BCB420 Week02 Tasks

Week 2 Tasks

In Class

• Questions
• Quiz 1 and pickup

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• Explore system definitions and system discovery processes in submitted papers.
• Discuss data relationships for functional annotation
  • Coexpression
  • Perturbation response (chemogenomics)
  • Interaction - physical and genetic
  • Similar genomic context
  • Gene fusion/fission events
  • Homology
  • Structure
  • Colocation
  • Literature
  • GO annotation
  • KEGG, Biocyc - other regulatory and metabolic pathways
  • First principles from systems theory (???)

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• Define Project
  • Objectives
  • Scope
  • Workflow
  • Milestones for preparation phases I - III
  • Work packages

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• Discuss Development topics
  • Habits (Projects, IDE and debugging, Version control)
  • Collaboration (Wiki, Git, Etherpad)
  • Development (TDD, Literate Development)
  • Testing (Unit testing, Integration testing)

• R Package - Latex tutorial (TBD)
• github tutorial (TBD)

 

For next week

• Work through Software development page
• Work through R Studio literal programming with knitr
• Study databases and strategies
• Draft project workflows
• Contribute to quiz questions
• More ... TBD

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