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Created page with ''''Title of script''': '''Getting started with CellDesigner''' '''Author: Sakina''' '''Keywords: Menubar, Toolbar, Component, Species,Reaction.''' {| style="border-spacing:0…'

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'''Title of script''': '''Getting started with CellDesigner'''

'''Author: Sakina'''

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

{| style="border-spacing:0;"
! <center>Visual Clue</center>
! <center>Narration</center>

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Welcome to the Spoken tutorial on Getting started with '''CellDesigner'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide

About CellDesigner

Menu and Tool bars in CellDesigner

Different areas in CellDesigner layout

Components – Species and Reactions

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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'''

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide

Create a simple network

Save a network

Export an image

Zooming the network
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| How to Create a simple network

Save a network

Export an image

How to zoom a network

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide -What is Celldesigner?
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| '''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)'''

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide - OS and versions

* Windows XP
* CellDesigner Version 4.2
* Works on Linux and Mac OS X also

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I am using Windows XP and CellDesigner Version 4.2

CellDesigner works on Linux and Mac OS X also.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the shortcut CellDesigner icon on the desktop
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| To open CellDesigner, double-click on the shortcut CellDesigner icon on the desktop.

Alternately, click on '''Start'''>'''All Programs'''>'''CellDesigner4.2'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"|
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| This will open CellDesigner window.

Now let us explore it.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Point to Menu bar and options
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| On the '''Menu''' bar you can see various Menu options

like '''File''', '''Edit''', '''Component''' ,'''View''', '''Database''' and others.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Point to the Toolbars and its options

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| 5 Different areas in CellDesigner and Component-Species&Reaction
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Let us learn about the different areas of the CellDesigner layout.

As you can see, there are 5 areas.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Draw Area

(highlight)
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| On the right hand side is the '''Draw''' area.

This is where we would be drawing the networks.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Component – General term for species, reaction,compartment
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Move the cursor on the CellDesigner window to point to the various species and reactions
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| One can see the list of all these symbols and their meanings from the CellDesigner website – '''www.celldesigner.org'''

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| List Area

(highlight)
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Below '''Draw''' area is the '''List''' area.

Here one can display and edit the list of components and functions of a model.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Notes Area

(highlight)
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| The '''Notes''' area is used to display and edit the notes of the component.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Tree Area

(highlight)
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| On the left hand side, there is a '''Tree''' area which lists the components in a tree structure.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Layer Area
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Below that is the '''Layer''' area which displays all the layers of the model.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Change the size and position of the areas.

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| The size of the areas can be changed by

dragging the borderlines.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Place the cursor on borderline of draw area and drag.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will place the cursor on the borderline . You can see a double headed arrow. Drag it to maximize or minimize the area.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Go to View>> Click on List and Select Right''' '''
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide-Show simple network

Explain the simple network

Point wherever necessary
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Creating simple network

Click File >> New
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Let us create this network .

Click on File and then New.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"|
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| A small dialog box named as ‘'''New Document'''’ will open.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Provide file name as “'''simple network'''”
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will type “'''simple network”''' in the '''Name''' field.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Point to the height and width fields
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Here one can change the height and width as required.

However, I will keep the default height and width.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click OK
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Click on '''OK'''. You can see the name appearing on the top left corner of the '''Draw '''area.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Go to Edit- Click Grid visible and Grid snap
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now, go to Edit, and enable '''Grid snap''' and '''Grid visible'''.

A grid will be visible in the '''Draw''' area.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Point to Grid visible
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| '''Grid snap''' will make the components to align properly with the grid.

You can de-select '''Grid visible '''once the network is complete.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Showing examples of species and reaction on CellDesigner window

Pointing the species

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Pointing the reactions
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now the reactions

'''State transition''', '''Heterodimer association''', '''Dissociation''', '''Catalysis, Inhibition '''etc.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Hover the mouse over Species Toolbar on upper right corner.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| '''Species''' toolbar is present on the upper right corner.

You can see various icons here.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the 1<sup>st</sup> icon from species toolbar.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| We will select the first icon by clicking on it.

This icon is for protein.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on Draw area to place the species
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Click anywhere on the '''Draw Area''' where you want to place this species.

I will place it on left side of the '''Draw area'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Provide the name for the species as 'A'
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| A small dialog box will open and ask for the species name.

I will name the new species as '''A''' and click on OK.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Add another species and name it as 'B'
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| As you can see we have added a new species

in the '''Draw area'''. Similarly I will add '''B'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Hover the mouse on the select icon
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on B

Drag B and keep next to A
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I want to place '''B''' besides '''A'''. So click on '''B''' and select it.

Drag and keep it next to '''A'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Changing size of the component
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now we will see, how to change the size of a component.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on A
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will click on '''A'''. We see small squares on it.

