Difference between revisions of "CellDesigner/C3/Customizing-Diagram-Layout/English-timed"

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|-
 
|-
 
| 00:01
 
| 00:01
−
|  Hello everyone.Welcome to this tutorial on '''‘Customizing Diagram Layout’'''.
+
|  Hello everyone. Welcome to this tutorial on '''‘Customizing Diagram Layout’'''.
  
 
|-
 
|-
 
|  00:08
 
|  00:08
−
|  In this tutorial, we will learn how to: Change color, shape and width of a '''Reaction line'''
+
|  In this tutorial, we will learn how to: change color, shape and width of a '''Reaction line''',
  
 
|-
 
|-
 
|  00:19
 
|  00:19
−
|Add '''Anchor points''' to a '''Reaction line , '''Align '''Components''' , Show/hide '''Reaction ids'''
+
|add '''Anchor points''' to a '''Reaction line , '''align '''Components''' , show/hide '''Reaction ids'''.
  
 
|-
 
|-
 
| 00:30   
 
| 00:30   
−
|  We will also learn how to: Add notes to '''Components''' , Edit '''Protein''' , Edit information ,
+
|  We will also learn how to: add notes to '''Components''' , edit '''Protein''' , edit information ,
  
 
|-
 
|-
 
|00:39
 
|00:39
−
| And get a '''bird’s eye view''' of the diagram.
+
| and get a '''bird’s eye view''' of the diagram.
  
 
|-
 
|-
 
| 00:44
 
| 00:44
−
|  To record this tutorial, I am using'''Ubuntu Linux OS 14.04''' '''CellDesigner version 4.3'''  '''Java version 1.7'''
+
|  To record this tutorial, I am using '''Ubuntu Linux OS 14.04''', '''CellDesigner version 4.3''', '''Java version 1.7'''.
  
 
|-
 
|-
 
|  01:01
 
|  01:01
−
|  To follow this tutorial, learners should be familiar with:'''Undergraduate Biochemistry '''and
+
|  To follow this tutorial, learners should be familiar with: undergraduate Biochemistry and
 
'''CellDesigner interface.'''
 
'''CellDesigner interface.'''
  
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|-
 
|-
 
| 01:22
 
| 01:22
−
|  The assignment for one of the previous tutorials was- To build a '''process diagram '''for '''Methionine Biosynthesis'''.
+
|  The assignment for one of the previous tutorials was to build a '''process diagram '''for '''Methionine Biosynthesis'''.
  
 
|-
 
|-
 
|  01:32
 
|  01:32
−
|  I am going to use that same diagram as the example for this tutorial.And I will demonstrate how to customize it.
+
|  I am going to use that same diagram as the example for this tutorial. And, I will demonstrate how to customize it.
  
 
|-
 
|-
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|-
 
|-
 
|  02:12
 
|  02:12
−
| Let us go back to the''' Cell designer '''interface
+
| Let us go back to the''' Cell designer '''interface.
  
 
|-
 
|-
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|-
 
|-
 
| 02:47
 
| 02:47
−
|  A dialog box named “'''Change color & shape”''' appears on the screen.
+
|  A dialog box named “'''Change color & shape”''' appears on the '''screen'''.
  
 
|-
 
|-
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|-
 
|-
 
|  03:02
 
|  03:02
−
| I will change this to 3.0
+
| I will change this to 3.0.
  
 
|-
 
|-
 
|  03:06
 
|  03:06
−
|  To change the color of the '''Reaction line''', go to the''' Color panel.'''
+
|  To change the color of the '''Reaction line''', go to the''' Color''' panel.
  
 
|-
 
|-
 
|  03:12
 
|  03:12
−
|  In the''' Color panel''' we can see a color wheel, with a pointer like handle.
+
|  In the''' Color''' panel, we can see a color wheel with a pointer like handle.
  
 
|-
 
|-
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|-
 
|-
 
|  03:34
 
|  03:34
−
| Now, Click and drop the small circle at the pointer.  
+
| Now, click and drop the small circle at the pointer.  
  
