Data, Services and Computational
Resources Integration at the INB
Oswaldo Trelles
University of Malaga, Spain
Integrated Bioinformatics - INB

O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

National Institute for Bioinformatics
www.inab.org
Integrated Bioinformatics

Computational Node 2
J.L. Gelpi– CEPBA/IBM

Cental Node
Bioinformatics & Proteomics

Protein Structure

M-Orozco – Univ. Barcelona

A.Valencia – CNIO

Computational Node 1
J.M. Carazo – CNB / PCM

Bioinformatics & Genomics
R.Guigó – IMIM

Functional
Genomicsl

J.Dopazo – CI.FP

Integrated Bioinformatics
O.Trelles – Univ. Málaga

Scalable & expandable “Virtual” Organization
O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

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O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

Main lines of work at GNV5Integration architecture
MOWServ client - connecting and presenting theservice offering of INB

BioMOBY proposals
Protocol improvements (error handling, async,mirroring)

Identification and restructuring of MOWServ internals
MOWServ is a generic client (uniform interface) but
more specific clients are needed (jORCA)

Development of software libraries
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Design specifications
After careful analysis, the open
source standard bioMOBY(Wilkinson and Links; 2002;
Wilkinson, et al.; 2003) –included
its pros and cons- was chosen as
the underlying protocol to sustain
inter-operational conjunction ofnodes.

Persistence of user data files
Controlled Ontology and Services Registry
Task scheduling, Robustness (long services)
Objects & tasks monitoring
Generic Client (extended set of facilities)
Creation & visualization functionality
Help & training support

Integrated Bioinformatics, INB-UMA

Although from the beginning werealized of some limitations in theprotocol, the advantages for a
rapid deployment of results aswell as the increasing number ofservices becoming available
under this platform were on top ofbenefits.
One of the important tasks fromthe INBG perspective was toextend the protocol to fulfil ourobjectives
O.Trelles, BioHackaton-Japan 08

The MOWServ-v1 Architecture

Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

jORCA -v1 : easily integration
http://www.bitlab-es.com/jorca

jORCA: new Desktop interactive client: management ofmoby, soap, grid-based and any other type of services

Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Controlled Registry System
One of the most important “procedural” MOWServ’s components

KW-based service description
Moving to semantics
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Browsing Objects,
Services & Namespaces
Quality control:
registering / daily
availability /documentation
Favourites section
Dynamic & automatic offer
deployment in browseable treeorganization

Intelligent client for integrating bioinformatics services”, Navas-Delgado, et al.
Bioinformatics, vol.22 no.1 2006 pages 106-111
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Advanced search: Example

Example: a user has a new sequence and wants to obtain a quality alignment using HMM in order to get the family sequence
where the query sequence belongs. Select GenericSequence as Input Object, and next HMMSearch_Report as output object.
In this way, 4 services are suggested. Then select Alignment in Service window, and only 2 services (the same with 2 mirrors):
runHMMSearchAgainstSeqs, are identified which is useful for the final target.
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Creation Services

Creation services: generic
Up-down load objects
Plug-in specific
Transparent to users
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Service invocation
Automatic / Uniform
Objects: online creation
Up-download
Online help services
Different protocols (soap / Moby /grid / ... jORCA: plug-in workers)
Security issues (anonymous data)
Controlled access to resources

Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Tasks & Objects Monitoring
Task monitoring
Objects persistence
Pipelining capabilities
The object object problem

O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

Viewing results
Plug-in based architecture:
Each object can be associated with a XSLT fileService providers can submit specialized viewers fortheir data (e.g. jMOL)
Results always viewable as XML or HTML.
Improvements: “Interactive” visualization / registering

Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Workflows

O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

2.- WF selection
WFs tab : public / private

Phylogenetictree

STEP 1: Sequence retrieval
STEP 2: Blast
STEP 3: Best hits
STEP 2: Multiple seq. alignment
STEP 3: Phylogenetic tree
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

3.- specialise

Input definition

CHY1_PAGMA
UniProtLaunch execution
O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

4.- Monitoring

In progress ....
...doneIntegrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

5.- Results

O.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

Open questions
Short term

Asynchronous services (& progress status notification)
Error handling
Replication (mirroring) system
Daily Service quality control
Service’s help system
Advanced service discovering
Collections
Large data sets (network overloading)Indirect (by reference) pass of data (locality of D & S)
Workflows (storage in the repository, WWE-jmf)
Semantic annotations (datatypes & Services)
Define services categories
New datatypes: Gene expression; images; ...
Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08

Open questions
long term

Review / redefine the repository data model
modular / distributed / users / persistence / security...
<<component>>Core Metadata Manager
ToolManager

FunctionalCategory
Manager+retrieve()+save()+delete()+retrieve()+save()+delete()<<use>>

Tool

DataType
Manager+retrieve()+save()+delete()...

<<use>><<use>>

DataType<<use>> FunctionalCategory<<use>><<use>><<use>><<use>><<use>>

FunctionalCatGraph

WorkflowNode<<use>> DataType
Graph<<use>>

Parameter

ToolLocation<<use>>

Operation<<use>>
CompuResource

QualityO.Trelles, BioHackaton-Japan 08

Integrated Bioinformatics, INB-UMA

Integrated Bioinformatics Nodewww.bitlab-es.com

Integrated Bioinformatics, INB-UMA

O.Trelles, BioHackaton-Japan 08