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Taverna: From Biology to Astronomy Dr Katy Wolstencroft University of Manchester my Grid OMII-UK What is Taverna? An environment for workflow design and execution User interface to a larger suite of middleware – my Grid Designed to support in silico experiments in biology Open source

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taverna from biology to astronomy

Taverna: From Biology to Astronomy

Dr Katy Wolstencroft

University of Manchester

myGrid

OMII-UK

what is taverna
What is Taverna?
  • An environment for workflow design and execution
  • User interface to a larger suite of middleware – myGrid
  • Designed to support in silico experiments in biology
  • Open source
omii open middleware infrastructure institute
OMII Open Middleware Infrastructure Institute
  • University of Manchester joined with the Universities of Edinburgh and Southampton in March 2006
  • OMII-UK aims to provide software and support to enable a sustained future for the UK e-Science community and its international collaborators.
  • A guarantee of development and support
the life science community
The Life Science Community

In silico Biology is an open Community

  • Open access to data
  • Open access to resources
  • Open access to tools
  • Open access to applications

Global in silico biological research

the community problems
The Community Problems
  • Everything is Distributed
    • Data, Resources and Scientists
  • Heterogeneous data
  • Very few standards
    • I/O formats, data representation, annotation
    • Everything is a string!

Integration of data and interoperability of resources is difficult

lots of resources
Lots of Resources

NAR 2007 – 968 databases

traditional bioinformatics
Traditional Bioinformatics

12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt 12481 aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt 12541 ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg 12601 tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga 12661 tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc 12721 atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa 12781 taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa

workflows as a solution
Workflows as a Solution
  • Describes whatyou want to do, not how you want to do it
  • High level description of the experiment
  • Easier to explain, share, relocate, reuse and repurpose.
  • Workflow <=> Model
  • Workflow is the integrator of knowledge
  • The METHODS section of a scientific publication
slide9

Taverna Workflow Components

Scufl Simple Conceptual Unified Flow Language

slide10

Taverna in an Open World

  • Open domain services and resources.
  • Taverna accesses 3000+ services
  • Third party – we don’t own them – we didn’t build them
  • All the major providers
    • NCBI, DDBJ, EBI …
  • Enforce NO common data model.
  • Quality Web Services considered desirable
what can you do with my grid
What can you do with myGrid?
  • ~33,000 downloads
  • Users worldwide

US, Singapore, UK, Europe, Australia

  • Systems biology
  • Proteomics
  • Gene/protein annotation
  • Microarray data analysis
  • Medical image analysis
  • Heart simulations
  • High throughput screening
  • Genotype/Phenotype studies
  • Health Informatics
  • Astronomy
  • Chemoinformatics
  • Data integration
examples early pioneers williams beuren syndrome

WBSCR21

WBSCR27

WBSCR24

WBSCR14

WBSCR18

WBSCR22

WBSCR28

CLDN3

CLDN4

STX1A

ELN

CTA-315H11

CTB-51J22

RP11-148M21

RP11-731K22

RP11-622P13

314,004bp extension

All nine known genes identified

(40/45 exons identified)

Examples – Early PioneersWilliams-Beuren Syndrome

Identifying new human genome sequence and genes contained within in an area of the genome associated with the disease

Improve understanding between genotype and phenotype

Four workflow cycles totalling ~ 10 hours

The gap was correctly closed and all known features identified

trypanosomiasis in africa
Trypanosomiasis in Africa
  • Resistance to parasites in different breeds of cattle
  • Involves:
  • Microarray analysis
  • Classical genetics
  • Biochemical pathway analysis

Large data sets, large results sets

http://www.genomics.liv.ac.uk/tryps/trypsindex.html

is taverna just for biologists
Is Taverna Just for Biologists?
  • Nothing in the code is specific to biology
  • The default list of services ARE bio services, but Taverna doesn’t care what they are
  • Services from other science disciplines can simply be slotted in
other examples
Other Examples
  • Medical imaging
    • MIAS-GRID –investigating cartilage thickness during drug trials
    • 2D and 3D brain image registration
  • Chemoinformatics
    • CDK-Taverna – project to provide the CDK chemoinformatics tool set as web services
    • Chimatica - Virtual Drug Candidate Production Environment
  • Health informatics
    • PsyGrid – investigating first episode psychosis
what taverna gives you
What Taverna Gives you
  • Automation
  • Implicit iteration
  • Implicit parallelisation
  • Support for nested workflow construction
  • Error handling
    • Retry, failover and automatic substitution of alternates
extensibility
Extensibility
  • Accepts many types of services:

- web services, beanshell scripts, local java scripts, JDBC connections…etc

  • Easy to add your own services
  • Plug-in architecture

Easy to build new processor types

Easy to extend to include alternative results viewers

could taverna be used for astronomy
Could Taverna be used for Astronomy?
  • Lots of data (although individual data items might be bigger)
  • Distributed data
  • Chains of analyses
  • MORE standards for data formatting/exchange

Investigated by AstroGrid and SAMPO

sampo european southern observatory project
Sampo - European Southern Observatory project

Workflows for data reduction

Reasons for choosing Taverna

 Open source

 Free

 Allows customisation

 Easy to use and adapt

 Designed for science

 Most workflow engines are meant for business applications

 Very robust

 Actively developed

 Good support for web services

slide21

AstroGrid Workflows

Evaluation of Taverna

Building plug-ins for AstroGird project

In the process of gathering AstroGrid requirements

Still things to address……..

coming soon taverna 2
Coming soon…Taverna 2

A complete redesign of Taverna from the ground up to enable:

  • Streaming data
  • Management of large volumes of data
  • Better remote workflow execution
  • Integration with grid resources
  • Monitoring and steering

Beta release due end summer 2007

my grid acknowledgements
myGrid acknowledgements

Carole Goble, Norman Paton, Robert Stevens, Anil Wipat, David De Roure, Steve Pettifer

  • OMII-UK Tom Oinn, Katy Wolstencroft, Daniele Turi, June Finch, Stuart Owen, David Withers, Stian Soiland, Franck Tanoh, Matthew Gamble, Alan Williams
  • Research Martin Szomszor, Duncan Hull, Jun Zhao, Pinar Alper, Antoon Goderis, Alastair Hampshire, Qiuwei Yu, Wang Kaixuan.
  • Current contributors Matthew Pocock, James Marsh, Khalid Belhajjame, PsyGrid project, Bergen people, EMBRACE people.
  • User Advocates and their bosses Simon Pearce, Claire Jennings, Hannah Tipney, May Tassabehji, Andy Brass, Paul Fisher, Peter Li, Simon Hubbard, Tracy Craddock, Doug Kell, Marco Roos, Matthew Pocock, Mark Wilkinson
  • Past Contributors Matthew Addis, Nedim Alpdemir, Tim Carver, Rich Cawley, Neil Davis, Alvaro Fernandes, Justin Ferris, Robert Gaizaukaus, Kevin Glover, Chris Greenhalgh, Mark Greenwood, Yikun Guo, Ananth Krishna, Phillip Lord, Darren Marvin, Simon Miles, Luc Moreau, Arijit Mukherjee, Juri Papay, Savas Parastatidis, Milena Radenkovic, Stefan Rennick-Egglestone, Peter Rice, Martin Senger, Nick Sharman, Victor Tan, Paul Watson, and Chris Wroe.
  • IndustrialDennis Quan, Sean Martin, Michael Niemi (IBM), Chimatica.
  • Funding EPSRC, Wellcome Trust.
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