CellDesigner/C2/Getting-Started-with-CellDesigner/English

Title of script: Getting started with CellDesigner

Author: Sakina

Keywords: Menubar, Toolbar, Component, Species,Reaction.

Visual Cue	Narration
Slide	Welcome to the Spoken tutorial on Getting started with CellDesigner.
Slide About CellDesigner Menu and Tool bars in CellDesigner Different areas in CellDesigner layout Components – Species and Reactions	In this tutorial we will learn About CellDesigner Menu and Tool bars in CellDesigner Different areas in the CellDesigner workspace Components of CellDesigner which includes Species and Reactions
Slide Create a simple network Save a network Export an image Zooming the network	How to Create a simple network Save a network Export an image How to zoom a network
Slide -What is Celldesigner?	CellDesigner is a process diagram editor for drawing gene-regulatory and biochemical networks. The process diagram was proposed by Kitano These diagrams are stored using the Systems Biology Markup Language (SBML)
Slide - OS and versions Windows XP CellDesigner Version 4.2 Works on Linux and Mac OS X also	I am using Windows XP and CellDesigner Version 4.2 CellDesigner works on Linux and Mac OS X also.
Click on the shortcut CellDesigner icon on the desktop	To open CellDesigner, double-click on the shortcut CellDesigner icon on the desktop. Alternately, click on Start>All Programs>CellDesigner4.2.
	This will open CellDesigner window. Now let us explore it.
Point to Menu bar and options	On the Menu bar you can see various Menu options like File, Edit, Component ,View, Database and others.
Point to the Toolbars and its options	Under the Main Menu you will see various Toolbars. There are Toolbars for editing, species, reactions, compartments, etc. We will learn about some of them as we go along.
5 Different areas in CellDesigner and Component-Species&Reaction	Let us learn about the different areas of the CellDesigner layout. As you can see, there are 5 areas.
Draw Area (highlight)	On the right hand side is the Draw area. This is where we would be drawing the networks.
Component – General term for species, reaction,compartment	Any shape you see on the Draw area, for eg - rectangle, an oval or a line segment, is called a Component. Component is a general term for species, reactions or a compartment.
Move the cursor on the CellDesigner window to point to the various species and reactions	One can see the list of all these symbols and their meanings from the CellDesigner website – www.celldesigner.org
List Area (highlight)	Below Draw area is the List area. Here one can display and edit the list of components and functions of a model.
Notes Area (highlight)	The Notes area is used to display and edit the notes of the component.
Tree Area (highlight)	On the left hand side, there is a Tree area which lists the components in a tree structure.
Layer Area	Below that is the Layer area which displays all the layers of the model.
Change the size and position of the areas.	The size of the areas can be changed by dragging the borderlines.
Place the cursor on borderline of draw area and drag.	I will place the cursor on the borderline . You can see a double headed arrow. Drag it to maximize or minimize the area.
Go to View>> Click on List and Select Right	To change the position of the List & Notes area go to View option>>click on List and select Right. It changes list to the right. Down is the default one.
Slide-Show simple network Explain the simple network Point wherever necessary	This is the simple network which we will create. In this network Protein A undergoes state transition to Protein B under catalysis of Protein C. Protein B inturn undergoes state transition to Protein D . This transition is inhibited by Protein E.
Creating simple network Click File >> New	Let us create this network . Click on File and then New.
	A small dialog box named as ‘New Document’ will open.
Provide file name as “simple network”	I will type “simple network” in the Name field.
Point to the height and width fields	Here one can change the height and width as required. However, I will keep the default height and width.
Click OK	Click on OK. You can see the name appearing on the top left corner of the Draw area.
Go to Edit- Click Grid visible and Grid snap	Now, go to Edit, and enable Grid snap and Grid visible. A grid will be visible in the Draw area.
Point to Grid visible	Grid snap will make the components to align properly with the grid. You can de-select Grid visible once the network is complete.
Showing examples of species and reaction on CellDesigner window Pointing the species	Before we begin to add components, let me show you some examples of species and reactions. The symbols are for generic protein, receptor, ion channel, truncated protein, gene, RNA etc.
Pointing the reactions	Now the reactions State transition, Heterodimer association, Dissociation, Catalysis, Inhibition etc.
