CellDesigner - Revision history

Bellatony911 at 15:12, 20 November 2019

2019-11-20T15:12:09Z

PoojaMoolya at 09:09, 7 May 2019

2019-05-07T09:09:07Z

PoojaMoolya at 05:44, 6 May 2019

2019-05-06T05:44:50Z

Nancyvarkey at 02:04, 27 March 2018

2018-03-27T02:04:53Z

Nancyvarkey at 02:59, 26 March 2018

2018-03-26T02:59:59Z

Nancyvarkey at 12:27, 9 August 2016

2016-08-09T12:27:17Z

Bellatony911: /* Intermediate Level */

2016-06-22T06:13:02Z

‎Intermediate Level

Bellatony911: /* Basic Level */

2016-06-22T06:11:39Z

‎Basic Level

Bellatony911: /* Basic Level */

2016-06-22T06:08:18Z

‎Basic Level

Bellatony911: /* All Level */

2016-06-21T10:24:28Z

‎All Level

@@ Line 67: / Line 67: @@
 #* How to see all the icons on the CellDesigner window.
 #* How to draw a Compartment and change position of the compartment name
 ==Intermediate Level==

@@ Line 21: / Line 21: @@
 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''': Bio-Chemistry students.
+'''Learners''': UG/PG Bio-Chemistry students.
 <blockquote style="background-color: lemonchiffon; border: solid thin grey;">

← Older revision		Revision as of 05:44, 6 May 2019
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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'.		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''': Bio-Chemistry students.

	<blockquote style="background-color: lemonchiffon; border: solid thin grey;">		<blockquote style="background-color: lemonchiffon; border: solid thin grey;">

@@ Line 21: / Line 21: @@
 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'.
+<blockquote style="background-color: lemonchiffon; border: solid thin grey;">
 ==Basic Level==

@@ Line 19: / Line 19: @@
 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'.
+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'.
 ==Basic Level==

@@ Line 67: / Line 67: @@
 ==Intermediate Level==
-# Create a Complex &nbsp; &nbsp;
-#* To create a complex
+# Build-and-Modify-Process-Diagram
-#* To modify the species within a complex
+#* Use of Macros
-#* To change the appearance of a complex
+#* How to move Components on the draw area
-# Edit Reactions &nbsp; &nbsp;
+#* Generic protein to Simplae molecule
-#* To change connection points of Reaction on Species
+#* Connect a reaction line around a species
-#* To add Anchor points
+#* Align and extend a reaction line
-#* To move a Species with a reaction
+#* Add a Product and a Reactant
-#* To change the shape of a Reaction line segment
+#* To build a process diagram for Methionine Biosynthesis
-#* To adjust a Reaction line automatically
+# Customizing Diagram Layout
-#* To change line width and color setting of a Reaction
+#* How to change color, shape and width of a Reaction line
-#* To make a reversible reaction
+#* How to add Anchor points to a Reaction line
-# Change Color and Shape of Components & Export Image &nbsp; &nbsp;
+#* How to align Components
-#* To change the default settings of the color and shape
+#* How to show/hide Reaction ids
-#* To change the color & shape of the individual components
+#* How to add notes to Components
-#* To export image in different format
+#* How to edit Protein
-# Add Model Description & Import and Export a Model &nbsp; &nbsp;
+#* How to edit information
-#* To add Model Description
+#* And get a Bird’s eye view of the diagram
-#* 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)
-# Open an SBML format &nbsp; &nbsp;
-#* To open an SBML file
-#* To save a model with SBO Terms
-# Compartments & Species &nbsp; &nbsp;
-#* 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
-# Species-Proteins, Gene, RNA and asRNA &nbsp; &nbsp;
-#* 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
-# Block Diagram-To check Relationship of a Species (*Proto-type) &nbsp; &nbsp;
-#* What is a Block Diagram
-#* To extract Regulation
-#* Modifications/Activations Relation
 ==Advanced Level==

@@ Line 53: / Line 53: @@
 #* Undo/Redo
 #* Change the size of the component
 #* Zoom
 # Installation of CellDesigner on Linux OS &nbsp; &nbsp;

@@ Line 27: / Line 27: @@
 ==Basic Level==
 # Overview of CellDesigner &nbsp; &nbsp;
-#* What is a CellDesigner
+#* Link for the Startup Guide Version 4.3
-#* Who can use CellDesigner
+#* Clippings of video tutorials available in  CellDesigner series
-#* Simple Examples in Cell Designer
-#* Motivation
-#* Major Features
-#* Citation of CellDesigner
 #Installation of CellDesigner 4.3 &nbsp; &nbsp;
 #* Software requirement
 #* Download & Installation of CellDesigner
-#* On Windows OS
+#* On Windows Operating System
 #* Adding a protein species
 # Getting Started with CellDesigner &nbsp; &nbsp;
 #* The Menu & Tool Bar
 #* Components, Species & Reaction
 #* Creating a simple network: Name & Size of the network
-#* Grid Visible , Grid Snap
+#* Save a network
 #* Change size of network
 #* Select a component
@@ Line 51: / Line 55: @@
 #* Save the Network
 #* Zoom
-# Creating a Simple Biological Network using CellDesigner4.3 &nbsp; &nbsp;
+# Installation of CellDesigner on Linux OS &nbsp; &nbsp;
-#* TO build a biological pathway
+#* Download and install CellDesigner 4.3 on Ubuntu Linux Operating System
-#* Adding new compartments
+#* Create a Compartment in the draw area of CellDesigner
-#* To put components in a compartment
+#* How to find out the details of the OS type of our machine
-#* To change the shape of a compartment
+#* How to see the Main menu bar clearly.
-#* To change the position of the compartment name
+#* To open a new document
-#* Adding Reactions:Association (Homodimer/Heterodimer), Dissociation & State Transition
+#* Significance of Select Mode
-#* Adding Catalysis or Modifier of the reaction:Activation, Inhibition
+#* How to change the position of the List & Notes area
-# Editing & Formatting Species of a Network &nbsp; &nbsp;
+#* How to change size of the areas
-## Change Identity-Species
+#* How to see all the icons on the CellDesigner window.
-##* Change Class
+#* How to draw a Compartment and change position of the compartment name
-##* Homomultimer
+# Build-and-Modify-Process-Diagram
-##* State
+#* Use of Macros
-## Edit protein
+#* How to move Components on the draw area
-##* Change type
+#* Generic protein to Simplae molecule
-##* Rename
+#* Connect a reaction line around a species
-##* Edit block diagram
+#* Align and extend a reaction line
-##* Edit residue (Change angle)
+#* Add a Product and a Reactant
-##* Add text (Reference/Information)
+#* To build a process diagram for Methionine Biosynthesis
-##*Change font, color & shape
+# Customizing Diagram Layout
-##* Replace species ID
+#* How to change color, shape and width of a Reaction line
-##* Replace reaction ID
+#* How to add Anchor points to a Reaction line
-## Format Reaction
+#* How to align Components
-##* Add anchor point
+#* How to show/hide Reaction ids
-##* Change Identity (name, type, reversible)
+#* How to add notes to Components
-##* Edit reaction-Creating a kinetic law
+#* How to edit Protein
-##* Change color shape-Add text
+#* How to edit information
-## Grid visible
+#* And get a bird’s eye view of the diagram
-# Simulation of Computational Model &nbsp; &nbsp;
-#* What is Simulation
-#* 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==