e-science tools for the genomic scale characterisation of bacterial secreted proteins tracy...
TRANSCRIPT
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e-Science Tools For The Genomic Scale Characterisation Of Bacterial Secreted Proteins
Tracy Craddock, Phillip Lord, Colin Harwood and Anil Wipat
Newcastle University
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Outline
Computational challenges of bioinformatics
Secretion in Bacillus Classification and analysis workflows Results and discussion
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Computational Challenges of Bioinformatics
New requirements from bioinformatics 3 major problems
Heterogeneity Distribution Autonomy
Experiments - series of workflows
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myGrid and Taverna
Scufl Simple Conceptual Unified Flow LanguageTaverna Writing, running workflows & examining resultsSOAPLAB Makes applications available
Freefluo Workflow engine to run workflows
Freefluo
SOAPLABWeb Service
Any Application
Web Service e.g. DDBJ BLAST
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Microbase
Grid-based system for microbial genome comparison and analysis
Information repository (and execution environment)
Pre-computed data
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Outline
Computational challenges of bioinformatics
Secretion in Bacillus Classification and analysis workflows Results and discussion
![Page 7: E-Science Tools For The Genomic Scale Characterisation Of Bacterial Secreted Proteins Tracy Craddock, Phillip Lord, Colin Harwood and Anil Wipat Newcastle](https://reader033.vdocuments.net/reader033/viewer/2022042822/56649ec95503460f94bd5fd2/html5/thumbnails/7.jpg)
Secretion in Bacillus
Predict characteristics & behavior of bacteria
Identify secreted proteins
Bacillus species diverse behaviour Soil inhabitants Harmful bacteria
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Importance of Secretion
Mechanism of interaction with environment
Reveal capabilities of an organism
Pathogens are of great interest
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Secretory Proteins
Cytoplasm
Medium
Membrane
Cell Wall
Signal Peptide
Lipoprotein
Cell wall binding
Transmembrane
LPXTG
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Outline
Computational challenges of bioinformatics
Secretion in Bacillus Classification and analysis workflows Results and discussion
![Page 11: E-Science Tools For The Genomic Scale Characterisation Of Bacterial Secreted Proteins Tracy Craddock, Phillip Lord, Colin Harwood and Anil Wipat Newcastle](https://reader033.vdocuments.net/reader033/viewer/2022042822/56649ec95503460f94bd5fd2/html5/thumbnails/11.jpg)
Bioinformatic Tools
Cytoplasm
Medium
Membrane
Cell Wall
Signal Peptide
Lipoprotein
Cell wall binding
Transmembrane
LPXTG
Signalp
TMHMMtmap
MEMSATLipoP
ps_scan
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Classification Workflow
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Process of Analysis
01
02
03
04
0
CP
00
00
01
AE
01
73
55
AE
01
72
25
AE
01
73
34
AE
01
68
79
AE
01
71
94
AE
01
68
77
AL
00
91
26
CP
00
00
02
AE
01
73
33
AP
00
66
27
BA
00
00
04
Putative secreted proteins
Protein families
Functional classification Relations
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Analysis Workflow
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Architecture
Custom-designed database Provenance tracking Analysis – computationally intensive Architecture differs from other systems
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Web Portal
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Outline
Computational challenges of bioinformatics
Secretion in Bacillus Classification and analysis workflows Results and discussion
![Page 18: E-Science Tools For The Genomic Scale Characterisation Of Bacterial Secreted Proteins Tracy Craddock, Phillip Lord, Colin Harwood and Anil Wipat Newcastle](https://reader033.vdocuments.net/reader033/viewer/2022042822/56649ec95503460f94bd5fd2/html5/thumbnails/18.jpg)
Classification Results
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Similar to unknown proteinsTransport/binding proteins and lipoproteinsCell WallMembrane bioenergeticsGerminationProtein secretionSporulationMetabolism of carbohydrates and related moleculesSpecific pathwaysTransformation/competenceMetabolism of lipidsMetabolism of phosphateTranscription regulationMetabolism of amino acids and related molecules
02
46
81
01
2
Functions of the Clusters
Num
ber
of
fam
ilies
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Biologist’s Outlook
Results available for subsequent analysis
Data and results are of great interest
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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
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Future Enhancements
Use notification to automatically analyse recently annotated genomes
Migrate workflows to a remote enclosed environment?
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Acknowledgments
Phillip Lord Colin Harwood Anil Wipat
myGrid Carole Goble Tom Oinn
… and the rest of the myGrid team
Microbase Yudong Sun Anil Wipat Matthew Pocock Pete A. Lee Paul Watson Keith Flanagan James T. Worthington