XML Documentation of Biopathways and Their Simulations in Genomic Object Net Speaker : Hungwei chen

XML Documentation of Biopathways XML Documentation of Biopathways and Their Simulations in Genomic Object Netand Their Simulations in Genomic Object Net

Speaker : Hungwei chen

Biopathway Biopathway Modeling & SimulationModeling & Simulation

A Software A Software TowardToward


A Software A Software TowardToward


Genomic Object NetGenomic Object Net

What is Genomic Object NetWhat is Genomic Object Net• Genomic Object Net is a software tools for Modeling and Simulation Biopathways

• Employing the notion of HFPN as its basic Architecture

• Using XML Documents for representation simulations and visualization for Biopathway

About Genomic Object NetAbout Genomic Object Net

• Genomic Object Net Assembler

• Genomic Object Net Describing tool.

• Genomic Object Net Visualizer

• Biopathway Describing Tool– helps to describe a biopathway according to the traditi

onal description methods in biology

– releasing users from the mathematical knowledge

• Genomic Object Net Assembler1. Designs HFPN which represents and simulates a syste

m of genomic objects.

2. Produces Biopathway Representation Source File as an XML document.

3. Produces Simulation Results Files (CSV format) each of which contains a time-series of the numerical values representing the behavior of places in HFPN.

In order for biosimulation tools to be accepted by users in

(1)Remove issues which are irrelevant to biological importance, 　　　　　　　　　　　　　　　

(2)Allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism

From these criteria, software tools currently developed might not be enough satisfactory.

• Metabolic Pathways

• Signaling Pathways

• Gene Regulatory Networks

Pathway Types for Modeling

Metabolic Pathway

Apoptosis induced by Fas

Cytoplasm

cascade

caspase

Signal

Fas ligand

Fas receptor

complex

Signaling Pathway

Switching Mechanism of Lambda Phage

Petri net

place

transition

arc

inhibitory arc

token

What is the Petri Net ??What is the Petri Net ??• A Petri Net is a collection of directed arcs

connecting places and transitions .

• Arcs have capacity 1 by default .

• Places may hold tokens

• transitions have no capacity, and cannot store tokens .

Simple Example of Petri NetSimple Example of Petri Net

How to enable token through transition

• A transition is enabled when the number of tokens in each of its input places is at least equal to the arc weight going from the place to the transition.

• An enabled transition may fire at any time. When fired, the tokens in the input places are moved to output place

Example of Petri Net GraphExample of Petri Net Graph

When arcs have different weightsWhen arcs have different weights

The inhibitor arcThe inhibitor arc

• This transition cannot fire, because the token in P2 inhibits it.

Petri Net TopologyPetri Net Topology

•

Example-the control of a vending machineExample-the control of a vending machine

A coin is ready to dropA coin is ready to drop

An accepted coin leads to dispensingAn accepted coin leads to dispensing

After inserting several coinsAfter inserting several coins

2H2 + O2 -> 2H2O

Hybrid Petri Net

•Easy to describe biological facts and biological phenomenon on computers and •Acceptable technical expression of the tool to biologists.

Extension to Hybrid Dynamic Net

© Copyright 2002 Satoru Miyano, Human Genome Center, University of Tokyo

Elements

Michaelis

- Menten

Equation

Hybrid Dynamic Net


Hybrid functional Petri net

)(2

1 , , 313322211 mmfmmfmmf

323213

1 , log2

2

1 1 megmmg m

•　 Assign any function to each arc

• Transition T fires as long as mi > 0 for all 1 < i < p


dimer monomers 1 2

discrete Petri net

1 1

1 1

hybrid dynamic net

1 2

hybrid functional Petri net

describe naturally

explosion of tokens

Not intuitive nor natural© Copyright 2002 Satoru Miyano, Human Genome Center, University of Tokyo

Lambda phage genetic switch feedback mecnanism

1. Identify main events in the biopathway of concern.2. placesplaces :• Continuous places (doubled circles) ： contain real numbers which represent concentrations of mRNA and Proteins.

• Discrete places (single circles) ： are corresponded to the promoter or operator sites for expressing the binding situation of transcription factor

Design of hybrid functional Petri net

• 3. transitionstransitions: interactions between objects – hidden interaction should also be identified

• 4. functionsfunctions assigned to transitions : – based on the logical structure in events and biol

ogical/biochemical knowledge about objects

• 5. Simulate, evaluate, and tune up the designed HFPN

3. transitiontransition :• Continuous transitions (white rectangles) ： are used for expressing the production/degradation speed of mRNAs or proteins.

Discrete transitions (black rectangles) ： are used for expressing the required time for RNA polymerase which moves between two genes.

Design of hybrid functional Petri net

XML Integration of Biopathway XML Integration of Biopathway in Genomic Object Netin Genomic Object Net

<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE hybridFunctionalPetriNet SYSTEM "SampleHFPNet.dtd"><HFPN> <place id="P1" type="continuos" variableName="m1"/> <place id="P2" type="continuos" variableName="m2"/> <transition id="T1" speedFunction="m1/2.5" type="continuos"/> <arc from="P1" to="T1" type="normal" weight="1"/> <arc from="T1" to="P2" type="normal" weight="m1/2"/></HFPN>

m1 m2

T1

1 m1/2

P1 P2

m1/2.5

XML　 representation of HFPN

XML Biopathway Visualization

(Upper left) Lambda phage chromosome – brightness or color of gene is changed according to t

he protein concentration level

(upper right) Concentrations of proteins N and CI– Direct display of csv file in Simulation Result Files

(bottom) CI and Cro binding to OR1, OR2, OR3

ConclusionConclusion• The HFPN model for representing and simulating

biopathways.

• XML documents for description and visualization of HFPN together with simulation results.

• The future plan of Genomic Object Net is to construct a knowledge database of biopathways which allow computer simulation and visualization.

Result Result

• For all biochemical passways are hard to

modeling in a good mathematical Knowledge

http://www.GenomicObject.Net

Thank you for your Thank you for your attentionattention