Difference between revisions of "CellDesigner/C3/Build-and-Modify-Process-Diagram/English-timed"

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'''Title of the Script''': Build and Modify Process Diagram
 
 
'''Author''': Bella Tony
 
 
'''Keywords''': Process Diagram, Macros, Alanine Biosythesis,
 
Generic Protein, Aminotransferase
 
  
 
{| border=1
 
{| border=1
 
|| '''Time'''
 
|| '''Time'''
 
|| '''Narration'''
 
|| '''Narration'''
 
  
 
|-
 
|-
 
|  00:01
 
|  00:01
|  Hello everyone. Welcome to this tutorial on''' ‘Build''' '''and Modify Process Diagram''' in''' CellDesigner’'''.
+
|  Hello everyone. Welcome to this tutorial on''' Build and Modify Process Diagram''' in''' CellDesigner'''.
  
 
|-
 
|-
 
| 00:08
 
| 00:08
|  In this tutorial, we will learn to: Use '''Macros''' , Move Components on the draw area , Connect a reaction line around a species,
+
|  In this tutorial, we will learn to: use '''Macros''' , move '''Components''' on the '''draw area''' , connect a '''reaction line''' around a '''species''',
  
 
|-
 
|-
 
|  00:18
 
|  00:18
Align and extend a reaction line , Add a '''Product''' and a '''Reactant'''.
+
align and extend a reaction line , add a '''Product''' and a '''Reactant'''.
  
 
|-
 
|-
 
|  00:23
 
|  00:23
|  For this tutorial, I am using'''Ubuntu Linux OS 14.04'''  '''CellDesigner '''version '''4.3''' '''Java version 1.7'''
+
|  For this tutorial, I am using'''Ubuntu Linux OS 14.04''', '''CellDesigner '''version '''4.3''', '''Java version 1.7'''.
  
 
|-
 
|-
 
| 00:35
 
| 00:35
|  To follow this tutorial, learners should be familiar with: Undergraduate''' Biochemistry.''' '''CellDesigner '''interface.
+
|  To follow this tutorial, learners should be familiar with: undergraduate''' Biochemistry,''' '''CellDesigner '''interface.
  
 
|-
 
|-
 
| 00:43
 
| 00:43
|If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website
+
|If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website.
  
 
|-
 
|-
 
|  00:51
 
|  00:51
|  Let us begin
+
|  Let us begin.
  
 
|-
 
|-
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|-
 
|-
 
|  00:58
 
|  00:58
|  Now, we’ll use '''CellDesigner''' to create this process diagram.
+
|  Now, we’ll use '''CellDesigner''' to create this '''process diagram'''.
  
 
|-
 
|-
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|-
 
|-
 
|  01:09
 
|  01:09
|  Now type '''./runCellDesigner4.3''' and press '''Enter'''.
+
|  Now type: '''./runCellDesigner4.3''' and press '''Enter'''.
  
 
|-
 
|-
 
|  01:20
 
|  01:20
|  CellDesigner window is now open on your terminal
+
|  CellDesigner window is now open on your terminal.
  
 
|-
 
|-
 
|  01:24
 
|  01:24
|  Open a new file by pressing''' CTRL+N''' and name it '''Build''' '''and Modify Process Diagram'''.
+
|  Open a new file by pressing''' CTRL+N''' and name it '''Build and Modify Process Diagram'''.
  
 
|-
 
|-
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|-
 
|-
 
|  01:47
 
|  01:47
|  On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the draw area.
+
|  On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the '''draw area'''.
  
 
|-
 
|-
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|-
 
|-
 
|  02:08
 
|  02:08
|  For that click on the ''''Edit'''' menu and then click on ''''Select All'.'''
+
|  For that, click on the '''Edit''' menu and then click on ''''Select All'.'''
  
 
|-
 
|-
 
| 02:16
 
| 02:16
|Alternately you may press '''Ctrl + A '''keys.
+
|Alternately, you may press '''Ctrl + A '''keys.
  
 
|-
 
|-
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|-
 
|-
 
|  02:24
 
|  02:24
|  Now click anywhere on the highlighted components and drag them to the desired location.
+
|  Now, click anywhere on the highlighted components and drag them to the desired location.
  
 
|-
 
|-
 
|  02:30
 
|  02:30
Let’s proceed.
+
Let's proceed.
  
 
|-
 
|-
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|-
 
|-
 
|  02:37
 
|  02:37
|  Again on the draw area, right click on the''' Generic Protein S1.'''
+
|  Again, on the draw area, right click on the''' Generic Protein S1.'''
  
