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Curation of models: Painstaking effort or rewarding activity?. Harish Dharuri Monday, October 20, 2014 Second Biomodels.net Training Camp. What makes it painstaking…. Incomplete information in the paper Missing Initial Conditions Parameter values

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curation of models painstaking effort or rewarding activity

Curation of models: Painstaking effort or rewarding activity?

Harish Dharuri

Monday, October 20, 2014

Second Biomodels.net Training Camp

what makes it painstaking
What makes it painstaking…
  • Incomplete information in the paper
    • Missing
      • Initial Conditions
      • Parameter values
  • Lack of correspondence between simulation result and figures given in the paper.
  • Typo’s in model equations or just outright wrong representation.
  • Unresponsive authors.
what makes it painstaking1
What makes it painstaking…
  • Software issues: SBML compliance.
  • Balance the need to make models compatible across the spectrum with aesthetics of model representation.
examples in model integration
Examples in Model Integration
  • Yeast Pheromone Pathway and Cell Cycle
    • BIOMD0000000032 and BIOMD0000000056
  • Calcium Dynamics
slide6

Yeast Pheromone Pathway

CDC28+Far1PP: Leads to Cell Cycle Arrest

recap
Recap
  • What we are doing…
    • Merging the Yeast Pheromone model and the Cell cycle model.
    • Far1PP-CDC28 (ComplexN) inhibits Cyclins (CLN1, CLN2 and CLN3) in the cell cycle model.
      • Inference made from literature.
  • What we hope to see…
    • Cell cycle stop in the G1 phase.
      • Needs to look like experimental data from CLN (1,2,3) mutants.
conclusions
Conclusions
  • What makes it painstaking
    • Issues with
      • Publications
      • Software
      • Authors don’t like me 
  • What makes it rewarding
    • Offers a terrific learning experience
    • Ideal training for a Systems Biology aspirant
conclusions1
Conclusions
  • Another Issue
    • Employability with this skill set
      • What is the market demand/perception