CellDesigner/C3/Build-and-Modify-Process-Diagram/English-timed - Revision history

Sandhya.np14 at 10:25, 7 June 2018

2018-06-07T10:25:29Z

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Sandhya.np14 at 06:24, 7 June 2018

2018-06-07T06:24:35Z

Pratik kamble at 10:49, 15 January 2018

2018-01-15T10:49:00Z

Pratik kamble at 10:48, 15 January 2018

2018-01-15T10:48:49Z

Sakinashaikh at 11:53, 15 December 2017

2017-12-15T11:53:36Z

Jyotisolanki at 06:28, 21 November 2017

2017-11-21T06:28:36Z

Jyotisolanki at 06:27, 21 November 2017

2017-11-21T06:27:45Z

Jyotisolanki at 06:26, 21 November 2017

2017-11-21T06:26:06Z

Jyotisolanki: Created page with "'''Title of the Script''': Build and Modify Process Diagram '''Author''': Bella Tony '''Keywords''': Process Diagram, Macros, Alanine Biosythesis, Generic Protein, Aminotra..."

2017-09-22T10:02:03Z

Created page with "'''Title of the Script''': Build and Modify Process Diagram '''Author''': Bella Tony '''Keywords''': Process Diagram, Macros, Alanine Biosythesis, Generic Protein, Aminotra..."

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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
|| '''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 using'''Ubuntu 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''' the 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.

|-
| 09:24
| The''' Spoken Tutorial Project '''Team conducts- Workshops using Spoken tutorials.

|-
| 09:29
| 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.

|}

← Older revision		Revision as of 10:48, 15 January 2018
Line 1:		Line 1:
−	~~'''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

@@ Line 6: / Line 6: @@
 |-
 |  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
-|  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
-|  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
-|  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'''.
 |-

@@ Line 3: / Line 3: @@
 || '''Time'''
 || '''Narration'''
 |-

@@ Line 422: / Line 422: @@
 |-
-|  09:24
+| 10:24
 |  The''' Spoken Tutorial Project '''Team conducts- Workshops using Spoken tutorials.
 |-
-| 09:29
+| 10:29
 | And gives certificates for those who pass an online test.

@@ Line 405: / Line 405: @@
 |-
 |  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
+|  For the assignment:Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner'''
 |-

@@ Line 17: / Line 17: @@
 |-
 | 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
-|  Align and extend a reaction line Add a '''Product''' and a '''Reactant'''
+|  Align and extend a reaction line , Add a '''Product''' and a '''Reactant'''
 |-
@@ Line 377: / Line 377: @@
 |-
 | 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'''
 |-
@@ Line 393: / Line 393: @@
 |-
 |  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
-|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
-|  Align and extend a reaction line  Add a '''Product''' and a '''Reactant'''
+|  Align and extend a reaction line, Add a '''Product''' and a '''Reactant'''
 |-