Sandhya.np14 at 09:27, 6 June 2018

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PoojaMoolya at 06:49, 28 February 2018

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PoojaMoolya at 10:53, 31 January 2018

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Jyotisolanki at 05:59, 21 November 2017

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Jyotisolanki at 09:36, 9 October 2017

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Jyotisolanki at 08:51, 9 October 2017

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Jyotisolanki at 07:24, 9 October 2017

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Jyotisolanki at 07:02, 5 October 2017

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Jyotisolanki at 06:35, 5 October 2017

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Jyotisolanki: Created page with "{| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Welcome to the Spoken tutorial on Getting started with '''CellDesigner'''. |- | 00:05 | In this tutorial we will le..."

2017-09-18T10:16:56Z

Created page with "{| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Welcome to the Spoken tutorial on Getting started with '''CellDesigner'''. |- | 00:05 | In this tutorial we will le..."

New page

{| border=1
|| '''Time'''
|| '''Narration'''

|-
| 00:01
| Welcome to the Spoken tutorial on Getting started with '''CellDesigner'''.

|-
| 00:05
| In this tutorial we will learn : About CellDesigner '''Menu''' and '''Tool''' bars in CellDesigner

|-
| 00:13
|Different '''areas''' in the CellDesigner workspace

|-
| 00:17
|'''Components''' of CellDesigner which includes '''Species''' and '''Reactions'''

|-
|00:23
| We will also learn How to Create a simple network

|-
| 00:27
|Save a network

|-
| 00:29
|Export an image

|-
| 00:30
|How to zoom a network

|-
| 00:33
| '''CellDesigner''' is a process diagram editor for drawing gene-regulatory and biochemical networks.

|-
| 00:40
| The process diagram was proposed by Kitano These diagrams are stored using the '''Systems Biology Markup Language (SBML)'''

|-
| 00:50
| I am using Windows XP and CellDesigner Version 4.2 CellDesigner works on Linux and Mac OS X also.

|-
| 01:00
| To open CellDesigner, double-click on the shortcut CellDesigner icon on the desktop.

|-
| 01:07
|This will open CellDesigner, Now lets explore .

|-
| 01:12
| On the '''Menu''' bar you can see various Menu options , like '''File''', '''Edit''', '''Component''' ,'''View''', '''Database''' and others.

|-
| 01:24
| Under the '''Main Menu ''' you will see various '''Toolbars'''.

|-
| 01:30
| There are '''Toolbars '''for editing, species, reactions, compartments, etc.

|-
| 01:38
| We will learn about some of them as we go along.

|-
| 01:42
| Let us learn about the different areas of the CellDesigner workspace.

|-
| 01:48
| As you can see, there are 5 areas.

|-
| 01:52
| On the right hand side is the '''Draw''' area.

|-
| 01:55
| This is where we would be drawing the networks.

|-
| 01:58
| Any shape you see on the '''Draw''' area, for eg - rectangle, an oval or a line segment, is called a '''Component'''.

|-
| 02:08
| Component is a general term for '''species''', '''reactions''' or a '''compartment'''.

|-
| 02:14
| One can see the list of all these symbols and their meanings from the CellDesigner website – That is '''www.celldesigner.org'''

|-
| 02:29
| I will click on the ''' Documents '''

|-
| 02:33
|Now let's Click on the Startup guide. That is also on another tab.

|-
| 02:40
|I will go directly to page number 82.

|-
| 02:45
|Here you can see various symbols and their meanings.

|-
| 02:51
|Let's go back to CellDesigner window.

|-
|02:55
| Below '''Draw''' area is the '''List''' area.

|-
| 02:59
| Here one can display and edit the list of components and functions of a model.

|-
| 03:06
| The '''Notes''' area is used to display and edit the notes of the component.

|-
| 03:12
| On the left hand side, there is a '''Tree''' area which lists the components in a tree structure.

|-
| 03:21
| Below that is the '''Layer''' area which displays all the layers of the model.

|-
| 03:27
| The size of the areas can be changed by dragging the borderlines.

|-
| 03:33
| I will place the cursor on the borderline . You can see a double headed arrow. Drag it to maximize or minimize the area.

|-
| 03:45
| To change the position of the '''List''' & '''Notes''' area

|-
| 03:50
| go to '''View''' option>>click on '''List''' and select '''Right'''.

|-
| 03:56
| It changes list to the right. Down is the default one.

|-
| 04:00
|Let us go back to the slide.

|-
| 04:05
| This is the simple network which we will create.

