e-Science Tools For The Genomic Scale Characterisation Of Bacterial Secreted Proteins Tracy Craddock, Phillip Lord, Colin Harwood and Anil Wipat Newcastle University

Outline  Computational challenges of bioinformatics  Secretion in Bacillus  Classification and analysis workflows  Results and discussion

Computational Challenges of Bioinformatics  New requirements from bioinformatics  3 major problems  Heterogeneity  Distribution  Autonomy  Experiments - series of workflows

my Grid and Taverna Scufl Simple Conceptual Unified Flow Language Taverna Writing, running workflows & examining results SOAPLAB Makes applications available Freefluo Workflow engine to run workflows Freefluo SOAPLAB Web Service Any Application Web Service e.g. DDBJ BLAST

Microbase  Grid-based system for microbial genome comparison and analysis  Information repository (and execution environment)  Pre-computed data

Outline  Computational challenges of bioinformatics  Secretion in Bacillus  Classification and analysis workflows  Results and discussion

Secretion in Bacillus  Predict characteristics & behavior of bacteria  Identify secreted proteins  Bacillus species diverse behaviour  Soil inhabitants  Harmful bacteria

Importance of Secretion  Mechanism of interaction with environment  Reveal capabilities of an organism  Pathogens are of great interest

Secretory Proteins Cytoplasm Medium Membrane Cell Wall Signal Peptide Lipoprotein Cell wall binding Transmembrane LPXTG

Outline  Computational challenges of bioinformatics  Secretion in Bacillus  Classification and analysis workflows  Results and discussion

Bioinformatic Tools Cytoplasm Medium Membrane Cell Wall Signal Peptide Lipoprotein Cell wall binding Transmembrane LPXTG Signalp TMHMM tmap MEMSAT LipoP ps_scan

Classification Workflow

Process of Analysis Putative secreted proteins Protein families Functional classification Relations

Analysis Workflow

Architecture  Custom-designed database  Provenance tracking  Analysis – computationally intensive  Architecture differs from other systems

Web Portal

Outline  Computational challenges of bioinformatics  Secretion in Bacillus  Classification and analysis workflows  Results and discussion

Classification Results

Functions of the Clusters Number of families

Biologist’s Outlook  Results available for subsequent analysis  Data and results are of great interest

eScientist’s Outlook  Microbase simplified data analysis But …  Autonomy - most services provided originally by external parties  Licensing – limits exposure of services  Distribution - difficulty came from the relatively large datasets

Future Enhancements  Use notification to automatically analyse recently annotated genomes  Migrate workflows to a remote enclosed environment?

Acknowledgments  Phillip Lord  Colin Harwood  Anil Wipat my Grid  Carole Goble  Tom Oinn … and the rest of the my Grid team Microbase  Yudong Sun  Anil Wipat  Matthew Pocock  Pete A. Lee  Paul Watson  Keith Flanagan  James T. Worthington