 
|-
 
|-
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|-
 
|-
 
| 03:55
 
| 03:55
−
|  Next we will learn how to add '''Anchor points '''on the '''Reaction line'''.
+
|  Next, we will learn how to add '''Anchor points '''on the '''Reaction line''',
  
 
|-
 
|-
 
|  04:01
 
|  04:01
−
|  And why '''Anchor points '''are useful to- Turn around the '''Reaction lines''' ,
+
|  and, why '''Anchor points '''are useful to turn around the '''Reaction lines''',
  
 
|-
 
|-
 
|  04:09
 
|  04:09
−
|Give them a proper shape And place them in the correct position on the '''draw area.'''.
+
|give them a proper shape and place them in the correct position on the '''draw area.'''.
  
 
|-
 
|-
 
|  04:16
 
|  04:16
−
|  Lets come back to the '''CellDesigner interface'''.
+
|  Let's come back to the '''CellDesigner interface'''.
  
 
|-
 
|-
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|-
 
|-
 
|  04:23
 
|  04:23
−
| I will select the same '''State Transition reaction line''' between- '''Homoserine''' and '''Succinyl Homoserine.'''
+
| I will select the same '''State Transition reaction line''' between '''Homoserine''' and '''Succinyl Homoserine.'''
  
 
|-
 
|-
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|-
 
|-
 
|  04:55
 
|  04:55
−
|  Let me show you how '''Anchor Points '''can help to modify a Reaction line.
+
|  Let me show you how '''Anchor Points '''can help to modify a '''Reaction line'''.
  
 
|-
 
|-
 
|  05:03
 
|  05:03
−
| Let me open a new window and name it '''Anchor. '''Click''' OK'''
+
| Let me open a new window and name it '''Anchor. '''Click''' OK'''.
  
 
|-
 
|-
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|-
 
|-
 
|  05:18
 
|  05:18
−
| And click anywhere on the draw area.
+
| and click anywhere on the '''draw area'''.
  
 
|-
 
|-
 
|  05:22
 
|  05:22
−
|Right-click on ''' Reaction line''' and click on ''' Add Anchor point'''
+
|Right-click on ''' Reaction line''' and click on ''' Add Anchor point'''.
  
 
|-
 
|-
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|-
 
|-
 
|  05:37
 
|  05:37
−
|  Next we will see how to '''align''' the components on the '''draw area.'''
+
|  Next we will see how to align the components on the '''draw area.'''
  
 
|-
 
|-
 
|  05:44
 
|  05:44
−
|  Let us come back to the''' Methionine '''biosynthesis process diagram window
+
|  Let us come back to the''' Methionine biosynthesis process diagram''' window.
  
 
|-
 
|-
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|-
 
|-
 
| 05:56
 
| 05:56
−
|  Now, hold the ''''Shift'''' key and click on multiple '''Species''' on the '''draw area.'''
+
|  Now, hold the '''Shift''' key and click on multiple '''Species''' on the '''draw area.'''
  
 
|-
 
|-
 
| 06:04
 
| 06:04
−
|  Go to '''Edit''' menu, scroll down select '''Alignment''' and click on the '''Alignment type'''.
+
|  Go to '''Edit''' menu, scroll down, select '''Alignment''' and click on the '''Alignment type'''.
  
 
|-
 
|-
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|-
 
|-
 
|  06:27
 
|  06:27
−
|  Let us undo the alignment and move ahead.
+
|  Let us '''undo''' the alignment and move ahead.
  
 
|-
 
|-
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|-
 
|-
 
|  06:48
 
|  06:48
−
| The '''Reaction ids''' on the respective reactions on the '''draw area''' will not be visible any more.
+
| The '''Reaction ids''' on the respective reactions, on the '''draw area''', will not be visible any more.
  
 
|-
 
|-
 
|  06:55
 
|  06:55
−
|  In case, you wish to show the '''Reaction Id do the following.'''
+
|  In case, you wish to show the '''Reaction Id''', do the following.
  
