Difference between revisions of "CellDesigner/C2/Getting-Started-with-CellDesigner/English-timed"

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|-
 
|-
 
| 00:01
 
| 00:01
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| Welcome to the Spoken tutorial on ''' Getting started with CellDesigner'''.
+
| Welcome to the '''Spoken tutorial''' on ''' Getting started with CellDesigner'''.
  
 
|-
 
|-
 
| 00:05
 
| 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 bar'''s in CellDesigner,
  
 
|-
 
|-
 
| 00:13
 
| 00:13
−
|Different '''areas''' in the CellDesigner workspace
+
|different areas in the CellDesigner '''workspace''',
  
 
|-
 
|-
 
| 00:17
 
| 00:17
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|'''Components''' of CellDesigner which includes  '''Species''' and '''Reactions'''
+
|components of CellDesigner which includes  '''Species''' and '''Reactions'''.
  
 
|-
 
|-
 
|00:23
 
|00:23
−
| We will also learn How to Create a simple network
+
| We will also learn how to: create a simple network,
  
 
|-
 
|-
 
| 00:27
 
| 00:27
−
|Save a network
+
|'''save''' a '''network''',
  
 
|-
 
|-
 
| 00:29
 
| 00:29
−
|Export an image
+
|'''export''' an '''image''',
  
 
|-
 
|-
 
| 00:30
 
| 00:30
−
|How to zoom a network
+
|how to zoom a network.
  
 
|-
 
|-
 
| 00:33
 
| 00:33
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| '''CellDesigner''' is a process diagram editor for drawing gene-regulatory and biochemical networks.
+
| '''CellDesigner''' is a '''process diagram editor''' for drawing gene-regulatory and biochemical networks.
  
 
|-
 
|-
 
| 00:40
 
| 00:40
−
| The process diagram was proposed by Kitano These diagrams are stored using the '''Systems Biology Markup Language (SBML)'''
+
| The process diagram was proposed by Kitano. These diagrams are stored using the '''Systems Biology Markup Language (SBML)'''.
  
 
|-
 
|-
 
| 00:50
 
| 00:50
−
| I am using Windows XP and CellDesigner Version 4.3 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.
  
 
|-
 
|-
 
| 01:00
 
| 01:00
−
| To open CellDesigner, double-click on the shortcut CellDesigner icon on the desktop.
+
| To open CellDesigner, double-click on the '''shortcut CellDesigner icon''' on the desktop.
  
 
|-
 
|-
 
| 01:07
 
| 01:07
−
|This will open CellDesigner, Now lets explore .
+
|This will open CellDesigner. Now let's explore .
  
 
|-
 
|-
 
| 01:12
 
| 01:12
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| On the '''Menu''' bar you can see various Menu options , like '''File''', '''Edit''', '''Component''' ,'''View''', '''Database''' and others.
+
| On the '''Menu''' bar, you can see various Menu options like- '''File''', '''Edit''', '''Component''' ,'''View''', '''Database''' and others.
  
 
|-
 
|-
 
| 01:24
 
| 01:24
−
| Under the '''Main Menu ''' you will see various '''Toolbars'''.  
+
| Under the '''Main Menu, ''' you will see various '''Toolbars'''.  
  
 
|-
 
|-
 
| 01:30
 
| 01:30
−
| There are '''Toolbars '''for editing, species, reactions, compartments, etc.
+
| There are '''Toolbars '''for editing, '''species''', '''reactions''', '''compartments''' etc.
  
 
|-
 
|-
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|-
 
|-
 
| 01:42
 
| 01:42
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| Let us learn about the different areas of the CellDesigner workspace.  
+
| Let us learn about the different areas of the '''CellDesigner workspace'''.  
  
 
|-
 
|-
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|-
 
|-
 
| 01:52
 
| 01:52
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| On the right hand side is the '''Draw''' area.  
+
| On the right hand side, is the '''Draw''' area.  
  
 
|-
 
|-
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|-
 
|-
 
| 02:14
 
| 02:14
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| One can see the list of all these symbols and their meanings from the CellDesigner website – That is  '''www.celldesigner.org'''
+
| One can see the list of all these symbols and their meanings from the CellDesigner website – that is  '''www.celldesigner.org'''
  
 
|-
 
|-
 
| 02:29
 
| 02:29
−
| I will click on the ''' Documents '''
+
| I will click on the ''' Documents. '''
  
 
|-
 
|-
 
| 02:33
 
| 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.
  
 
|-
 
|-
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|-
 
|-
 
|02:55
 
|02:55
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| Below '''Draw''' area is the '''List''' area.  
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| Below '''Draw''' area, is the '''List''' area.  
  
 
|-
 
|-
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|-
 
|-
 
| 03:21
 
| 03:21
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| Below that is the '''Layer''' area which displays all the layers of the model.
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| Below that, is the '''Layer''' area which displays all the layers of the model.
  
