Portals and myGrid

Stefan Rennick EgglestoneMixed Reality LaboratoryUniversity of Nottingham

Introduction to myGrid

• a computer science pilot project working in the field of bioinformatics

• a consortium of the European Bioinformatics Institute, IT Innovations, 5 universities and some industrial partners

• ends June 2005 and other projects will develope infrastructure further

Presentation aims

• Introduce myGrid• Introduce bioinformatics• Introduce portal work in myGrid• Show some screenshots of portlets

Introduction to bioinformatics

• how to store, process and publish large volumes of biological data

• large databases, access and analysis services

• composite processes involve multiple databases and services

• Automation through workflows

Data in bioinformatics

• Commonly genetic sequences– DNA: GCGCATAGCGATGA– Protein: MAHPLGPHGVANA

• Meta information– Species, chromosome– Interesting features– Equipment used– First published paper referring to sequence

Data storage

• 3 international databases aim to store all DNA sequences (EMBL, GenBank, DDBJ)

• Protein sequences in SwissProt• Journals require submission before

publication• Smaller databases hold specialist

information

Using bioinformatics data

• Database access services– Fetch sequence for given ID– Fetch similar sequences

• Sequence analysis– Look for interesting regions of sequence

• Sequence prediction– Predict proteins generated by DNA sequence

Service interface types

• Web-page• Command-line tool set• Programming language library client• SOAP web-service with WSDL interface

Using services

• Often need to combine services with different interface types

• Cut-and-paste from web-page to file and run command-line tool

• Repetitive and time-consuming• Can be automated using scripts

Workflows

myGrid workflow technology

• Freefluo workflow enactor• Taverna – graphical workbench allowing

users to – Author workflows– Enact and browse results

• myGrid Information Repository

Authoring a workflow

Enacting a workflow

Browsing results

Including services in workflows

• Service invocation done by processor• Generic processor for SOAP/WSDL web-

services• Custom processor can wrap custom client• SOAPlab exposes command-line tools as

web-service

Portal in myGrid

• Taverna/Freefluo is production workflow system, so interface can’t be hacked around with

• Some interface limitiations– Difficult to start new workflow running using

results of enactment– Complex interface, so takes time to master

Text services work

• If enactment of a workflow produces a SwissProt protein sequence record, can extract from this PubMed ID of first paper referring to this protein

• Add extra workflow stages which look up related papers

• Might like to re-run these stages as a separate workflow on any new papers found

Input form

Monitoring progress

Results

MIR portal work

• Taverna/Freefluo/MIR interface caters for expert user

• Large numbers of users who won’t write workflows but might enact them

• Provide a simpler workflow enactment interface

• Portal useful – all biologists have browser on their desk

Collections of workflows

View workflow

View workflow results

View individual output param

Further details

• www.mygrid.org.uk• Twiki.mygrid.org.uk• Stefan Rennick Egglestone (

sre@cs.nott.ac.uk0• Ian Roberts (i.roberts@dcs.sheff.ac.uk)• Presentation and notes will be at

www.mrl.nott.ac.uk/~sre