 
|-
 
|-
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|-
 
|-
 
|  07:08
 
|  07:08
−
| The '''Reaction ids''' will appear on the respective '''reactions''' on the '''draw area.'''
+
| The '''Reaction ids''' will appear on the respective '''reactions''', on the '''draw area.'''
  
 
|-
 
|-
 
|  07:15
 
|  07:15
−
|  We can also add notes to all the '''Components''' (Compartment, Species or Reaction) on the '''draw area'''.
+
|  We can also add notes to all the '''Components''' ('''Compartment, Species''' or '''Reaction''') on the '''draw area'''.
  
 
|-
 
|-
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|-
 
|-
 
|  07:35
 
|  07:35
−
| A pop up menu is displayed
+
| A pop up menu is displayed.
  
 
|-
 
|-
 
|  07:38
 
|  07:38
−
|  A dialog box ''''Species Notes'''' pops up.  Type the text related to the '''Species'''  
+
|  A dialog box ''''Species Notes'''' pops up.  Type the text related to the '''Species'''.
  
 
|-
 
|-
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|-
 
|-
 
|  08:21
 
|  08:21
−
| Type the text related to the '''Species'''-
+
| Type the text related to the '''Species'''.
  
 
|-
 
|-
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|-
 
|-
 
|  09:59
 
|  09:59
−
|  For this demo, I will select- '''Size '''as 15 and'''Angle''' 38
+
|  For this demo, I will select '''Size '''as 15 and'''Angle''' 38.
  
 
|-
 
|-
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|-
 
|-
 
|  10:14
 
|  10:14
−
|  And close the box.
+
|  and close the box.
  
 
|-
 
|-
 
|  10:17
 
|  10:17
−
|  As we do not require to add region in the '''Methionine Biosynthesis, '''I will undo these changes.
+
|  As we do not require to add region in the '''Methionine Biosynthesis, '''I will '''undo''' these changes.
  
 
|-
 
|-
 
|  10:25
 
|  10:25
−
|  Next, let us learn to edit information.
+
|  Next, let us learn to '''edit''' information.
  
 
|-
 
|-
 
|  10:30
 
|  10:30
−
|  Right-click on the '''component '''on the '''draw area'''.
+
|  Right-click on the '''component, '''on the '''draw area'''.
  
 
|-
 
|-
 
|  10:33
 
|  10:33
−
| I will click on Homoserine.
+
| I will click on '''Homoserine'''.
  
 
|-
 
|-
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|-
 
|-
 
|  10:41
 
|  10:41
−
| A dialog box '''‘Edit Information’''' appears on screen
+
| A dialog box '''‘Edit Information’''' appears on '''screen'''.
  
 
|-
 
|-
 
| 10:46
 
| 10:46
−
|  In the dialog box do the following'''- '''  Under the tab ‘'''state'''’ select '''Open. '''
+
|  In the dialog box, do the following'''- '''  under the tab ‘'''state'''’, select '''Open, '''
  
 
|-
 
|-
 
|  10:54
 
|  10:54
−
|  Under the tab ‘'''prefix'''’ select '''mt. '''
+
|  under the tab ‘'''prefix'''’, select '''mt. '''
 
   
 
   
 
|-
 
|-
 
|  10:59
 
|  10:59
−
| Under the tab '''‘label’ '''select '''dna.'''
+
| under the tab '''‘label’, '''select '''dna.'''
  
 
|-
 
|-
 
|  11:04
 
|  11:04
−
|  Click''' '''on '''‘Ok’.'''
+
|  Click on '''‘Ok’.'''
  
 
|-
 
|-
 
|  11:07
 
|  11:07
−
| You can see the information '''mt:dna''' displayed on the draw area
+
| You can see the information '''mt:dna''' displayed on the '''draw area'''.
  
 
|-
 
|-
 
|  11:15
 
|  11:15
−
|  I will undo '''Edit Information,''' as we do not require it in '''Methionine Biosynthesis.'''
+
|  I will '''undo''' '''Edit Information,''' as we do not require it in '''Methionine Biosynthesis.'''
  