Hover the mouse over Species Toolbar on upper right corner.	Species toolbar is present on the upper right corner. You can see various icons here.
Click on the 1st icon from species toolbar.	We will select the first icon by clicking on it. This icon is for protein.
Click on Draw area to place the species	Click anywhere on the Draw Area where you want to place this species. I will place it on left side of the Draw area.
Provide the name for the species as 'A'	A small dialog box will open and ask for the species name. I will name the new species as A and click on OK.
Add another species and name it as 'B'	As you can see we have added a new species in the Draw area. Similarly I will add B.
Hover the mouse on the select icon	You are required to select a component before you edit or move it. Click on the component to select them. Make sure the select icon is on before you do so.
Click on B Drag B and keep next to A	I want to place B besides A. So click on B and select it. Drag and keep it next to A.
Changing size of the component	Now we will see, how to change the size of a component.
Click on A	I will click on A. We see small squares on it. These are the handles to change the size.
Keep the cursor on one square on the edge of species A & Drag	I will keep the cursor on this edge and drag. We see the size of A has changed. There is another way of changing the size of component which we will learn in later tutorial.
Press Ctrl-Z Show the undo and redo icons	You can “undo" the previous actions with Ctrl-Z . I am pressing Ctrl-Z. If you want to “re-do”, press Ctrl-Y. Also you can do this directly by click on the icons for undo and redo
Adding Reactions	Now let’s add reactions. A reaction is the interaction between two objects.
Click on the icon for State transition in the reaction toolbar.	This is a state transition reaction. So I will click on the icon for State transition in the Reaction toolbar.
Click on edge of A & then B	Click on any edge of A and then on B. Thus, you can see the reaction arrow now joins A and B.
Point to A	The component selected first is considered as the reactant. So always remember to select the reactants first.
Point to re1.	The default reaction id comes as re1.
Add species and name it as 'C'.	Now lets add species C and keep at appropriate position as shown in the earlier slide.
Click on the icon for Catalysis in the reaction toolbar	I am selecting this icon from the Reaction toolbar. It is for Catalysis .
Click on the edge of specie C and square symbol of State transition reaction	I will click on the edge of C, and the square symbol of the State transition reaction.
Add species and name it as 'D'.	Now i will add species D and place it besides B.
Click on the icon for State transition in the reaction toolbar.	Lets add a State transition reaction from B to D. The default reaction id is re2.
Add species and name it as 'E'.	I will add species E and keep at appropriate position as shown in the earlier slide.
Select inhibition reaction icon from reaction toolbar	Now I will select this icon from the Reaction toolbar, which represents the Inhibition reaction.
Click on the edge of specie E and square symbol of State transition reaction	I will click on the edge of E and this square symbol of the State transition reaction. This will join the two points.
	We can see the simple network now.
Save The File Click File > Save as	Let us save our work. Go to File. Click on Save as.
Type “Simple Network” Click Save	I will name it as “Simple Network” . This will save our work in .xml format. Click on Save.
Export The Image Go to File > Export Image	Now we will learn how to Export an image. To do this, Go to File>Export Image.
Type “Simple Network”.	Give a file name to the image. I will type “Simple Network”.
Click Save.	You can save the image in various formats like pdf, png, jpeg etc. I will save it as a jpeg image. Click on Save.
Zooming the network Click on Zoom In icon twice Click on Zoom Reset	Let us see how to zoom the network. We have 4 options for zoom - Zoom In, Zoom Out, Zoom Fit. Zoom Reset. I will click on the Zoom In icon twice. We can see the magnified image. Now I will click on Zoom Reset. The network comes back to the original size.
Slide- Summary	This brings us to the end of the spoken tutorial on. Getting started with CellDesigner. To Summarize , we learnt about Menu and Tool bar in CellDesigner. Different areas in CellDesigner. Components like Species and Reactions. We created a simple network using the species and reaction components. Also we learnt how to zoom, save a network and exporting an image.
Assignment- Slide- A Network	As an assignment Construct a network with the help of CellDesigner 4.2 In this network, A and B protein associates to form a complex(Complex1) in presence of catalyst protein C. This complex gets degraded when catalyst protein D is present.
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	This is Sakina Shaikh from IIT Bombay signing off. Thanks for joining. Goodbye.

Contributors and Content Editors

PoojaMoolya, Sakinashaikh