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Enhancing Biological Modeling with a Graphical Rule Editor for Pathway Logic Assistant

This paper discusses the development of a graphical rule editor designed to improve the usability of Pathway Logic Assistant, a tool for analyzing biological systems. Motivated by the need for intuitive representations of complex biological processes, the graphical interface aims to simplify rule editing and understanding. By linking formal logic with visual representations, biologists can more effectively interact with their models without requiring extensive training in logic. The goal is to create a user-friendly environment that fosters better comprehension of pathway logic models.

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Enhancing Biological Modeling with a Graphical Rule Editor for Pathway Logic Assistant

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  1. Towards a graphical rule editor for the Pathway Logic AssistantAmnaAbbas1 Carolyn Talcott2Merrill Knapp 2Oliver Ray 11University of Bristol, UK2SRI International, USALDSSB’12, Bristol, UK24th September 2012

  2. Motivation • “Symbolic Systems Biology is the qualitative and quantitative study of biological processes as integrated systems rather than isolated parts.” • ... • “The aim is to develop formal models that are as close as possible to domain experts (biologists) mental models.” • P. Lincoln and C. Talcott • in M.S.Iyengar(ed.) Symbolic Systems Biology: Theory and Methods • Jones and Bartlett, 2010, p.2

  3. Background • Pathway Logic • symbolic approach for reasoning about biological entities and processes • based on a rewriting logic system (Maude) • developed at SRI International (Lincoln, Talcott) • pl.csl.sri.com • Pathway Logic Assistant • tool for browsing and analysing pathway logic models • applied to large signalling and metabolic networks

  4. Background • Representation • entities (metabolites, species, genes, ...) • reactions (substrates, products, modifiers) • Reasoning • static analysis • forward simulation • forward search • backward search • model checking • constraint solving • meta-analysis

  5. Example: Maude Definition • this is what the biologists at SRI actually work with !

  6. Example: Maude Definition • this is what the biologists at SRI actually work with ! • substrates • products • modifiers

  7. Example: Petri net representation • even when rules are displayed graphically they are still hard to understand !

  8. Example: Petri net representation • even when rules are displayed graphically they are still hard to understand ! • complex formation • species location • species modification

  9. Introducing Our Graphical Rule Editor • our graphical interface should make editing and understanding rules easier !

  10. Introducing Our Graphical Rule Editor • our graphical interface should make editing and understanding rules easier ! • “right brain” vs. “left brain” (spatial representation of locations, complexes) • biologists “think in” cartoons (and actually write them down as before/after) • link formal representation to intuitive model

  11. Conclusion • Biologists should not need special training in logic to use symbolic systems biology tools • We have focused on providing intuitive graphical support for simple rule editing (making modifications, locations, and the before and after states more intuitive) • But the greater challenge is to provide interactive graphical feedback for complex modes of logical inference (input queries and output results).

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