Difference between revisions of "CellDesigner"

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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.   
 
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 a free and open software and can be downloaded from [http://celldesigner.org  http://celldesigner.org]
 
  
 
CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X.
 
CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X.
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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 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'.  
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The Spoken Tutorial Effort for CellDesigner is being contributed by '''Dr. Bella Tony''' from IIT Bombay.  Ms. Dasaka Kavita & Ms. Sakina Shaikh from IIT Bombay also created 2 tutorials. Other contributors who helped in the creation of the scripts include Dr. Snehalatha, Mr. Anil Patel & Ms. Reshma Patil from IIT Bombay who have contributed as 'Domain experts'.
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'''Learners''': UG/PG Bio-Chemistry students.
  
 
<blockquote style="background-color: lemonchiffon; border: solid thin grey;">
 
<blockquote style="background-color: lemonchiffon; border: solid thin grey;">
'''CellDesigner Slide Template''' [[Media:CellDesigner_template.zip | (TEX Format)]]  &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
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[[Glossary_for_CellDesigner | Glossary]]
[[Glossary_for_CellDesigner | Glossary]] </blockquote>
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</blockquote>
  
 
==Basic Level==
 
==Basic Level==
 
# Overview of CellDesigner &nbsp; &nbsp;  
 
# Overview of CellDesigner &nbsp; &nbsp;  
#* What is a CellDesigner
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#* Link for the Startup Guide Version 4.3
#* Who can use CellDesigner
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#* Clippings of video tutorials available in CellDesigner series
#* Simple Examples in Cell Designer
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#Installation of CellDesigner 4.3 &nbsp; &nbsp;  
#* Motivation
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#* Major Features
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#* Citation of CellDesigner
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#Download & Installation of CellDesigner 4.2 &nbsp; &nbsp;  
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#* Software requirement
 
#* Software requirement
#* Pre-requisites
 
 
#* Download & Installation of CellDesigner
 
#* Download & Installation of CellDesigner
#* On Windows OS
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#* On Windows Operating System
#* On Linux OS
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#* Adding a protein species
#* On Mac OS
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#* List of Plugins & Utilities
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# Getting Started with CellDesigner &nbsp; &nbsp;  
 
# Getting Started with CellDesigner &nbsp; &nbsp;  
#* General view of CellDesigner
 
 
#* The Menu & Tool Bar
 
#* The Menu & Tool Bar
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#* 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
#* Grid Visible , Grid Snap
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#* Save a network
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#* Export an image
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#* 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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#* Undo/Redo
 
#* Undo/Redo
 
#* Change the size of the component
 
#* Change the size of the component
#* Save the Network
 
 
#* Zoom
 
#* Zoom
# Creating Model of a Biological Network &nbsp; &nbsp;  
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# Installation of CellDesigner on Linux OS &nbsp; &nbsp;  
#* Example of a Biological Network:Enzyme-Substrate Reaction
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#* Download and install CellDesigner 4.3 on Ubuntu Linux Operating System
#* Prerequisites for a Network Model
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#* Create a Compartment in the draw area of CellDesigner
#* New Compartment:Name & Shape of Compartment
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#* How to find out the details of the OS type of our machine
#* To put components in a compartment
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#* How to see the Main menu bar clearly.
#* To change the shape of a compartment
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#* To open a new document
#* To change the position of the compartment name
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#* Significance of Select Mode
#* Adding Reactions:Association (Homodimer/Heterodimer), Dissociation & State Transition
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#* How to change the position of the List & Notes area
#* Adding Catalysis or Modifier of the reaction:Activation, Inhibition
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#* How to change size of the areas
# Editing & Formatting Species of a Network &nbsp; &nbsp;
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#* How to see all the icons on the CellDesigner window.
## Change Identity-Species
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#* How to draw a Compartment and change position of the compartment name
##* Change Class
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# Create and Edit Components
##* Homomultimer
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#* Open an already saved .xml file
##* State
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#* Change the following in a Compartment- Size, shape, color and  thickness of the border
## Edit protein
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#* Create multiple files in CellDesigner
##* Change type
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#* Learn about Start-point and End-point of a Species
##* Rename
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#* Change identity of Species and Reaction
##* Edit block diagram
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##* Edit residue (Change angle)
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##* Add text (Reference/Information)
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##*Change font, color & shape
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##* Replace species ID
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##* Replace reaction ID
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## Format Reaction
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##* Add anchor point
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##* Change Identity (name, type, reversible)
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##* Edit reaction-Creating a kinetic law
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##* Change color shape-Add text
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## Grid visible
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# Developing a Computational Model &nbsp; &nbsp;
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#* Prerequisite for a Computational Model
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#* Setting Initial Conditions: Amount of substance & Unit of amount
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#* Getting started with kinetic law window: Introduction
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#* Add new parameters: Name, ID, Unit of parameter
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#* Set Kinetics of elementary reactions (by keyboard): zero order, first order etc.
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#* Set Kinetics by using mouse
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#* Change view of equation: Replace ID with name, convert view of equation into mathematical form
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#* Change view of kinetic law window: Hide/unhide sections of kinetic window
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#* View kinetics from desktop of CellDesigner
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# Simulation of Computational Model &nbsp; &nbsp;
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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
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==Intermediate Level==
 
