An overview of the MGS modeling system

Min Zeng

Department of Computer Science

What is MGS

• A programming language for the simulation of biological processes

• Focus on dynamical systems with a dynamical structure

• Provide a unified view on several computational mechanisms

Dynamical System With Dynamical Structure

• State of the system changes with time

• Structure of the state also changes with time

• Example: cell-division

• Idea: Multiset rewriting

T

C T(C )

AB

C

T

T(C) T(T(C))

Problem with Multiset--rewriting

• Lack of spatial organization! The cell can not be thought as a chemical reactor where the chemicals are homogeneously diluted. The cell exhibit a highly organized spatial structure.

A G T T C A C C A A

A

B

C

Observation

• Neighborhood relationships are important!

• Neighborhood relationships must be flexible.

• Can we define a data structure through the specification of the neighborhood of its elements?

Collection

monoidalrecord pair array

set bag seq

…

Datatypes in MGS

trans max = x,y/(x>y) => x

max[fixrule]( (1,2,5,3,4,set:()) )

max[fixrule]( (5,2,5,3,4,bag:()) )

5, set:()

5,5,bag:()

trans Sort = (x,y /y<x) => y,x

Sort[fixrule] ((2,4,3,1,6,seq:()))

(1,2,3,4,6, seq:())

collection DNA = seq;;collection TUBE = bag;;

trans Restriction = { EcoRI = X+,(“G”,“A”,“A”,”T”,”T”,”C”), Y+ =>(X,“G”)::(“A”,“A”,“T”,“T”,“C”,Y)::TUBE:(); Void = X+ => X:: TUBE:();}

trans React = { dna => hd(restriction(dna)) }

gbf Hexagon = <east, north, northeast; north = east + northeast>

northeast

C

Eden’s Model

Trans Eden = { x, <undef> / x => x, true }

Turing diffusion-reaction process on a ring

Future work

• Compare MGS with other languages (e.g. the L+C system at UofC)

• Implement some models myself using MGS