Difference between revisions of "CellDesigner"

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==Basic Level==
 
==Basic Level==
 
# Overview of CellDesigner      
 
# Overview of CellDesigner      
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#* What is a CellDesigner
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#* Link for the Startup Guide Version 4.3
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#* Who can use CellDesigner
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#* Clippings of video tutorials available in CellDesigner series
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#* Simple Examples in Cell Designer
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−
#* Motivation
+
−
#* Major Features
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−
#* Citation of CellDesigner
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#Installation of CellDesigner 4.3      
 
#Installation of CellDesigner 4.3      
 
#* Software requirement
 
#* Software requirement
 
#* Download & Installation of CellDesigner
 
#* Download & Installation of CellDesigner
−
#* On Windows OS
+
#* On Windows Operating System
 
#* Adding a protein species
 
#* Adding a protein species
 
# Getting Started with CellDesigner      
 
# Getting Started with CellDesigner      
−
#* General view of CellDesigner
 
 
#* The Menu & Tool Bar
 
#* The Menu & Tool Bar
 +
#* Different areas in the CellDesigner workspace
 
#* Components, Species & Reaction
 
#* Components, Species & Reaction
 
#* Creating a simple network: Name & Size of the network
 
#* Creating a simple network: Name & Size of the network
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#* Grid Visible , Grid Snap
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#* Save a network
 +
#* Export an image
 +
#* What is Celldesigner?
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#* How to Open CellDesigner from the shortcut CellDesigner icon on the desktop
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#* Symbols for generic protein, receptor, ion channel, truncated protein, gene, RNA etc
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#* Symbols for  State transition, Heterodimer association, Dissociation, Catalysis, Inhibition etc
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#* How to change the size of a component
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#* How to zoom a network
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#* Grid Visible, Grid Snap
 
#* Change size of network
 
#* Change size of network
 
#* Select a component
 
#* Select a component
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#* Save the Network
 
#* Save the Network
 
#* Zoom
 
#* Zoom
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# Creating a Simple Biological Network using CellDesigner4.3      
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# Installation of CellDesigner on Linux OS      
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#* TO build a biological pathway
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#* Download and install CellDesigner 4.3 on Ubuntu Linux Operating System
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#* Adding new compartments
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#* Create a Compartment in the draw area of CellDesigner
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#* To put components in a compartment
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#* How to find out the details of the OS type of our machine
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#* To change the shape of a compartment
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#* How to see the Main menu bar clearly.
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#* To change the position of the compartment name
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#* To open a new document
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#* Adding Reactions:Association (Homodimer/Heterodimer), Dissociation & State Transition
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#* Significance of Select Mode
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#* Adding Catalysis or Modifier of the reaction:Activation, Inhibition
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#* How to change the position of the List & Notes area
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# Editing & Formatting Species of a Network    
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#* How to change size of the areas
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## Change Identity-Species
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#* How to see all the icons on the CellDesigner window.
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##* Change Class
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#* How to draw a Compartment and change position of the compartment name
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##* Homomultimer
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# Build-and-Modify-Process-Diagram
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##* State
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#* Use of Macros
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## Edit protein
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#* How to move Components on the draw area
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##* Change type
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#* Generic protein to Simplae molecule
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##* Rename
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#* Connect a reaction line around a species
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##* Edit block diagram
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#* Align and extend a reaction line
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##* Edit residue (Change angle)
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#* Add a Product and a Reactant
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##* Add text (Reference/Information)
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#* To build a process diagram for Methionine Biosynthesis
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##*Change font, color & shape
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# Customizing Diagram Layout
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##* Replace species ID
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#* How to change color, shape and width of a Reaction line
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##* Replace reaction ID
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#* How to add Anchor points to a Reaction line
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## Format Reaction
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#* How to align Components
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##* Add anchor point
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#* How to show/hide Reaction ids
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##* Change Identity (name, type, reversible)
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#* How to add notes to Components
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##* Edit reaction-Creating a kinetic law
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#* How to edit Protein
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##* Change color shape-Add text
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#* How to edit information
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## Grid visible
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#* And get a bird’s eye view of the diagram
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# Simulation of Computational Model    
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−
#* What is Simulation
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#* Prerequisite for Simulation
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−
#* Set value of parameter or initial conditions for the simulation
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−
#* Set simulation time and tolerance
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#* Plot graphs, hide/unhide graphs
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#* Export results
+
  
 
==Intermediate Level==
 
==Intermediate Level==

Revision as of 15:54, 21 June 2016

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    
    • Link for the Startup Guide Version 4.3
    • Clippings of video tutorials available in CellDesigner series
  2. Installation of CellDesigner 4.3    
    • Software requirement
    • Download & Installation of CellDesigner
    • On Windows Operating System
    • Adding a protein species
  3. Getting Started with CellDesigner    
    • The Menu & Tool Bar
    • Different areas in the CellDesigner workspace
    • Components, Species & Reaction
    • Creating a simple network: Name & Size of the network
    • Save a network
    • Export an image
    • What is Celldesigner?
    • How to Open CellDesigner from the shortcut CellDesigner icon on the desktop
    • Symbols for generic protein, receptor, ion channel, truncated protein, gene, RNA etc
    • Symbols for State transition, Heterodimer association, Dissociation, Catalysis, Inhibition etc
    • How to change the size of a component
    • How to zoom a 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. Installation of CellDesigner on Linux OS    
    • Download and install CellDesigner 4.3 on Ubuntu Linux Operating System
    • Create a Compartment in the draw area of CellDesigner
    • How to find out the details of the OS type of our machine
    • How to see the Main menu bar clearly.
    • To open a new document
    • Significance of Select Mode
    • How to change the position of the List & Notes area
    • How to change size of the areas
    • How to see all the icons on the CellDesigner window.
    • How to draw a Compartment and change position of the compartment name
  5. Build-and-Modify-Process-Diagram
    • Use of Macros
    • How to move Components on the draw area
    • Generic protein to Simplae molecule
    • Connect a reaction line around a species
    • Align and extend a reaction line
    • Add a Product and a Reactant
    • To build a process diagram for Methionine Biosynthesis
  6. Customizing Diagram Layout
    • How to change color, shape and width of a Reaction line
    • How to add Anchor points to a Reaction line
    • How to align Components
    • How to show/hide Reaction ids
    • How to add notes to Components
    • How to edit Protein
    • How to edit information
    • And get a bird’s eye view of the diagram

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

Contributors and Content Editors

Bellatony911, Kavita, Minal, Nancyvarkey, PoojaMoolya, Sakinashaikh

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