==Intermediate Level==
# Create a Complex &nbsp; &nbsp;
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#* To create a complex
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# Build-and-Modify-Process-Diagram
#* To modify the species within a complex
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#* Use of Macros
#* To change the appearance of a complex
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#* How to move Components on the draw area
# Edit Reactions &nbsp; &nbsp;
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#* Generic protein to Simplae molecule
#* To change connection points of Reaction on Species
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#* Connect a reaction line around a species
#* To add Anchor points
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#* Align and extend a reaction line
#* To move a Species with a reaction
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#* Add a Product and a Reactant
#* To change the shape of a Reaction line segment
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#* To build a process diagram for Methionine Biosynthesis
#* To adjust a Reaction line automatically
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# Customizing Diagram Layout
#* To change line width and color setting of a Reaction
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#* How to change color, shape and width of a Reaction line
#* To make a reversible reaction
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#* How to add Anchor points to a Reaction line
# Change Color and Shape of Components & Export Image &nbsp; &nbsp;
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#* How to align Components
#* To change the default settings of the color and shape
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#* How to show/hide Reaction ids
#* To change the color & shape of the individual components
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#* How to add notes to Components
#* To export image in different format
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#* How to edit Protein
# Add Model Description & Import and Export a Model &nbsp; &nbsp;
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#* How to edit information
#* To add Model Description
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#* And get a Bird’s eye view of the diagram
#* To Save a Model
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#* To Save a Model in pure SBML format
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#* To Import a Model SBML file
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#* To Export a Model to a pure SBML file
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#* To Export a Model to a BioPax format file (.owl)
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# Open an SBML format &nbsp; &nbsp;
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#* To open an SBML file
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#* To save a model with SBO Terms
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# Compartments & Species &nbsp; &nbsp;
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#* To Edit a Compartment
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#* To edit Species
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#* To change font size
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#* Find a species in the List area
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#* To export the list to CSV files
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# Species-Proteins, Gene, RNA and asRNA &nbsp; &nbsp;
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#* Check & Change the Properties ona Protein/Gene/RNA/asRNA
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#* To Change the type of Protein
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#* To add a Residue/Binding Region of a Protein/Gene/RNA/asRNA
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#* To specify the Modification of a residue
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#* To Change the State of a Protein
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#* Add notes to a Protein, Gene, RNA or asRNA
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# Block Diagram-To check Relationship of a Species (*Proto-type) &nbsp; &nbsp;
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#* What is a Block Diagram
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#* To extract Regulation
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#* Modifications/Activations Relation
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==Advanced Level==
 
==Advanced Level==

Latest revision as of 20:42, 20 November 2019

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 Dr. Bella Tony from IIT Bombay. Ms. Dasaka Kavita & Ms. Sakina Shaikh from IIT Bombay also created 2 tutorials. Other contributors who helped in the creation of the scripts include Dr. Snehalatha, Mr. Anil Patel & Ms. Reshma Patil from IIT Bombay who have contributed as 'Domain experts'.

Learners: UG/PG Bio-Chemistry students.

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
    • 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. Create and Edit Components
    • Open an already saved .xml file
    • Change the following in a Compartment- Size, shape, color and thickness of the border
    • Create multiple files in CellDesigner
    • Learn about Start-point and End-point of a Species
    • Change identity of Species and Reaction

Intermediate Level

  1. 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
  2. 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

Advanced Level

Contributors and Content Editors

Bellatony911, Kavita, Minal, Nancyvarkey, PoojaMoolya, Sakinashaikh