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CellDesigner Tutorial
Laurence Calzone, Andrei Zinovyev
UMR U900 INSERM/Institut Curie/Ecole des Mines de Paris
Wednesday, April 30th
Outline
• CellDesigner
• Tutorial - Practice
• Example
Variety of models: example of NFkB
A model can be represented in many different ways:
Many representations for the same model.
=> Each modeler uses its own representation
=> Need to read the paper to understand the model
=> Before being able to use or translate models into
mathematics, need to understand the modeler’s symbols
=> Need for a standard format to be able to
- use models
- exchange models
- compare models
- compose models
- etc.
Standard formats
SBML (Systems Biology Markup Language)
format for representing models of biochemical reaction networks
Over 100 software packages support SBML
BioPAX (Biological PAthway eXchange)
format for storing biological pathway data;
ontology for describing biochemical processes and their
hierarchies
SBGN (Systems Biology Graphical Notation)
format for representing graphically biological interactions e.g.
protein-protein interaction, gene regulatory networks, etc.
CellDesigner: a short overview
What is CellDesigner?
CellDesigner is a structured diagram
editor for drawing gene-regulatory and
biochemical networks that uses standard
formats.
CellDesigner content
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Full SBML support
Graphical notation (SBGN)
Possibility for mathematical simulations
Database connection
Export to PDF, PNG, …
Freely available
Supported Environment
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Windows (2000 or later)
Mac OS X
Linux
What is CellDesigner good for?
CellDesigner:
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Offers an « easy-to-use » graphical representation of a network
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Facilitates exchange of models developed by different groups, using a
standard language (SBML: Systems Biology Markup Language)
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Allows to annotate the reactions, proteins, genes, etc.
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Proposes links to other databases (PubMed, IHOP, BioModels, KEGG,
etc.)
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Organizes a lot of information in a unique diagram
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Allows an exchange with other modeling tools
Install and Start CellDesigner
Download CellDesigner version 4.0 β from http://celldesigner.org
Download:
Setup:
Launch:
Start CellDesigner
CellDesigner screen
General view
TREE AREA
displays all the list of the
components in a tree
structure.
DRAW AREA
is the area where the
model is built from the tool
bar items.
Tree
Drawing
LIST AREA
displays and edits the list
of the components of the
model (species, proteins,
genes, RNAs, etc.)
NOTES AREA
displays and edits the
notes of each component
(reactions, protein,
complex, etc.)
Layer
List
Notes
The menu
Compartment
menu
Chemical species
menu
Visualization
Reaction
menu
menu
Boolean logic
menu
The chemical species
The reactions
The compartments
Compartments can be:
- Cytoplasm
- Nucleus
- Nucleolus
- etc.
Boolean gates
Introduce boolean logic information into the diagram
Start with a simple network
- Open a new document:
[File] => [New]
- Name your network
(MichaelisMenten)
- Choose the dimension
of the graph
(by default: 600 by 400
but can be changed later)
Add proteins
- Choose to add a protein
from the Species menu
- A pop-up window opens:
name your protein
- Repeat the process as
many times as needed
Add complexes
- Choose to add a
complex from the Species
menu
- Name it
- Insert the proteins that
compose the complexes
(you must copy/paste the
proteins from the diagram
itself and move them
inside the complex)
Connect species
- Choose the heretodimer
association to connect the
proteins E, S and the
complex ES (there are
many reaction types to
link two species)
- An alternative: a macro,
allows to do all these
steps in just one step
Examples of macros
Small network
This biochemical reaction
E  S 
 ES 
EP
re1 , re4
re3
is translated into this
diagram
Note: There is a possibility to include dynamics into the diagram by defining
the parameters re1, re4, re3… We will not describe this process today…
Or more simply…
This reaction
is translated into this
diagram
You choose the level of details…
E
S

P
Some functions
Drawing tips:
- Choose from the [Edit] menu, Grid Snap, to help you draw your
network.
- You can also make the grid visible
Grid Snap On or OFF indicated here
Database Connection
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Search Database by Notes:
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PubMed: PMID: 123456
Entrez Gene: GeneID: 4015
Database Connection
Import model from BioModels.net
Practice
Inventory of features
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Open a new model
Create a reaction
Add anchor point
Add catalytic reaction
Set active state
Change color
Include compartment
Add residue to protein
Change position of residue
Create complex
Include genes and RNAs
Connect to databases
Choose layout
Demo
First mathematical model of NFkB