Curation of models: Painstaking effort or rewarding activity?

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Curation of models Painstaking effort or
rewarding activity?

• Harish Dharuri
• Tuesday, April 01, 2014
• Second Biomodels.net Training Camp

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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.
• Typos in model equations or just outright wrong
  representation.
• Unresponsive authors.

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What makes it painstaking

• Software issues SBML compliance.
• Balance the need to make models compatible across
  the spectrum with aesthetics of model
  representation.

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What makes it rewardingand there are many
reasons

• Learning
• Learning
• Learning

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Examples in Model Integration

• Yeast Pheromone Pathway and Cell Cycle
• BIOMD0000000032 and BIOMD0000000056
• Calcium Dynamics

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Yeast Pheromone Pathway
CDC28Far1PP Leads to Cell Cycle Arrest
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Far1PP-CDC28 time profile
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Budding Yeast Cell Cycle, Chen et al (2004)
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Time Series Cell Cycle Model
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Kegg Pathway
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CLN1,2,3 Mutant G1 Arrest
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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.

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Dynamics of the Merged Model - DNA synthesis
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Dynamics of the Merged Model CKI profile
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Calcium signaling pathway
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Conclusions

• What makes it painstaking
• Issues with
• Publications
• Software
• Authors dont like me ?
• What makes it rewarding
• Offers a terrific learning experience
• Ideal training for a Systems Biology aspirant

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Conclusions

• Another Issue
• Employability with this skill set
• What is the market demand/perception