CellDesigner%20Tutorial

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CellDesigner Tutorial

• Laurence Calzone, Andrei Zinovyev
• UMR U900 INSERM/Institut Curie/Ecole des Mines de
  Paris
• Wednesday, April 30th

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Outline

• CellDesigner
• Tutorial - Practice
• Example

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Variety of models example of NFkB

• A model can be represented in many different
  ways

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• Many representations for the same model.
• gt Each modeler uses its own representation
• gt Need to read the paper to understand the model
• gt Before being able to use or translate models
  into mathematics, need to understand the
  modelers symbols
• gt Need for a standard format to be able to
• - use models
• - exchange models
• - compare models
• - compose models
• - etc.

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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.

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CellDesigner a short overview
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What is CellDesigner?

• CellDesigner is a structured diagram editor for
  drawing gene-regulatory and biochemical networks
  that uses standard formats.

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CellDesigner content

• Full SBML support
• Graphical notation (SBGN)
• Possibility for mathematical simulations
• Database connection
• Export to PDF, PNG,
• Freely available
• Supported Environment
• Windows (2000 or later)
• Mac OS X
• Linux

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What is CellDesigner good for?

• CellDesigner
• Offers an  easy-to-use  graphical
  representation of a network
• Facilitates exchange of models developed by
  different groups, using a standard language
  (SBML Systems Biology Markup Language)
• Allows to annotate the reactions, proteins,
  genes, etc.
• Proposes links to other databases (PubMed, IHOP,
  BioModels, KEGG, etc.)
• Organizes a lot of information in a unique
  diagram
• Allows an exchange with other modeling tools

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Install and Start CellDesigner

• Download CellDesigner version 4.0 ß from
  http//celldesigner.org
• Download
• Setup
• Launch

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Start CellDesigner
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CellDesigner screen
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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.
• 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.)

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The menu
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The chemical species
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The reactions
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The compartments

• Compartments can be
• Cytoplasm
• Nucleus
• Nucleolus
• etc.

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Boolean gates

• Introduce boolean logic information into the
  diagram

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Start with a simple network

• - Open a new document
• File gt New
• - Name your network
• (MichaelisMenten)
• - Choose the dimension of the graph
• (by default 600 by 400 but can be changed later)

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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

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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)

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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

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Examples of macros
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Small network
This biochemical reaction 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
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Or more simply
This reaction is translated into this diagram
You choose the level of details
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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
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Database Connection

• Search Database by Notes
• PubMed PMID 123456
• Entrez Gene GeneID 4015

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Database Connection

• Import model from BioModels.net

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Practice
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Inventory of features

• 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

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Demo
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First mathematical model of NFkB
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