These are the handles to change the size.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Keep the cursor on one square on the edge of species A & Drag
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Press Ctrl-Z

Show the undo and redo icons
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Adding Reactions
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now let’s add reactions.

A reaction is the interaction between two objects.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the icon for State transition in the reaction toolbar.

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| This is a state transition reaction.

So I will click on the icon for '''State transition''' in the '''Reaction''' toolbar.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on edge of '''A''' & then '''B'''
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Click on any edge of '''A''' and then on '''B'''.

Thus, you can see the reaction arrow now joins '''A '''and '''B'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Point to '''A'''
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| The component selected first is considered as the reactant.

So always remember to select the reactants first.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Point to '''re1.'''
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| The default reaction id comes as '''re1'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Add species and name it as 'C'.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now lets add species C and keep at appropriate position as shown in the earlier slide.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the icon for Catalysis in the reaction toolbar
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I am selecting this icon from the '''Reaction''' toolbar. It is for '''Catalysis''' .

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the edge of specie C and square symbol of State transition reaction
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will click on the edge of '''C''', and the square symbol of the '''State transition''' reaction.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Add species and name it as 'D'.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now i will add species D and place it besides B.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the icon for State transition in the reaction toolbar.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Lets add a '''State transition '''reaction from B to D. The default reaction id is re2.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Add species and name it as 'E'.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will add species E and keep at appropriate position as shown in the earlier slide.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Select inhibition reaction icon from reaction toolbar
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now I will select this icon from the '''Reaction '''toolbar, which represents the '''Inhibition reaction'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click on the edge of specie E and square symbol of State transition reaction
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will click on the edge of '''E''' and this square symbol of the '''State transition '''reaction. This will join the two points.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"|
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| We can see the simple network now.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Save The File

Click''' '''File''' > '''Save as
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Let us save our work.

Go to '''File'''. Click on '''Save as'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Type “'''Simple Network”'''

Click Save
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| I will name it as “'''Simple Network”''' .

This will save our work in '''.xml '''format.

Click on '''Save.'''

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Export The Image

Go to File > Export Image
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Now we will learn how to Export an image.

To do this,

Go to '''File'''>'''Export Image'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Type “'''Simple Network”'''.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| Give a file name to the image.

I will type “'''Simple Network'''”.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Click Save.
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| You can save the image in various formats like pdf, png, jpeg etc.

I will save it as a''' jpeg''' image. Click on '''Save'''.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Zooming the network

Click on Zoom In icon twice

Click on '''Zoom Reset'''
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Slide-

Summary
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Assignment-

Slide- A Network

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| 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.

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Show About Slide

About the Spoken Tutorial Project

* Watch the video available at-<br/> [http://spoken-tutorial.org/What_is_a_Spoken_Tutorial http://spoken-tutorial.org/What_is_a_Spoken_Tutorial]
* It summarises the Spoken Tutorial project
* If you do not have good bandwidth, you can download and watch it

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| * Watch the video available at the following link

* It summarises the Spoken Tutorial project
* If you do not have good bandwidth, you can download and watch it

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Show About Slide

Spoken Tutorial Workshops

The Spoken Tutorial Project Team

* Conducts workshops using spoken tutorials

* Gives certificates for those who pass an online test

* For more details, please write to contact@spoken-tutorial.org

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team

* Conducts workshops using spoken tutorials

* Gives certificates for those who pass an online test

* For more details, please write to contact at spoken hyphen tutorial dot org

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"| Show Slide

Funding Support

* Spoken Tutorial Project is a part of the Talk to a Teacher project

* It is supported by the National Mission on Education through ICT, MHRD, Government of India

* More information on this Mission is available at

* [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro]

| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| * Spoken Tutorial Project is a part of the Talk to a Teacher project

* It is supported by the National Mission on Education through ICT, MHRD, Government of India

* More information on this Mission is available at

* spoken hyphen tutorial dot org slash NMEICT hyphen Intro

|-
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:none;padding:0.097cm;"|
| style="border-top:none;border-bottom:0.035cm solid #000000;border-left:0.035cm solid #000000;border-right:0.035cm solid #000000;padding:0.097cm;"| This is Sakina Shaikh from IIT Bombay signing off. Thanks for joining. Goodbye.

|}

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

PoojaMoolya at 05:57, 17 June 2014

Sakinashaikh: Created page with ''''Title of script''': '''Getting started with CellDesigner''' '''Author: Sakina''' '''Keywords: Menubar, Toolbar, Component, Species,Reaction.''' {| style="border-spacing:0…'

@@ Line 8: / Line 8: @@
 {| style="border-spacing:0;"
-! <center>Visual Clue</center>
+! <center>Visual Cue</center>
 ! <center>Narration</center>