 
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|-
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|-
 
|-
 
| 03:45
 
| 03:45
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| To change the position of the '''List''' & '''Notes''' area
+
| To change the position of the '''List''' & '''Notes''' area,
  
 
|-
 
|-
 
| 03:50
 
| 03:50
−
| go to '''View''' option>>click on '''List''' and select '''Right'''.
+
| go to '''View''' option >> click on '''List''' and select '''Right'''.
  
 
|-
 
|-
 
| 03:56
 
| 03:56
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| It changes list to the right. Down is the default one.
+
| It changes list to the '''right'''. '''Down''' is the default one.
  
 
|-
 
|-
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|-
 
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| 04:10
 
| 04:10
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| In this network Protein '''A''' undergoes state transition to Protein '''B '''under catalysis of Protein '''C'''.
+
| In this network, Protein '''A''' undergoes state transition to Protein '''B ''', under catalysis of Protein '''C'''.
  
 
|-
 
|-
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|-
 
|-
 
| 04:39
 
| 04:39
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|Now Click on File and then New.
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|Now click on '''File''' and then '''New'''.
  
 
|-
 
|-
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|-
 
|-
 
| 04:48
 
| 04:48
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| This is ''' name ''' field.
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| This is ''' Name ''' field.
  
 
|-
 
|-
 
| 04:50
 
| 04:50
−
| I will type “'''simple network”'''  
+
| I will type “'''simple network”'''.
  
 
|-
 
|-
 
| 04:53
 
| 04:53
−
| Here one can change the height and width as required. However, I will keep the default height and width.  
+
| Here, one can change the height and width as required. However, I will keep the default height and width.  
  
 
|-
 
|-
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|-
 
|-
 
| 05:12
 
| 05:12
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| Now, go to Edit, and enable '''Grid snap''' and '''Grid visible'''.  
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| Now go to '''Edit''' and enable '''Grid snap''' and '''Grid visible'''.  
  
 
|-
 
|-
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|-
 
|-
 
| 05:34
 
| 05:34
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| Before we begin to add components, let me show you some examples of species and reactions.
+
| Before we begin to add '''component'''s, let me show you some examples of '''species''' and '''reactions'''.
  
 
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|-
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|-
 
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| 05:45
 
| 05:45
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| The symbols here are for '''generic protein, receptor, ion''' '''channel, truncated protein, gene,''' '''RNA''' etc.  
+
| The symbols here are for '''generic protein, receptor, ion''', '''channel, truncated protein, gene,''' '''RNA''' etc.  
  
 
|-
 
|-
 
| 05:58
 
| 05:58
−
| Now let us see the  reactions  first is the  '''State transition''', '''Heterodimer association''', '''Dissociation''', '''Catalysis, Inhibition '''etc.
+
| Now let us see the  reactions. First is the  '''State transition''', '''Heterodimer association''', '''Dissociation''', '''Catalysis, Inhibition '''etc.
  
 
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|-
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| 06:39
 
| 06:39
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| I will name the new species as '''A''' and click on OK.
+
| I will name the new species as '''A''' and click on '''OK'''.
 
   
 
   
 
|-
 
|-
 
| 06:46
 
| 06:46
−
|See the change in the list area too.
+
|See the change in the '''list''' area too.
  
 
|-
 
|-
 
| 06:50
 
| 06:50
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| As you can see we have added a new species ,in the '''Draw area'''. Similarly I will add '''B'''.
+
| As you can see, we have added a new species in the '''Draw area'''. Similarly I will add '''B'''.
  
 
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|-
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| 07:21
 
| 07:21
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| Now we will see, how to change the size of a component.
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| Now we will see how to change the size of a component.
  
 
|-
 
|-
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| 07:29
 
| 07:29
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| These are the handles to change the size.  
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| These are the '''handles''' to change the size.  
  
 
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|-
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| 07:54
 
| 07:54
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| Also you can do this directly by click on the icons for undo and redo
+
| Also you can do this directly by click on the icons for '''undo''' and '''redo'''.
  
 
|-
 
|-
 
| 08:03
 
| 08:03
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| Now let’s add reactions.  
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| Now let’s add '''reaction'''s.  
  
