000/dashttp://biocomp.cnb.uam.es:9000/das

[?param=value]

?query=EMD1017

?segment=EMD1017

?segmet=FFT0005


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List of available data sources: http://biocomp.cnb.uam.es:9000/das/dsn

<?xml version="1.0" standalone="no"?><!DOCTYPE DASDSN SYSTEM 'http://www.biodas.org/dtd/dasdsn.dtd' ><DASDSN> <DSN> <SOURCE id="3DEM_EMDB" version="1.02.20060508">3DEM_EMDB</SOURCE> <MAPMASTER>http://bioweb:9000/das/3DEM_EMDB/</MAPMASTER> <DESCRIPTION> Annotation server for 3D-EM volume data. Most textual data parsed from EMDB. </DESCRIPTION> </DSN> <DSN> <SOURCE id="3DEM_Fitting" version="1.02.20060503">3DEM_Fitting</SOURCE> <MAPMASTER>http://bioweb:9000/das/3DEM_Fitting/</MAPMASTER> <DESCRIPTION>Annotation server for fitting experiments (PDB structures into 3D-EM volumes).</DESCRIPTION> </DSN> <DSN> <SOURCE id="3DEM" version="1.02.20060503">3DEM</SOURCE> <MAPMASTER>http://bioweb:9000/das/3DEM/</MAPMASTER> <DESCRIPTION>Reference server for 3D-EM volume map data from EMDB.</DESCRIPTION> </DSN></DASDSN>


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List of available entry points in a data source:

<?xml version="1.0" standalone="no"?><!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"><DASEP> <ENTRY_POINTS href="http://bioweb:9000/das/3DEM/entry_points" version="1.0.2"> <SEGMENT id="EMD1001" class="volume_map" type="ccp4" release_date="20/06/2002">EMD1001</SEGMENT> <SEGMENT id="EMD1003" class="volume_map" type="ccp4" release_date="22/08/2002">EMD1003</SEGMENT> <SEGMENT id="EMD1004" class="volume_map" type="ccp4" release_date="29/08/2003">EMD1004</SEGMENT> <SEGMENT id="EMD1005" class="volume_map" type="ccp4" release_date="30/08/2003">EMD1005</SEGMENT> <SEGMENT id="EMD1006" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1006</SEGMENT> <SEGMENT id="EMD1007" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1007</SEGMENT> <SEGMENT id="EMD1008" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1008</SEGMENT> <SEGMENT id="EMD1009" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1009</SEGMENT> <SEGMENT id="EMD1010" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1010</SEGMENT> <SEGMENT id="EMD1011" class="volume_map" type="ccp4" release_date="09/10/2002">EMD1011</SEGMENT> <SEGMENT id="EMD1012" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1012</SEGMENT> <SEGMENT id="EMD1013" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1013</SEGMENT>

… <SEGMENT id="EMD1212" class="volume_map" type="ccp4" release_date="03/04/2007">EMD1212</SEGMENT> <SEGMENT id="EMD1213" class="volume_map" type="ccp4" release_date="03/04/2006">EMD1213</SEGMENT> </ENTRY_POINTS></DASEP>

http://biocomp.cnb.uam.es:9000/das/3DEM/entry_points


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Known annotations for an entry point:

<?xml version='1.0' standalone='yes'?><!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd"><DASGFF> <GFF version="1.5" href="http://bioweb:9000/das/3DEM_EMDB/features"> <SEGMENT id="EMD1017" version="1.0" start="1" stop=""> <FEATURE id="1017" label="1017"> <TYPE id="Description" reference="no" subparts="no" superparts="no">Description</TYPE> <START>1</START> <END>0</END> <SCORE>-</SCORE> <ORIENTATION>0</ORIENTATION> <PHASE>-</PHASE> <NOTE>Sample: "DnaB.DnaC complex from Escherichia coli "; Author: "M.Barcena,T.Ruiz,L.E.Donate,S.E.Brown,N.E.Dixon,M.Radermacher,J.M.Carazo"</NOTE> <LINK href="ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/emd-1017/map/emd_1017.map.gz">Retrive 17/10/2003 from EMDB</LINK> <GROUP id="1" type="Summary" /> </FEATURE> </SEGMENT> </GFF></DASGFF>

http://biocomp.cnb.uam.es:9000/das/3DEM/features?segment=emd_1017


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DAS Registry:


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• Client•PeppeR


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Structural DAS:

ServersReference

•Uniprot•PDB

Alignment serverMSD

ClientSPICE

Prlic A, Down A, Hubbard TJ (2005). Adding some SPICE to DAS. Bioinformatics, 2005, 21 Suppl 2, ii40-ii41


Structural DAS

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Structures(reference) Structures(reference)

Features /Annotations

Genomic DAS

Sequences(reference)Sequences(reference)

Alignmentserver

Alignmentserver

SPICEStructural

Client


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SPICE

http://www.efamily.org.uk/software/dasclients/spice/


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• Client•PeppeR


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Molecular Fitting:

High-resolutionTechniques

High-resolutionTechniques

CrystallographyRMN, etc.

Medium to Low-resolutionTechniques

Medium to Low-resolutionTechniques

3D Electron Microscopy

Hybrid ModelHybrid Model


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3D-EM DAS

Features /Annotations

Genomic DAS

Sequences(reference)Sequences(reference)

New

Fitting resultsFitting results

New

EMDBannotations

EMDBannotations

New

3D-EMvolume maps

(reference)

3D-EMvolume maps

(reference)

Structures(reference) Structures(reference)

Structure DAS

Alignmentserver

Alignmentserver

PeppeR3D-EM DAS

Client

NewNew


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• Java implementation- Architecture independent

• Windows• Unix / Linux• Mac

- Java Web Start deployment• launched directly from a web link

• AstexViewer for map / pdb structures display• Features (annotations) panels from SPICE library

3D-EM DAS client: PeppeR


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3d-em das

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