Difference between revisions of "CellDesigner"

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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.
  
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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;">
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'''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]]
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[[Glossary_for_CellDesigner | Glossary]] </blockquote>
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</blockquote>
  
 
==Basic Level==
 
==Basic Level==
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#* Undo/Redo
 
#* Undo/Redo
 
#* Change the size of the component
 
#* Change the size of the component
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#* Save the Network
 
 
#* Zoom
 
#* Zoom
 
# Installation of CellDesigner on Linux OS &nbsp; &nbsp;  
 
# Installation of CellDesigner on Linux OS &nbsp; &nbsp;  
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#* How to see all the icons on the CellDesigner window.
 
#* How to see all the icons on the CellDesigner window.
 
#* How to draw a Compartment and change position of the compartment name
 
#* How to draw a Compartment and change position of the compartment name
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# Create and Edit Components
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#* Open an already saved .xml file
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#* Change the following in a Compartment- Size, shape, color and  thickness of the border
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#* Create multiple files in CellDesigner
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#* Learn about Start-point and End-point of a Species
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#* Change identity of Species and Reaction
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==Intermediate Level==
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# Build-and-Modify-Process-Diagram
 
# Build-and-Modify-Process-Diagram
 
#* Use of Macros
 
#* Use of Macros
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#* How to edit Protein
 
#* How to edit Protein
 
#* How to edit information
 
#* How to edit information
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#* And get a bird’s eye view of the diagram
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#* And get a Bird’s eye view of the diagram
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==Intermediate Level==
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# Create a Complex &nbsp; &nbsp;
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#* To create a complex
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#* To modify the species within a complex
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#* To change the appearance of a complex
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# Edit Reactions &nbsp; &nbsp;
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#* To change connection points of Reaction on Species
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#* To add Anchor points
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#* To move a Species with a reaction
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#* To change the shape of a Reaction line segment
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#* To adjust a Reaction line automatically
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#* To change line width and color setting of a Reaction
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#* To make a reversible reaction
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# Change Color and Shape of Components & Export Image &nbsp; &nbsp;
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#* To change the default settings of the color and shape
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#* To change the color & shape of the individual components
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#* To export image in different format
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# Add Model Description & Import and Export a Model &nbsp; &nbsp;
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#* To add Model Description
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#* 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

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