Streptomyces IGF bioinformatics support service

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Streptomyces IGF bioinformatics support service

• (1) data capture

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Plan

• IGF initiative
• bioinformatics goals my role
• Data capture in action

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Investigating Genome Function

• The IGF initiative was launched in 1999 to fund
  consortia to develop access to high throughput
  genomics technologies (eg micro-arrays and
  proteomics) and associated resources (eg mutant
  populations) for communities working on organisms
  key to the BBSRC remit.

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COGEME / Streptomyces IGF Support Service
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Who am I?
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The Friendly Face of Bioinformatics
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My role

• Support
• Deposition
• Analysis
• Consultancy
• Policies
• Data standards
• IT infrastructure

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Consultancy

• Working group
• Policies
• Data deposition
• Data analysis services
• IPR credit
• Terms for describing experiments
• Rate my attributes
• IT infrastructure
• charting Pipeline requirements
• feeding back maxd bugs

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Support

• StreptoBASE
• Portal web site
• Support Centre
• Microarray Data Repository
• built with maxd
• MIAME

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Support Centre
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Microarray Data Repository
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Microarray Data Repository
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Microarray Data Capture

• Whats in it for you

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Direct benefits 1

• Force thought about experimental design
• Ability to export MAGE-ML files
• Satisfying demands of high-end journals
• Allow various systems to interpret your data
• Databases, querying and analysis tools

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Direct benefits 2

• Post-docs and students leave
• Data not fully exploited
• Unexplored avenues
• Comparisons with future results
• Lab books vary in quality

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Direct Benefits 3

• Support
• Deposition
• Analysis
• Conditions
• Data must be deposited
• Acknowledgement / Collaboration

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Indirect Benefits 1

• A transcriptome resource for everyone
• Numbers meaningless alone
• Resource stores the context
• Complex queries
• E.g., please find all the genes upregulated under
  drug treatment x in experiment 204 from Jones
  lab, where transcription is not significantly
  affected in any of mutant in list y of
  experiments 14-58 in Smiths lab, that have
  ontology terms related to metabolism and

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Indirect Benefits 2

• Pipeline

DNA
RNA
proteins
metabolites
Normalisation QC Analysis
really complex queries
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Indirect Benefits 3

• Dialog
• Model tool validation
• Foster links between you and CS

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Help!

• StreptoBASE Pipeline need data
• Raison dêtre
• Needs testing with real experiments
• Need to foster collaboration between CS and
  biology groups

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