4 1. Gene Hereditary (inheritance) information unit Defines every organism development What does genes operation mean?
5 2. Gene operation (gene activity) Responsible for producing its special protein Protein amount is the characteristic that can be measured Production rate varies from cell to cell What does it depend on?
6 3. Genes interaction Some proteins can have positive or negative influence on production rates of other proteins This is the way genes can interact with each other May occur within one cell or throughout a part of organism
7 4. Gene network System of gene interactions Usually represented by a directed graph: –Vertices represent genes –Arcs represent interaction facts
8 5. Gene network representation gene B activates gene A (positive interaction) gene B suppresses gene A (negative interaction) Real network exampleElementary interactions
16 Gene model Outer state – amount of protein Inner state – protein generation ability Speed of protein degradation (gradual decrease of protein amount) Block flag – to manipulate gene operation explicitly
17 Universal mechanism of describing both vital activity and interaction processes Interaction rules
18 Cell group structure Systems main orientation is simulation of plant development
19 Cell group structure Hemisphere structure is an approximation to plants cell group giving birth to the whole upper part of plant
20 Cell group structure However, the structure can be used for simulation of many other vital processes in different organisms
21 Simulation flow Step-by-step Each step corresponds to one cell group state: –cell group structure –cell parameters –gene parameters
24 Interface tendencies Simplification: –Network creation similar to common drawing –Use of algebraic notation in interaction rule expressions Visual aids –3D model of cell structure –Graphical indication of simulation flow details –Graphs for cell and gene parameters
25 Extensibility Multilevel architecture Use of design patterns Cross platform –OpenGL –MFC => wxWidgets –Program core (most part of code) is platform- independent
32 System advantages comparing to analogs For gene network simulation : –takes cell localization of interaction processes into consideration For all-purpose simulation: –a simpler interface, does not demand programming skills from a user