Difference between revisions of "CellDesigner"

Revision as of 15:57, 29 October 2013

CellDesigner is a process diagram editor for drawing gene-regulatory and biochemical networks. Intuitive user-interface helps to draw a diagram in rich graphical representation with our own design. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano.

CellDesigner is used for

• User-friendly visualization
• Modeling and simulation of genetic regulatory networks
• Protein networks and metabolic networks.

CellDesigner is SBML compliant software. SBML (System Biology Markup Language) is a standard computer-readable format for representing models of biochemical and gene-regulatory networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench. CellDesigner uses SBML (System Biology Markup Language) to describe models and allow simulation of models using an integrated SBML ODE solver.

Cell Designer = SBML + Simulation + Databases Connections

In this tutorial we will learn about the basic components of the software, developing graphical model of a network, developing computational model & simulation of the model.

CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X.

The current version of CellDesigner requires JRE (Java Runtime Environment). The installers for Windows & Linux include JRE 1.6, so no need to install Java before installing CellDesigner. On MacOS X, Java 1.6 is required.

The Spoken Tutorial Effort for CellDesigner is being contributed by Ms. Dasaka Kavita & Ms. Sakina Shaikh from IIT Bombay. Other contributors who helped in the creation of the scripts include Mr. Anil Patel & Ms. Reshma Patil from IIT Bombay who have contributed as 'Domain experts'.

CellDesigner Slide Template (TEX Format)                                                                                                                              

Glossary

Basic Level

1. Overview of CellDesigner    
   • What is a CellDesigner
   • Who can use CellDesigner
   • Simple Examples in Cell Designer
   • Motivation
   • Major Features
   • Citation of CellDesigner
2. Installation of CellDesigner 4.3    
   • Software requirement
   • Download & Installation of CellDesigner
   • On Windows OS
3. Getting Started with CellDesigner    
   • General view of CellDesigner
   • The Menu & Tool Bar
   • Components, Species & Reaction
   • Creating a simple network: Name & Size of the network
   • Grid Visible , Grid Snap
   • Change size of network
   • Select a component
   • Move/Delete a component
   • Undo/Redo
   • Change the size of the component
   • Save the Network
   • Zoom
4. Creating Model of a Biological Network    
   • Example of a Biological Network:Enzyme-Substrate Reaction
   • Prerequisites for a Network Model
   • New Compartment:Name & Shape of Compartment
   • To put components in a compartment
   • To change the shape of a compartment
   • To change the position of the compartment name
   • Adding Reactions:Association (Homodimer/Heterodimer), Dissociation & State Transition
   • Adding Catalysis or Modifier of the reaction:Activation, Inhibition
5. Editing & Formatting Species of a Network    
   1. Change Identity-Species
      • Change Class
      • Homomultimer
      • State
   2. Edit protein
      • Change type
      • Rename
      • Edit block diagram
      • Edit residue (Change angle)
      • Add text (Reference/Information)
      • Change font, color & shape
      • Replace species ID
      • Replace reaction ID
   3. Format Reaction
      • Add anchor point
      • Change Identity (name, type, reversible)
      • Edit reaction-Creating a kinetic law
      • Change color shape-Add text
   4. Grid visible
6. Developing a Computational Model    
   • Prerequisite for a Computational Model
   • Setting Initial Conditions: Amount of substance & Unit of amount
   • Getting started with kinetic law window: Introduction
   • Add new parameters: Name, ID, Unit of parameter
   • Set Kinetics of elementary reactions (by keyboard): zero order, first order etc.
   • Set Kinetics by using mouse
   • Change view of equation: Replace ID with name, convert view of equation into mathematical form
   • Change view of kinetic law window: Hide/unhide sections of kinetic window
   • View kinetics from desktop of CellDesigner
7. Simulation of Computational Model    
   • Prerequisite for Simulation
   • Set value of parameter or initial conditions for the simulation
   • Set simulation time and tolerance
   • Plot graphs, hide/unhide graphs
   • Export results

Intermediate Level

1. Create a Complex    
   • To create a complex
   • To modify the species within a complex
   • To change the appearance of a complex
2. Edit Reactions    
   • To change connection points of Reaction on Species
   • To add Anchor points
   • To move a Species with a reaction
   • To change the shape of a Reaction line segment
   • To adjust a Reaction line automatically
   • To change line width and color setting of a Reaction
   • To make a reversible reaction
3. Change Color and Shape of Components & Export Image    
   • To change the default settings of the color and shape
   • To change the color & shape of the individual components
   • To export image in different format
4. Add Model Description & Import and Export a Model    
   • To add Model Description
   • To Save a Model
   • To Save a Model in pure SBML format
   • To Import a Model SBML file
   • To Export a Model to a pure SBML file
   • To Export a Model to a BioPax format file (.owl)
5. Open an SBML format    
   • To open an SBML file
   • To save a model with SBO Terms
6. Compartments & Species    
   • To Edit a Compartment
   • To edit Species
   • To change font size
   • Find a species in the List area
   • To export the list to CSV files
7. Species-Proteins, Gene, RNA and asRNA    
   • Check & Change the Properties ona Protein/Gene/RNA/asRNA
   • To Change the type of Protein
   • To add a Residue/Binding Region of a Protein/Gene/RNA/asRNA
   • To specify the Modification of a residue
   • To Change the State of a Protein
   • Add notes to a Protein, Gene, RNA or asRNA
8. Block Diagram-To check Relationship of a Species (*Proto-type)    
   • What is a Block Diagram
   • To extract Regulation
   • Modifications/Activations Relation

Advanced Level