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CellDesigner - modeling tool for gene-regulatory and biochemical networks

By Prof Kannan Moudgalya - Principal Investigator of Spoken Tutorial Project   |   Indian Institute of Technology Bombay
Learners enrolled: 4203
This course comprises 7 audio-video spoken tutorials, using which you can self-learn CellDesigner with ease. 

STEP 1-
First of all install CellDesigner by following the steps given in the Installation tutorials.
  1. These tutorials give the steps to install CellDesigner on Linux and Windows OS.
  2. Open the tutorials, follow the instructions for your OS and install the CellDesigner on your machine.
  3. Cross-verify (as mentioned in the tutorials) to confirm successful installation.
STEP 2-
Next, read this sheet. https://spoken-tutorial.org/CellDesigner-Instruction-Sheet-English.pdf/
  1. This sheet explains how to learn from spoken tutorials.
  2. This sheet also mentions some important information about the text editors while coding, how to use the command prompt (in Windows OS), how to use the Code Files, how to do the Assignments, etc.
  3. Read this sheet carefully and make a note of all the information, before you begin.
STEP 3-
Follow the side-by-side learning methodology while learning from spoken tutorials - watch the video, listen to the instructions, pause the video, try out the command on your system.  You should get the exact same results as shown in the video.  If successful, proceed with the video.  Else, rewind and watch the video again and replicate the commands shown.

Complete all the videos in the given sequence one by one.
The Assignment for each tutorial is for your self-assessment only.  Do not upload it anywhere for evaluation.

Summary
Course Status : Upcoming
Course Type : Elective
Category :
  • Biological Sciences & Bioengineering
Credit Points : 1
Level : Undergraduate/Postgraduate

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Course layout

Introduction to CellDesigner - for drawing gene-regulatory and biochemical networks

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 to describe models and allow simulation of models using an integrated SBML ODE solver.

Cell Designer = SBML + Simulation + Databases Connections

In this series, 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.  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.

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