|-
| 04:10
| In this network Protein '''A''' undergoes state transition to Protein '''B '''under catalysis of Protein '''C'''.

|-
| 04:21
| Protein''' B''' inturn undergoes state transition to Protein '''D''' .

|-
| 04:27
| This transition is inhibited by Protein '''E'''.

|-
| 04:32
| Let us create this network .

|-
| 04:34
|I will go back to CellDesigner window.

|-
| 04:39
|Now Click on File and then New.

|-
| 04:43
| A small dialog box named as ‘'''New Document'''’ will open.

|-
| 04:48
| This is ''' name ''' field.

|-
| 04:50
| I will type “'''simple network”'''

|-
| 04:53
| Here one can change the height and width as required. However, I will keep the default height and width.

|-
| 05:03
| Click on '''OK'''. You can see the name appearing on the top left corner of the '''Draw '''area.

|-
| 05:12
| Now, go to Edit, and enable '''Grid snap''' and '''Grid visible'''.

|-
| 05:21
|A grid will be visible in the '''Draw''' area.

|-
| 05:25
| '''Grid snap''' will make the components to align properly with the grid.

|-
| 05:29
| You can de-select '''Grid visible '''once the network is complete.

|-
| 05:34
| Before we begin to add components, let me show you some examples of species and reactions.

|-
| 05:42
| Let us first see the species.

|-
| 05:45
| The symbols here are for '''generic protein, receptor, ion''' '''channel, truncated protein, gene,''' '''RNA''' etc.

|-
| 05:58
| Now let us see the reactions first is the '''State transition''', '''Heterodimer association''', '''Dissociation''', '''Catalysis, Inhibition '''etc.

|-
| 06:11
| We will select the first icon in the '''Species''' toolbar by clicking on it. This icon is for protein.

|-
| 06:22
| Click anywhere on the '''Draw Area''' where you want to place this species.

|-
| 06:28
| I will place it on left side of the '''Draw area'''.

|-
| 06:33
| A small dialog box will open and ask for the species name.

|-
| 06:39
| I will name the new species as '''A''' and click on OK.

|-
| 06:46
|See the change in the list area too.

|-
| 06:50
| As you can see we have added a new species ,in the '''Draw area'''. Similarly I will add '''B'''.

|-
| 06:58
| You are required to select a component before you edit or move it.

|-
| 07:03
| Click on the component to select them. Make sure the select icon is on before you do so.

|-
| 07:12
| I want to place '''B''' besides '''A'''. So click on '''B''' and select it.

|-
| 07:17
| Drag and keep it next to '''A'''.

|-
| 07:21
| Now we will see, how to change the size of a component.

|-
| 07:24
| I will click on '''A'''. We see small squares on it.

|-
| 07:29
| These are the handles to change the size.

|-
| 07:32
| I will keep the cursor on this edge and drag.

|-
| 07:36
| We see the size of '''A''' has changed.

|-
| 07:39
| There is another way of changing the size of component which we will learn in later tutorial.

|-
| 07:46
| You can “undo" the previous actions with Ctrl-Z .

|-
| 07:52
| If you want to “re-do”, press Ctrl-Y.

|-
| 07:54
| Also you can do this directly by click on the icons for undo and redo

|-
| 08:03
| Now let’s add reactions.

|-
| 08:06
| A reaction is the interaction between two objects.

|-
| 08:09
| This is a state transition reaction.

|-
| 08:12
| So I will click on the icon for '''State transition''' in the '''Reaction''' toolbar.
|-
| 08:18
| Click on any edge of '''A''' and then on '''B'''.

|-
| 08:23
| Thus, you can see the reaction arrow now joins '''A '''and '''B'''.

|-
| 08:30
| The component selected first is considered as the reactant.

|-
| 08:35
| So always remember to select the reactants first.

|-
| 08:39
| The default reaction id comes as '''re1'''.

|-
| 08:43
| Now lets add species C and keep at appropriate position as shown in the earlier slide.

|-
| 08:54
| I am selecting this icon from the '''Reaction''' toolbar. It is for '''Catalysis''' .

|-
|09:00
| I will click on the edge of '''C''', and the square symbol of the '''State transition''' reaction.
|-
| 09:08
| Now i will add species D and place it besides B.

|-
| 09:15
| Lets add a '''State transition '''reaction from B to D. The default reaction id is re2.

|-
| 09:26
| I will add species E and keep at appropriate position as shown in the earlier slide.