 
|-
 
|-
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|-
 
|-
 
|  11:37
 
|  11:37
−
|  Click the '''Bird's eye''' '''view '''icon.
+
|  Click the '''Bird's eye view '''icon.
  
 
|-
 
|-
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|-
 
|-
 
|  11:56
 
|  11:56
−
|  Let us summarize. In this tutorial, we have learnt how to: Change- color, shape and width of a '''Reaction line''',
+
|  Let us summarize. In this tutorial, we have learnt how to: change- color, shape and width of a '''Reaction line''',
  
 
|-
 
|-
 
|  12:07
 
|  12:07
−
| Add '''Anchor points''' to a '''Reaction line''' , Align '''Components'''  And show/hide '''Reaction id’s'''
+
| add '''Anchor points''' to a '''Reaction line''' , align '''Components'''  and show/hide '''Reaction id’s'''.
  
 
|-
 
|-
 
|  12:18
 
|  12:18
−
|  We have also learnt how to- Add notes to '''Components''',
+
|  We have also learnt how to- add notes to '''Components''',
 
   
 
   
 
|-
 
|-
 
|  12:23
 
|  12:23
−
| Edit '''Protein/Gene''' Edit Information,
+
| edit '''Protein/Gene''', edit Information,
 
   
 
   
 
|-
 
|-
 
|  12:27
 
|  12:27
−
| And get the '''Bird’s Eye View '''of the diagram.
+
| and get the '''Bird’s Eye View '''of the diagram.
  
 
|-
 
|-
 
|  12:32
 
|  12:32
−
|  For Assignment Create a Glycolysis Process Diagram using tools in CellDesigner.
+
|  For Assignment: create a '''Glycolysis Process Diagram''' using tools in CellDesigner.
 
   
 
   
 
|-
 
|-
 
|  12:41
 
|  12:41
−
| Explore different shapes of '''Reaction line'''
+
| Explore different shapes of '''Reaction line'''.
  
 
|-
 
|-
 
|  12:47
 
|  12:47
−
| Watch the video at the following link It summarizes the Spoken Tutorial project.
+
| Watch the video at the following link. It summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
 
|  12:52
 
|  12:52
−
|  If you do not have a good bandwidth please download and watch it.
+
|  If you do not have a good bandwidth, please download and watch it.
  
 
|-
 
|-
 
| 12:57
 
| 12:57
−
|  The''' Spoken Tutorial Project '''Team - Conducts Workshops And gives certificates for those who pass an online test.
+
|  The''' Spoken Tutorial''' project team - conducts Workshops and gives certificates for those who pass an online test.
  
 
|-
 
|-
 
|  13:06
 
|  13:06
−
| For more details, please write to contact@spoken-tutorial.org
+
| For more details, please write to '''contact@spoken-tutorial.org'''
  
 
|-
 
|-
 
|  13:13
 
|  13:13
−
|  Spoken Tutorial Project is a part of '''Talk to a Teacher project.''' It is funded by '''NMEICT, MHRD, Government of India'''. More information on this Mission is available at the given link.
+
|  Spoken Tutorial Project is a part of '''Talk to a Teacher project.''' It is funded by '''NMEICT, MHRD, Government of India'''. More information on this mission is available at the given link.
  
 
|-
 
|-
 
|  13:29
 
|  13:29
−
|  This is Bella Tony''' '''from''' IIT Bombay''' signing off.
+
|  This is Bella Tony''' '''from''' IIT Bombay''', signing off.
  
 
Thank you for joining.
 
Thank you for joining.
  
 
|}
 
|}

Latest revision as of 16:55, 7 June 2018

Time Narration
00:01 Hello everyone. Welcome to this tutorial on ‘Customizing Diagram Layout’.
00:08 In this tutorial, we will learn how to: change color, shape and width of a Reaction line,
00:19 add Anchor points to a Reaction line , align Components , show/hide Reaction ids.
00:30 We will also learn how to: add notes to Components , edit Protein , edit information ,
00:39 and get a bird’s eye view of the diagram.
00:44 To record this tutorial, I am using Ubuntu Linux OS 14.04, CellDesigner version 4.3, Java version 1.7.
01:01 To follow this tutorial, learners should be familiar with: undergraduate Biochemistry and

CellDesigner interface.

