Pathway Modelling and Curationusing CellDesigner + Payao --Yukiko

CellDesigner

How to Build Pathway?

species (nodes)
reaction
litreature

Model Representation <> Modelling tools <> Databases

SBML (Systems Biology Markup Language)
SBGN (Systems Biology Graphical Notation):

MAPK pathway

SBML <> SBGN

Read SBML file, add graphical notation, stored in CD annotation

Database Connection

Annotation:
Notes: model, species, protein/RNA/DNA;
MIRIAM;
Layer text

Simulation: via control panel; via SBW menu

SBW= systems biology workbench

SBML features and supporting tools

Models For Simulation

Plugin Development

Model Curation

Pathway Modelling Case Study

Mapathon: 15 members: ERATO wet lab virologists/biologists etc.
read 60 papers

Payao: community base pathway enrichment paltform

Public> Map> Community A