View source for CellDesigner/C3/Build-and-Modify-Process-Diagram/English-timed


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|| '''Time'''
|| '''Narration'''

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|  00:01
|  Hello everyone. Welcome to this tutorial on''' Build and Modify Process Diagram''' in''' CellDesigner'''.

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| 00:08
|  In this tutorial, we will learn to: use '''Macros''' , move '''Components''' on the '''draw area''' , connect a '''reaction line''' around a '''species''',

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|  00:18
|  align and extend a reaction line , add a '''Product''' and a '''Reactant'''.

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|  00:23
|  For this tutorial, I am using'''Ubuntu Linux OS 14.04''',  '''CellDesigner '''version '''4.3''', '''Java version 1.7'''.

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| 00:35
|  To follow this tutorial, learners should be familiar with: Undergraduate''' Biochemistry.''' '''CellDesigner '''interface.

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| 00:43
|If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website

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|  00:51
|  Let us begin

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|  00:53
|  What you see here is the conventional diagram for '''Alanine Biosynthesis.'''

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|  00:58
|  Now, we’ll use '''CellDesigner''' to create this process diagram.

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|  01:02
|  Open the '''terminal''' by pressing '''Ctrl+Alt+T''' keys simultaneously.

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|  01:09
|  Now type '''./runCellDesigner4.3''' and press '''Enter'''.

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|  01:20
|  CellDesigner window is now open on your terminal

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|  01:24
|  Open a new file by pressing''' CTRL+N''' and name it '''Build''' '''and Modify Process Diagram'''.

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|  01:34
|  Keep the default width and height and click on the '''Ok''' button.

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|   01:39
|  Now let us learn what are ‘'''Macros’'''.

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|  01:42
|  '''Macros''' are frequently used''' Components''' sets that help in drawing the diagrams easily.

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|  01:47
|  On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the draw area.

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| 01:57
|We now have a '''Macros-Catalysis reaction '''on the draw area.

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|  02:02
|  Let’s learn to move all the components to another side of the draw area.

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|  02:08
|  For that click on the ''''Edit'''' menu and then click on ''''Select All'.'''

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| 02:16
|Alternately you may press '''Ctrl + A '''keys.

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| 02:21
|All the '''Components''' are now highlighted. 

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|  02:24
|  Now click anywhere on the highlighted components and drag them to the desired location.

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|  02:30
|  Let’s proceed.

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|  02:32
|  Click anywhere on the draw area to uncheck the highlighted components.

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|  02:37
|  Again on the draw area, right click on the''' Generic Protein S1.'''

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|  02:43
|  Then click on the option ''''Change Identity''''.

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|  02:47
|  In the ''''class'''' box, change the '''Protein''' to''' Simple Molecule.'''

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|  02:53
|  Type the''' Name '''as: '''2-keto-isovalerate'''.

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| 02:58
|And then click on the '''‘Apply’''' button.

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|  03:02
|  In the dialog box ‘'''The Same Species Exists'''’, click '''‘No’.'''

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|  03:10
|  However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.Here, I will click''' ‘No’'''

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| 03:20
|  Observe the''' Generic Protein S1, '''is now a '''simple molecule '''named '''2-keto-isovalerate.'''

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| 03:30
|I will drag the molecule to accomodate the name.

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|  03:34
|  Right-click in the center of the''' end-point,''' '''Generic protein'''-'''S1 '''which is a '''product'''.

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| 03:42
|Change identity to''' Simple Molecule '''and name''' '''it '''Valine.'''

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| 03:50
|  Click on the '''Apply''' button.

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| 03:52
|You have''' Valine''' on the draw area.

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|  03:36
|  Next, rename catalyst''' S2.''' Right-click on it and select '''Edit Protein.'''

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| 04:06
|In the '''‘name’''' field, type '''Aminotransferase.''' 

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| 04:11
|  Click on '''Update''' and close the dialog box.

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| 04:16
|Drag the corner of the molecule to accomodate the name.

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|  04:21
|  Next, let’s change the position of the linked reaction.

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|  04:25
|  Click in the center of the ''''end-point'''' '''species''' i.e.''' Valine '''and drag and drop at the desired location'''.'''

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|  04:33
|  Repeat the same with '''Aminotransferase'''

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|  04:37
|  Observe that the linked reaction follows wherever the ‘'''end-point’ Species '''moves.

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|  04:44
|  We will now learn how to connect a '''reaction line''' around a '''species'''.

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|  04:49
|  A '''Reaction line '''can be connected to any of the 16 connection points around a '''Species'''. 

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| 04:56
|I will show you how to do so.