 
|-
 
|-
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|-
 
|-
 
|  03:10
 
|  03:10
|  However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.Here, I will click''' ‘No’'''
+
|  However, if you want to reflect the change to all '''components''' of the '''species''', click ‘'''Yes'''’. Here, I will click''' ‘No’'''.
  
 
|-
 
|-
 
| 03:20
 
| 03:20
|  Observe the''' Generic Protein S1, '''is now a '''simple molecule '''named '''2-keto-isovalerate.'''
+
|  Observe the''' Generic Protein S1 '''is now a simple molecule named '''2-keto-isovalerate.'''
  
 
|-
 
|-
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|-
 
|-
 
|  03:34
 
|  03:34
|  Right-click in the center of the''' end-point,''' '''Generic protein'''-'''S1 '''which is a '''product'''.
+
|  Right-click in the center of the''' end-point ''' '''Generic protein'''-'''S1 ''' which is a '''product'''.
  
 
|-
 
|-
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|-
 
|-
 
|  04:25
 
|  04:25
|  Click in the center of the ''''end-point'''' '''species''' i.e.''' Valine '''and drag and drop at the desired location'''.'''
+
|  Click in the center of the ''''end-point species''' i.e.''' Valine '''and drag and drop at the desired location.
  
 
|-
 
|-
 
|  04:33
 
|  04:33
|  Repeat the same with '''Aminotransferase'''
+
|  Repeat the same with '''Aminotransferase'''.
  
 
|-
 
|-
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|-
 
|-
 
|  05:08
 
|  05:08
|  Keep the default width and height and click on '''Ok''' the button.
+
|  Keep the default width and height and click on '''OK''' button.
  
 
|-
 
|-
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|-
 
|-
 
|  05:23
 
|  05:23
|  In the main menu,click on the icon for '''State Transition'''.
+
|  In the main menu, click on the icon for '''State Transition'''.
  
 
|-
 
|-
 
| 05:28
 
| 05:28
|Then, on the draw area, hover the mouse on ‘'''start-point'''' '''Species, Protein 1'''.
+
|Then, on the draw area, hover the '''mouse''' on ‘'''start-point'''' '''Species, Protein 1'''.
  
 
|-
 
|-
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|-
 
|-
 
|  05:53
 
|  05:53
|  In the same manner, hover the mouse on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''.
+
|  In the same manner, hover the '''mouse''' on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''.
  
 
|-
 
|-
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|-
 
|-
 
|  06:27
 
|  06:27
|  If we hover the mouse on either of the 2 '''process nodes''', a ‘'''plus’''' sign appears.
+
|  If we hover the mouse on either of the 2 '''process nodes''', a plus sign appears.
  
 
|-
 
|-
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|-
 
|-
 
|  06:43
 
|  06:43
|  Click anywhere on the draw area to uncheck the highlighted components.
+
|  Click anywhere on the '''draw area''' to uncheck the highlighted components.
  
 
|-
 
|-
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|-
 
|-
 
|  07:07
 
|  07:07
|  From here on, we will proceed with the Process diagram.
+
|  From here on, we will proceed with the '''Process diagram'''.
  
 
|-
 
|-
 
|  07:12
 
|  07:12
|  Let us come back to the '''Build''' '''and Modify Process Diagram''' window.
+
|  Let us come back to the '''Build and Modify Process Diagram''' window.
  
 
|-
 
|-
 
|  07:16
 
|  07:16
|  Let’s add a '''Reactant '''and a '''Product''', to the existing reaction.
+
|  Let’s add a '''Reactant '''and a '''Product''' to the existing reaction.
  
 
|-
 
|-
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|-
 
|-
 
|  08:07
 
|  08:07
|  Click on the''' '''highlighted '''process node.'''
+
|  Click on the highlighted '''process node.'''
  
 
|-
 
|-
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|-
 
|-
 
| 09:09
 
| 09:09
|From the toolbar use the icons: '''State Transition''' , '''Simple Molecule''',  '''Generic Protein''' and '''Catalysis'''
+
|From the toolbar, use the icons: '''State Transition''' , '''Simple Molecule''',  '''Generic Protein''' and '''Catalysis'''.
  
 
|-
 
|-
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|-
 
|-
 
|  09:36
 
|  09:36
|  Let us summarize. In this tutorial, we have learnt to Use '''Macros'''.
+
|  Let us summarize. In this tutorial, we have learnt: to use '''Macros''',
 
   
 