|-
| 09:35
| Now I will select this icon from the '''Reaction '''toolbar, which represents the '''Inhibition reaction'''.

|-
| 09:44
| I will click on the edge of '''E''' and this square symbol of the '''State transition '''reaction. This will join the two points.
|-
| 09:54
| We can see the simple network now.

|-
| 09:57
| Let us save our work.

|-
| 10:00
| Go to '''File'''. Click on '''Save as'''.

|-
| 10:04
| I will name it as “'''Simple Network”''' .

|-
| 10:06
| This will save our work in '''.xml '''format. Click on '''Save.'''

|-
| 10:12
| Now we will learn how to Export an image. To do this, Go to '''File'''>'''Export Image'''.

|-
| 10:22
| You can save the image in various formats like pdf, png, jpeg etc.

|-
| 10:29
| I will save it as a''' jpeg''' image. Click on '''Save'''.

|-
| 10:35
| Let us see how to zoom the network.

|-
| 10:38
| We have 4 options for zoom - ''' Zoom In, Zoom Out, Zoom Fit. Zoom Reset '''.

|-
| 10:47
| I will click on the '''Zoom In''' icon twice. We can see the magnified image.

|-
| 10:54
| Now I will click on '''Zoom Reset'''. The network comes back to the original size.

|-
|11:02
| This brings us to the end of the spoken tutorial on. Getting started with CellDesigner.

|-
| 11:08
| To Summarize , we learnt about Menu and Tool bar in CellDesigner.

|-
| 11:14
| Different areas in CellDesigner. Components like Species and Reactions.

|-
| 11:20
| We created a simple network using the species and reaction components.

|-
| 11:26
| Also we learnt how to zoom, save a network and exporting an image.

|-
| 11:32
| As an assignment Construct a network with the help of CellDesigner 4.2

|-
| 11:39
| In this network, A and B protein associates to form a complex(Complex1) in presence of catalyst protein C.

|-
| 11:51
| This complex gets degraded when catalyst protein D is present.

|-
| 11:58
|You should get a network like this.

|-
| 12:01
| 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

|-
| 12:13
| 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

|-
| 12:28
| 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

|-
| 12:41
| More information on this Mission is available at spoken hyphen tutorial dot org slash NMEICT hyphen Intro

|-
| 12:53
|This is Sakina Shaikh from IIT Bombay signing off. Thanks for joining. Goodbye.

|}

@@ Line 5: / Line 5: @@
 |-
 | 00:01
-| Welcome to the Spoken tutorial on ''' Getting started with '''CellDesigner'''.
+| Welcome to the Spoken tutorial on ''' Getting started with CellDesigner'''.
 |-

@@ Line 459: / Line 459: @@
 |-
 | 11:32
-| As an assignment Construct a network with the help of CellDesigner 4.2
+| As an assignment Construct a network with the help of CellDesigner 4.3
 |-

@@ Line 45: / Line 45: @@
 |-
 | 00:50
-| I am using Windows XP and CellDesigner Version 4.2 CellDesigner works on Linux and Mac OS X also.
+| I am using Windows XP and CellDesigner Version 4.3 CellDesigner works on Linux and Mac OS X also.
 |-

@@ Line 9: / Line 9: @@
 |-
 | 00:05
-| In this tutorial we will learn : About CellDesigner  '''Menu''' and '''Tool''' bars in CellDesigner
+| In this tutorial we will learn : About CellDesigner ,  '''Menu''' and '''Tool''' bars in CellDesigner
 |-
@@ Line 338: / Line 338: @@
 | 08:12
 | So I will click on the icon for '''State transition''' in the '''Reaction''' toolbar.
 |-
 | 08:18

@@ Line 313: / Line 313: @@
 |-
 | 07:46
-| You can “undo" the previous actions with Ctrl-Z .
+| You can '''“undo"''' the previous actions with '''Ctrl-Z''' .
 |-
 | 07:52
-| If you want to “re-do”, press Ctrl-Y.
+| If you want to “re-do”, press '''Ctrl-Y'''.
 |-

@@ Line 277: / Line 277: @@
 |-
 | 07:03
-| Click on the component to select them. Make sure the select icon is on before you do so.
+| Click on the '''component''' to select them. Make sure the select icon is on before you do so.
 |-

@@ Line 105: / Line 105: @@
 |-
 | 02:33
-|Now let's Click on the Startup guide. That is also on another tab.
+|Now let's Click on the '''Startup guide'''. That is also on another tab.
 |-

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