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| 04:59
|  Open a new window by pressing''' CTRL+N'''.

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| 05:04
|Name this file as''' Connection points.'''

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|  05:08
|  Keep the default width and height and click on '''Ok''' the button.

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|  05:14
|  On the draw area, draw two '''generic proteins '''and name them '''Protein 1 '''and '''Protein 2.'''

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|  05:23
|  In the main menu,click on the icon for '''State Transition'''.

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| 05:28
|Then, on the draw area, hover the mouse on ‘'''start-point'''' '''Species, Protein 1'''.

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|  05:36
|  Observe that all 16 connection points are highlighted in grey color.

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|  05:42
|  Note that when the cursor is pointed to one of these connection points, it will change to blue color.

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|  05:49
|  Let’s click on one of the connection points.

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|  05:53
|  In the same manner, hover the mouse on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''.

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|  06:00
|  Again, as explained above, click on the required connection point.

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|  06:05
|  A '''State Transition '''reaction line is formed between the selected connection points.

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|  06:12
|  Next, we will align the '''Reaction line.'''

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|  06:16
|  Click on the '''State transition reaction line '''between '''Protein 1 '''and '''Protein 2'''

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| 06:21
|  Note that the 2 '''process nodes''' on the '''reaction line''' get highlighted.

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|  06:27
|  If we hover the mouse on either of the 2 '''process nodes''', a ‘'''plus’''' sign appears.

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|  06:34
|  Click on one of the '''process nodes.''' 

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| 06:37
|Now drag and place the pointer on the preferred '''connection point.'''

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|  06:43
|  Click anywhere on the draw area to uncheck the highlighted components.

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|  06:49
|  To extend or stretch the '''reaction line''', first click on it.

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|  06:54
|  Now click on either of the '''process nodes '''located on the '''start-point''' or '''end-point Species'''.

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|  07:01
|  Drag the mouse to stretch the '''reaction line '''till the preferred connection point.

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|  07:07
|  From here on, we will proceed with the Process diagram.

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|  07:12
|  Let us come back to the '''Build''' '''and Modify Process Diagram''' window.

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|  07:16
|  Let’s add a '''Reactant '''and a '''Product''', to the existing reaction.

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|   07:21
|  From the toolbar, click and place 2 '''simple molecules''' on the draw area.

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|   07:27
|  Name them '''Glutamate''' and''' 2-Oxoglutarate'''.

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|   07:36
|  Drag and place them adjacent to the '''Simple molecules:''' '''2-keto-isovalerate '''and '''Valine.'''

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|   07:44
|  As explained earlier, let us align the components on the draw area.

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|  07:49
|  From what was explained earlier, I have now completed aligning the components.

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|   07:55
|  On the toolbar, click on the icon for''' ‘Add Product’.'''

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|   08:00
|  Now hover the mouse on the''' State Transition '''reaction between''' 2-keto-isovalerate '''and '''Valine.'''

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|  08:07
|  Click on the''' '''highlighted '''process node.'''

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|  08:10
|  Next, hover the mouse on '''2-Oxoglutarate.'''

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| 08:17
|Click on any one of the 16 highlighted '''process nodes.'''

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|  08:21
|  Observe, a '''reaction line '''appears between '''State Transition '''and '''2-Oxoglutarate.'''

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|  08:29
|  Similarly, click on '''‘Add Reactant’''' icon.

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|  08:34
|  Hover the mouse on '''Glutamate''' and click on one of the 16 highlighted''' process nodes.'''

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|  08:40
|  Next, hover the mouse on the''' State Transition '''reaction and click on the '''process node.'''

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|  08:49
|  Observe, a '''reaction line '''appears between '''State Transition '''and''' Glutamate'''.

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|  08:55
|  We now have a complete '''Catalysis '''reaction with a '''Reactant''' and a '''Product'''.

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|  09:01
|  I will align the '''reaction''' to accommodate other '''components''' in the process diagram.

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| 09:09
|From the toolbar use the icons: '''State Transition''' , '''Simple Molecule''',  '''Generic Protein''' and '''Catalysis'''

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|  09:18
|  This is the completed process diagram.

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|  09:22
|  To view it properly, go to '''View '''on the main menu bar and click on''' Zoom Fit'''

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| 09:32
|You now see the completed '''Process Diagram'''

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|  09:36
|  Let us summarize. In this tutorial, we have learnt to Use '''Macros'''.
 
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| 09:42
|Move Components on the draw area , Connect a reaction line around a species.

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|  09:48
|  Align and extend a reaction line, Add a '''Product''' and a '''Reactant'''

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|  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

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|  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 [mailto:contact@spoken-tutorial.org 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.

|}