This document discusses using programming languages to model biological systems. It describes how traditional biology experiments focus on isolated parts of systems, while systems biology examines interactions between many components. Modeling biological systems requires abstracting away details like individual molecules. Previous approaches include differential equations and pathway databases, but process calculi may provide a better foundation by modeling each entity as a concurrent computational process. The document proposes a process calculus called PML for describing biological systems at multiple levels of abstraction in a biologically meaningful way.

1. Programming Languages for Biology Bor-Yuh Evan Chang November 25, 2003 OSQ Group Meeting

2. Biological Perspective F [http://www.nocturnalvisions.freeservers.com/page6.html] FF [Matsudaira et al. Molecular Cell Biology 4.0 . Freeman, 2000] F FF FF FF

7. Example “Textbook” Description http://vcell.ndsu.nodak.edu/~christjo/vcell/animationSite/lacOperon/

16. Informal Graphical Diagrams Protein Enzyme Protein Enzyme Enzyme Protein k k -1 k cat domains rules sites

17. PML: Enzyme bind_substrate parameterized declared in outer scope interactions within the complex Enzyme

18. PML: Protein bind_substrate bind_product Protein Protein

19. PML: A Simple System

26. Bonus Slides

27. Compartments

29. PML: Simple Compartments Example MolB bind_a bind_a MolA

30. PML: Simple Compartments Example MolA MolB ER Cytosol CytERBridge

31. PML: Simple Compartments Example MolB ER Cytosol CytERBridge MolA

32. Semantics of PML

35. Syntax of PML

36. Syntax of PML

37. Syntax of PML

38. Example: Cotranslational Translocation

40. Example: Cotranslational Translocation

41. Example: Cotranslational Translocation

42. Example: Cotranslational Translocation

43. Example: Cotranslational Translocation

44. Example: Cotranslational Translocation

45. Example: Cotranslational Translocation

46. Example: Cotranslational Translocation