01:12 If not, for relevant CellDesigner tutorials, please visit the Spoken Tutorial website.
01:20 Let us begin.
01:22 The assignment for one of the previous tutorials was to build a process diagram for Methionine Biosynthesis.
01:32 I am going to use that same diagram as the example for this tutorial. And, I will demonstrate how to customize it.
01:43 Let me switch to CellDesigner interface.
01:47 What you see here is the process diagram for Methionine Biosynthesis.
01:53 Pause the tutorial here and open the Methionine Biosynthesis process diagram that you created.
02:01 If you do not have a saved file, you may open from the code file provided.
02:08 Now, let me start customizing the diagram.
02:12 Let us go back to the Cell designer interface.
02:16 To start with, I will change the width and color of a Reaction line.
02:22 To do so, I am selecting the State Transition between Homoserine and Succinyl homoserine.
02:30 Now, go to “Component” in the main menu bar.
02:35 And click on “Change color & shape” option.
02:39 Alternately, you may right-click on a Reaction line and select “Change color & shape” option.
02:47 A dialog box named “Change color & shape” appears on the screen.
02:53 For a thicker Reaction line, change the Line Width from 1.0 to a higher value.
03:02 I will change this to 3.0.
03:06 To change the color of the Reaction line, go to the Color panel.
03:12 In the Color panel, we can see a color wheel with a pointer like handle.
03:19 Click and hold the pointer and rotate to select the preferred color.
03:25 I will select a shade of blue.
03:28 Next, click anywhere inside the color triangle.
03:34 Now, click and drop the small circle at the pointer.
03:40 After all the modifications are done, click on Apply and then on Ok.
03:48 Observe that the Reaction line is now thicker and in shade of blue.
03:55 Next, we will learn how to add Anchor points on the Reaction line,
04:01 and, why Anchor points are useful to turn around the Reaction lines,
04:09 give them a proper shape and place them in the correct position on the draw area..
04:16 Let's come back to the CellDesigner interface.
04:20 Select any Reaction line.
04:23 I will select the same State Transition reaction line between Homoserine and Succinyl Homoserine.
04:31 On this line, using the cursor, choose the exact position where the Anchor point has to be placed.
04:39 Upon selection of the exact point, right-click and select Add Anchor Point.
04:47 You will see the newly added Anchor point at the exact chosen position on the Reaction line.
04:55 Let me show you how Anchor Points can help to modify a Reaction line.
05:03 Let me open a new window and name it Anchor. Click OK.
05:11 Now click on the icon for GTP/GDP
05:18 and click anywhere on the draw area.
05:22 Right-click on Reaction line and click on Add Anchor point.
05:29 Drag and drop the Reaction line anywhere on the draw area.
05:37 Next we will see how to align the components on the draw area.
05:44 Let us come back to the Methionine biosynthesis process diagram window.
05:50 Click anywhere on the draw area to uncheck the highlighted Reaction line.
05:56 Now, hold the Shift key and click on multiple Species on the draw area.
06:04 Go to Edit menu, scroll down, select Alignment and click on the Alignment type.
06:15 Alternately, click on the icon for Alignment on the toolbar.
06:21 Explore other Alignment options on the toolbar on your own.
06:27 Let us undo the alignment and move ahead.
06:31 While working on a Reaction, how can we show/hide Reaction ids on a process diagram?
06:39 Let’s learn that.
06:41 Go to 'View', scroll down and uncheck the 'Show Reaction Id'.
06:48 The Reaction ids on the respective reactions, on the draw area, will not be visible any more.
06:55 In case, you wish to show the Reaction Id, do the following.
07:01 Go to 'View', scroll down and click on the 'Show Reaction Id'.
07:08 The Reaction ids will appear on the respective reactions, on the draw area.
07:15 We can also add notes to all the Components (Compartment, Species or Reaction) on the draw area.