   
 
|-
 
|-
 
| 09:42
 
| 09:42
|Move Components on the draw area , Connect a reaction line around a species.
+
|move '''Components''' on the '''draw area''' , connect a reaction line around a species,
  
 
|-
 
|-
 
|  09:48
 
|  09:48
Align and extend a reaction line, Add a '''Product''' and a '''Reactant'''
+
align and extend a reaction line, add a '''Product''' and a '''Reactant'''.
  
 
|-
 
|-
 
|  09:54
 
|  09:54
|  For the assignment:Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner'''   
+
|  For the assignment: Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner'''.  
Explore the '''Macros''' for '''GTP/GD''',
+
Explore the '''Macros''' for '''GTP/GD'''.
Find out how to create a ’Curve’ reaction line
+
Find out how to create a ’Curve’ reaction line.
  
 
|-
 
|-
 
|  10:11
 
|  10:11
|  About the Spoken Tutorial project-  
+
|  About the '''Spoken Tutorial''' project-  
  
 
|-
 
|-
 
| 10:14
 
| 10:14
|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.
  
 
|-
 
|-
 
| 10:19
 
| 10:19
| 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.
  
 
|-
 
|-
| 09:24
+
| 10:24
|  The''' Spoken Tutorial Project '''Team conducts- Workshops using Spoken tutorials.
+
|  The''' Spoken Tutorial Project '''team: conducts- workshops using Spoken tutorials
  
 
|-
 
|-
| 09:29
+
| 10:29
| And gives certificates for those who pass an online test.
+
| and gives certificates for those who pass an online test.
  
 
|-
 
|-
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|-
 
|-
 
|  10:40
 
|  10:40
|  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.
  
 
|-
 
|-
 
|  10:54
 
|  10:54
|  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 15:55, 7 June 2018

