Software for the Data-Driven Researcher of the Future Dr. Paul Fisher

What is myGrid? An e-Science Collaboration Since 2001 Numerous partners involved: –Manchester –Southampton –Oxford –EMBL-EBI It provides sustainable and production quality software –Supported by OMII-UK, EPSRC and BBSRC Mixture of developers, bioinformaticians and researchers Software | Services | Content | Skills | Community

myGrid Open Suite of Tools Client User Interfaces Workflow GUI Workbench and 3 rd party plug-ins Workflow Repository Service Catalogue Programming and APIs Web Portals Activity and Service Plug-in Manager Provenance Store Workflow Server Open Provenance Model Secure Service Access, and Programming APIs

Huge amounts of data 100+ Genes QTL regions Microarray Genes How do I look at ALL the genes systematically? Next Gen Sequencing 10,000+ Genes

Issues with current approaches Scale of analysis task overwhelms researchers – lots of data User bias and premature filtering of datasets – cherry picking Hypothesis-Driven approach to data analysis Constant changes in data - problems with re-analysis of data Implicit methodologies (hyper-linking through web pages) Error proliferation from any of the listed issues – notably human error Solution Automate

Web Services –Technology and standard for exposing code and data resources by an means that can be consumed by a third party remotely –Describes how to interact with it, e.g. service parameters Workflows –General technique for describing and executing a process –Describes what you want to do, including the services to use

What kind of Services? WSDL Web Services REST BioMart R-processor BioMoby SoapLab Grid Services Local Java services Beanshell Workflows

Who Provides the Services? Open domain services and resources Taverna accesses services (11,874 operations) Third party – we don’t own them – we didn’t build them All the major providers –NCBI, DDBJ, EBI … Enforce NO common data model. Can include your own services and resources too !!!

Where can I find these services?

A public centralised and curated registry of Life Science Web Services ‘Web 2.0’-style website and API Allow anyone to register, discover and curate Web Services Community oriented with expert guidance Open content, open source, open platform

Available services Workflow diagram Workflow Explorer

What are Workflows used for?

Taverna Taverna first released 2004 Current version Taverna 2.2 Currently users per month, 350+ organizations, ~40 countries, 80,000+ downloads across versions Freely available, open source LGPL Windows, Mac OS, and Linux User and developer workshops Documentation Public Mailing list and direct support

Trypanosomiasis in Africa Andy Brass Steve Kemp + many Others

Reuse, Recycle, Repurpose Workflows Dr Paul Fisher Dr Jo Pennock Identify biological pathways implicated in resistance to Trypanosomiasis in cattle using mouse as a model organism. Identify the biological pathways colitis and helminth infections in the mouse model DOI: /ibd | PMID:

Where can I find workflows?

Recycling, Reuse, Repurposing Share Search Re-use Re-purpose Execute Communicate Record

Bringing myExperiment to the Taverna user Taverna Plug-in

Take a breath….. myGrid Taverna –Workflows good for automation –Reduce errors BioCatalogue –Publicly curated repository of Web Services myExperiment –Web 2.0 repository supporting Workflow discovery and re-use

Taverna and the ‘Cloud’ Analysing Next Generation Sequencing Data +

Analysing African Cattle with Taverna 2.2 Different breeds of African Cattle 10,000 years separation African Livestock adaptations: More productive Increases disease resistance Potential outcomes: Food security Understanding resistance Understanding environmental Understanding diversity

The study Lots of sites involved in Study: –Univeristy of Liverpool –University of Manchester –ILRI (Nairobi)…… Genetic variation in cattle species –African breeds: N’dama, Boran and Sahiwal Resistance to African trypanosomiasis infection ( sleeping sickness ) –Genetic differences to make one species more resistant? –Potential consequences of those genetic differences? –Pathways are affected by those changes?

The Analysis Problem Sequenced DNA from 3 cattle breeds using SOLiD / Illumina 22 million SNPs for Sahiwal alone –N’Dama, Boran ~ 11 millions SNPs each –Large data Comparing new data with reference genomes Identifying interesting differences –e.g. non-synonymous SNPs, stop lost, stop gained, splicing regions etc

The Analysis Pipeline (in Perl) MAP FILTER ANALYSIS Input SNP data from sequencer Map between Genome Builds (Liftover) Filter for SNPs in Exons SNP consequences Identifying damaging SNPs (Polyphen) Harry Noyes – University of Liverpool

Workflow and phases Input SNP file Populate DB with start SNP’s and resource version numbers Lift-over: maps between UMD3 and BTA4 cow assemblies Exon positions from ENSMBL Find SNPs in Exon regions PolyPhen to mark “dangerous” SNP’s The result can be either a MySQL database or TSV / CSV download MSc Student - Mohammad Khodadadi

Taverna and the ‘Cloud’ +

What we will demonstrate 1.Uploading Next Generation Sequencing SNP data to the cloud 2.Creating a new experiment 3.Running a workflow on multiple cloud instances 4.Showing result output, including links to annotated SNPs

Demo

Managing and Processing Data

Accessing Taverna on the Cloud

Jobs Status Input Provenance Experiment Metadata Input data summary Loading inputs

Summary of Workflow Output Non-synonymous coding SNPs Polyphen predictions: probably damaging 11 Million SNP for N’ Dama N.B. Number variances due to workflow and polyphen filtering process

New Developments in myGrid

Essential for cloud Taverna Taverna 2.2 execution engine –Large data processing –Pause, resume and cancelling workflows –Retry and parallelisation layer Taverna 2.2 server –Remote workflow execution –Workflows launched from web pages –Workflows executed on the cloud

Other New features Validation reporting Loading and sharing service sets Support for offline editing New provenance features

ISMB 10 BioCatalogue Plug-in

Training Tutorials and Training –58+ tutorials to >900 people. –>20 universities, Life Science Institutes, and networks. –Major Bio conferences –Summer schools in Biology and Middleware Developer and User Days –Annotation Jamborees Undergraduate and Postgraduate Bioinformatics in > 30 universities.

More Information myGrid – Taverna – myExperiment – BioCatalogue –

Visit us at the myGrid Silver Sponsor Stand

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