 
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|-
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| 08:09
 
| 08:09
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| This is a state transition reaction.  
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| This is a '''state transition''' reaction.  
  
 
|-
 
|-
 
| 08:12
 
| 08:12
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| So I will click on the icon for '''State transition''' in the '''Reaction''' toolbar.
+
| So, I will click on the icon for '''State transition''' in the '''Reaction''' toolbar.
  
 
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| 08:35
 
| 08:35
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| So always remember to select the reactants first.
+
| So, always remember to select the reactants first.
  
 
|-
 
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| 08:39
 
| 08:39
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| The default reaction id comes as '''re1'''.
+
| The default '''reaction id''' comes as '''re1'''.
  
 
|-
 
|-
 
| 08:43
 
| 08:43
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| Now lets add species C and keep at appropriate position as shown in the earlier slide.
+
| Now, let's add '''species C''' and keep at appropriate position as shown in the earlier slide.
  
 
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|09:00
 
|09:00
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| I will click on the edge of '''C''', and the square symbol of the '''State transition''' reaction.
+
| I will click on the edge of '''C''' and the square symbol of the '''State transition''' reaction.
 
|-
 
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| 09:08
 
| 09:08
−
| Now i will add species D and place it besides B.
+
| Now, I will add '''species D''' and place it besides '''B'''.
  
 
|-
 
|-
 
| 09:15
 
| 09:15
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| Lets add a '''State transition '''reaction from B to D. The default reaction id is re2.  
+
| Let's add a '''State transition '''reaction from B to D. The default reaction-id is '''re2'''.  
  
 
|-
 
|-
 
| 09:26
 
| 09:26
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| I will add species E and keep at appropriate position as shown in the earlier slide.
+
| I will add '''species E''' and keep at appropriate position as shown in the earlier slide.
  
 
|-
 
|-
 
| 09:35
 
| 09:35
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| Now I will select this icon from the '''Reaction '''toolbar, which represents the '''Inhibition reaction'''.  
+
| Now I will select this icon from the '''Reaction '''toolbar which represents the '''Inhibition reaction'''.  
  
 
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| 09:57
 
| 09:57
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| Let us save our work.  
+
| Let us '''save''' our work.  
  
 
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| 10:12
 
| 10:12
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| Now we will learn how to Export an image. To do this, Go to '''File'''>'''Export Image'''.
+
| Now we will learn how to '''Export''' an '''image'''. To do this, Go to '''File > Export Image'''.
  
 
|-
 
|-
 
| 10:22
 
| 10:22
−
| You can save the image in various formats like pdf, png, jpeg etc.  
+
| You can save the image in various formats like '''pdf, png, jpeg''' etc.  
  
 
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| 10:38
 
| 10:38
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| We have 4 options for zoom - ''' Zoom In, Zoom Out, Zoom Fit. Zoom Reset '''.  
+
| We have 4 options for zoom - ''' Zoom In, Zoom Out, Zoom Fit, Zoom Reset '''.  
  
 
|-
 
|-
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|11:02
 
|11:02
−
| This brings us to the end of the spoken tutorial on. Getting started with CellDesigner.
+
| This brings us to the end of the spoken tutorial on '''Getting started with CellDesigner'''.
  
 
|-
 
|-
 
| 11:08
 
| 11:08
−
| To Summarize , we learnt about Menu and Tool bar in CellDesigner.
+
| To Summarize : we learnt about Menu and Tool bar in CellDesigner,
  
 
|-
 
|-
 
| 11:14
 
| 11:14
−
| Different areas in CellDesigner. Components like Species and Reactions.
+
| different areas in CellDesigner, components like Species and Reactions.
  
 
|-
 
|-
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|-
 
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| 11:32
 
| 11:32
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| As an assignment Construct a network with the help of CellDesigner 4.3
+
| As an assignment, construct a network with the help of CellDesigner 4.3
  
 
|-
 
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| 12:01
 
| 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  
+
| 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
 
| 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  
+
| 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
 
| 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  
+
|  '''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
 
| 12:41
−
| More information on this Mission is available at spoken hyphen tutorial dot org slash NMEICT hyphen Intro  
+
| More information on this mission is available at '''spoken hyphen tutorial dot org slash NMEICT hyphen Intro'''.
  
 
|-
 
|-
 
| 12:53
 
| 12:53
−
|This is Sakina Shaikh from IIT Bombay signing off. Thanks for joining. Goodbye.  
+
|This is Sakina Shaikh from IIT Bombay, signing off. Thanks for joining. Goodbye.  
  
 
|}
 
|}

Latest revision as of 14:57, 6 June 2018

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 4.3. 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 let's 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, let's 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 Let's 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 4.3
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.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya, Sandhya.np14

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