Time Narration
00:01 Hello everyone. Welcome to this tutorial on Build and Modify Process Diagram in CellDesigner.
00:08 In this tutorial, we will learn to: use Macros , move Components on the draw area , connect a reaction line around a species,
00:18 align and extend a reaction line , add a Product and a Reactant.
00:23 For this tutorial, I am usingUbuntu Linux OS 14.04, CellDesigner version 4.3, Java version 1.7.
00:35 To follow this tutorial, learners should be familiar with: undergraduate Biochemistry, CellDesigner interface.
00:43 If not, for relevant CellDesigner tutorials, please visit the Spoken Tutorial website.
00:51 Let us begin.
00:53 What you see here is the conventional diagram for Alanine Biosynthesis.
00:58 Now, we’ll use CellDesigner to create this process diagram.
01:02 Open the terminal by pressing Ctrl+Alt+T keys simultaneously.
01:09 Now type: ./runCellDesigner4.3 and press Enter.
01:20 CellDesigner window is now open on your terminal.
01:24 Open a new file by pressing CTRL+N and name it Build and Modify Process Diagram.
01:34 Keep the default width and height and click on the Ok button.
01:39 Now let us learn what are ‘Macros’.
01:42 Macros are frequently used Components sets that help in drawing the diagrams easily.
01:47 On the toolbar, click on the Macros icon for Catalysis and click on the draw area.
01:57 We now have a Macros-Catalysis reaction on the draw area.
02:02 Let’s learn to move all the components to another side of the draw area.
02:08 For that, click on the Edit menu and then click on 'Select All'.
02:16 Alternately, you may press Ctrl + A keys.
02:21 All the Components are now highlighted.
02:24 Now, click anywhere on the highlighted components and drag them to the desired location.
02:30 Let's proceed.
02:32 Click anywhere on the draw area to uncheck the highlighted components.
02:37 Again, on the draw area, right click on the Generic Protein S1.
02:43 Then click on the option 'Change Identity'.
02:47 In the 'class' box, change the Protein to Simple Molecule.
02:53 Type the Name as: 2-keto-isovalerate.
02:58 And then click on the ‘Apply’ button.
03:02 In the dialog box ‘The Same Species Exists’, click ‘No’.
03:10 However, if you want to reflect the change to all components of the species, click ‘Yes’. Here, I will click ‘No’.
03:20 Observe the Generic Protein S1 is now a simple molecule named 2-keto-isovalerate.
03:30 I will drag the molecule to accomodate the name.
03:34 Right-click in the center of the end-point Generic protein-S1 which is a product.
03:42 Change identity to Simple Molecule and name it Valine.
03:50 Click on the Apply button.
03:52 You have Valine on the draw area.
03:36 Next, rename catalyst S2. Right-click on it and select Edit Protein.
04:06 In the ‘name’ field, type Aminotransferase.
04:11 Click on Update and close the dialog box.
04:16 Drag the corner of the molecule to accomodate the name.
04:21 Next, let’s change the position of the linked reaction.
04:25 Click in the center of the 'end-point species i.e. Valine and drag and drop at the desired location.
04:33 Repeat the same with Aminotransferase.
04:37 Observe that the linked reaction follows wherever the ‘end-point’ Species moves.
04:44 We will now learn how to connect a reaction line around a species.
04:49 A Reaction line can be connected to any of the 16 connection points around a Species.
04:56 I will show you how to do so.
04:59 Open a new window by pressing CTRL+N.
05:04 Name this file as Connection points.
05:08 Keep the default width and height and click on OK button.
05:14 On the draw area, draw two generic proteins and name them Protein 1 and Protein 2.
05:23 In the main menu, click on the icon for State Transition.
05:28 Then, on the draw area, hover the mouse on ‘start-point' Species, Protein 1.
05:36 Observe that all 16 connection points are highlighted in grey color.
05:42 Note that when the cursor is pointed to one of these connection points, it will change to blue color.
05:49 Let’s click on one of the connection points.
05:53 In the same manner, hover the mouse on the ‘end-point' Species i.e. Protein 2.
06:00 Again, as explained above, click on the required connection point.
06:05 A State Transition reaction line is formed between the selected connection points.
06:12 Next, we will align the Reaction line.
06:16 Click on the State transition reaction line between Protein 1 and Protein 2
06:21 Note that the 2 process nodes on the reaction line get highlighted.
06:27 If we hover the mouse on either of the 2 process nodes, a plus sign appears.
06:34 Click on one of the process nodes.
06:37 Now drag and place the pointer on the preferred connection point.
06:43 Click anywhere on the draw area to uncheck the highlighted components.
06:49 To extend or stretch the reaction line, first click on it.
06:54 Now click on either of the process nodes located on the start-point or end-point Species.
07:01 Drag the mouse to stretch the reaction line till the preferred connection point.
07:07 From here on, we will proceed with the Process diagram.
07:12 Let us come back to the Build and Modify Process Diagram window.
07:16 Let’s add a Reactant and a Product to the existing reaction.
07:21 From the toolbar, click and place 2 simple molecules on the draw area.
07:27 Name them Glutamate and 2-Oxoglutarate.
07:36 Drag and place them adjacent to the Simple molecules: 2-keto-isovalerate and Valine.
07:44 As explained earlier, let us align the components on the draw area.
07:49 From what was explained earlier, I have now completed aligning the components.
07:55 On the toolbar, click on the icon for ‘Add Product’.
08:00 Now hover the mouse on the State Transition reaction between 2-keto-isovalerate and Valine.
08:07 Click on the highlighted process node.
08:10 Next, hover the mouse on 2-Oxoglutarate.
08:17 Click on any one of the 16 highlighted process nodes.
08:21 Observe, a reaction line appears between State Transition and 2-Oxoglutarate.
08:29 Similarly, click on ‘Add Reactant’ icon.
08:34 Hover the mouse on Glutamate and click on one of the 16 highlighted process nodes.
08:40 Next, hover the mouse on the State Transition reaction and click on the process node.
08:49 Observe, a reaction line appears between State Transition and Glutamate.
08:55 We now have a complete Catalysis reaction with a Reactant and a Product.
09:01 I will align the reaction to accommodate other components in the process diagram.
09:09 From the toolbar, use the icons: State Transition , Simple Molecule, Generic Protein and Catalysis.
09:18 This is the completed process diagram.
09:22 To view it properly, go to View on the main menu bar and click on Zoom Fit
09:32 You now see the completed Process Diagram
09:36 Let us summarize. In this tutorial, we have learnt: to use Macros,
09:42 move Components on the draw area , connect a reaction line around a species,
09:48 align and extend a reaction line, add a Product and a Reactant.
09:54 For the assignment: Build a process diagram for Methionine Biosynthesis using tools in CellDesigner.

Explore the Macros for GTP/GD. Find out how to create a ’Curve’ reaction line.

10:11 About the Spoken Tutorial project-
10:14 Watch the video at the following link. It summarizes the Spoken Tutorial project.
10:19 If you do not have a good bandwidth, please download and watch it.
10:24 The Spoken Tutorial Project team: conducts- workshops using Spoken tutorials
10:29 and gives certificates for those who pass an online test.
10:34 For more details, please write to contact@spoken-tutorial.org
10:40 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.
10:54 This is Bella Tony from IIT Bombay, signing off.

Thank you for joining.

Contributors and Content Editors

Jyotisolanki, Pratik kamble, Sakinashaikh, Sandhya.np14