07:21 Let us learn how to do that.
07:24 Right-click on a Species on the draw area.
07:28 I will click on CoA.
07:32 Scroll down and click on the ‘Species Notes’.
07:35 A pop up menu is displayed.
07:38 A dialog box 'Species Notes' pops up. Type the text related to the Species.
07:46 I will type the following.
07:49 Click 'OK'.
07:51 Observe that the notes information is displayed in the Notes Area.
07:58 Alternately, to add notes to a Species, click on a Species on the draw area.
08:06 I will click on Succinate.
08:09 Then, click on Edit Notes tab, located at the bottom right corner of the CellDesigner window.
08:18 A pop up window will appear.
08:21 Type the text related to the Species.
08:25 I will type and click 'OK'.
08:30 In the same manner we can edit a Protein.
08:35 To do so, right-click on a component on the draw area.
08:40 I will click on Homoserine succinyl transferase.
08:46 Scroll down and click on Edit Protein.
08:51 A dialog box named Protein appears on the screen.
08:55 Enter the name of the Protein in the name box.
09:00 I will type O-succinyltransferase in the name box.
09:06 Click on ‘Update’ and close the dialog box.
09:11 We can also add regions to a Protein.
09:15 Right-click on a Protein on the draw area.
09:19 I will right click on O-succinyltransferase.
09:24 Scroll down and click on Edit Protein.
09:29 A dialog box, Protein, appears on the screen.
09:33 Under the tab ‘residues/regions’, click on the 'Add' button.
09:40 In the dialog box - ModificationResidue/Bindingregion:
09:46 Select the ‘Type’ from the drop down menu as ‘Binding region.
09:52 Change the size and angle by moving the cursor at the required value.
09:59 For this demo, I will select Size as 15 andAngle 38.
10:09 Then click on ‘Close’.
10:12 Click on the Update
10:14 and close the box.
10:17 As we do not require to add region in the Methionine Biosynthesis, I will undo these changes.
10:25 Next, let us learn to edit information.
10:30 Right-click on the component, on the draw area.
10:33 I will click on Homoserine.
10:37 Scroll down and click on ‘Edit Information’.
10:41 A dialog box ‘Edit Information’ appears on screen.
10:46 In the dialog box, do the following- under the tab ‘state’, select Open,
10:54 under the tab ‘prefix’, select mt.
10:59 under the tab ‘label’, select dna.
11:04 Click on ‘Ok’.
11:07 You can see the information mt:dna displayed on the draw area.
11:15 I will undo Edit Information, as we do not require it in Methionine Biosynthesis.
11:23 In some cases, the process diagram can be a complicated one.
11:28 In such cases, Bird's eye view can help as it is convenient to navigate inside a big model.
11:37 Click the Bird's eye view icon.
11:41 Drag the red square in the Bird’s Eye View.
11:46 Observe that the view on the draw area moves accordingly.
11:52 This brings us to the end of this tutorial.
11:56 Let us summarize. In this tutorial, we have learnt how to: change- color, shape and width of a Reaction line,
12:07 add Anchor points to a Reaction line , align Components and show/hide Reaction id’s.
12:18 We have also learnt how to- add notes to Components,
12:23 edit Protein/Gene, edit Information,
12:27 and get the Bird’s Eye View of the diagram.
12:32 For Assignment: create a Glycolysis Process Diagram using tools in CellDesigner.
12:41 Explore different shapes of Reaction line.
12:47 Watch the video at the following link. It summarizes the Spoken Tutorial project.
12:52 If you do not have a good bandwidth, please download and watch it.
12:57 The Spoken Tutorial project team - conducts Workshops and gives certificates for those who pass an online test.
13:06 For more details, please write to contact@spoken-tutorial.org
13:13 Spoken Tutorial Project is a part of Talk to a Teacher project. It is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the given link.
13:29 This is Bella Tony from IIT Bombay, signing off.

Thank you for joining.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14

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