Biological Modelling

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Biological Modelling

• A New Kind of Programming Language?

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Collaborators

• Traditional in bio-sciences talks
• Katinka Apagyi
• (Biochemistry, University of Cambridge)
• Jasmin Fisher
• (Computational Biology Division, MSR Cambridge)
• Alan Blackwell
• (Crucible, University of Cambridge)
• Thomas Green
• All mistakes remain mine

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Why?

• Poorly understood
• We increasingly know the code
• Reduction vs. Abstraction
• Expensive to model

Challenges
Usability Barrier

• Tolerance of incompleteness
• Low viscosity
• Comprehensible
• Support social construction

• Adoption
• Errors
• Social context

Abstraction
Reverse Engineering

• Unknown system
• Design determinism
• Translucent abstractions
• BioAbstractions are arbitrary
• Expressive enough to be useful

• Parametric results
• Negative results
• Noisy results

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Summary

• Unknown domain abstractions
• Understanding the code is the point
• Abstraction determinism is dangerous
• Social construction of knowledge is the primary
  activity
• Abstractions?
• Translucent
• low viscosity
• Provisional
• New analytical methods
• Errors Mental model transfer?