Difference between revisions of "CellDesigner/C2/Build-and-Modify-Process-Diagram/English"

Latest revision as of 16:38, 21 October 2015

Title of the Script: Build and Modify Process Diagram

Author: Bella Tony

Keywords: Process Diagram, Macros, Alanine Biosythesis, Generic Protein, Aminotransferase

Visual Cue	Narration
Slide Number 1 Title Slide	Hello everyone. Welcome to this tutorial on ‘Build and Modify Process Diagram in CellDesigner’.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to: Use Macros Move Components on the draw area Connect a reaction line around a species
Slide Number 3 Learning Objectives contd. ...	Align and extend a reaction line Add a Product and a Reactant
Slide Number 4 System Requirement	For this tutorial, I am using Ubuntu Linux OS 14.04 CellDesigner version 4.3 Java version 1.7
Slide Number 5 Pre-requisites	To follow this tutorial, learners should be familiar with: Undergraduate Biochemistry. CellDesigner interface. If not, for relevant CellDesigner tutorials, please visit the Spoken Tutorial website
	Let us begin
Slide 6 Conventional diagram for Alanine biosynthesis	What you see here is the conventional diagram for Alanine Biosynthesis.
	Now, we’ll use CellDesigner to create this process diagram.
Open terminal by pressing Ctrl+Alt+T keys	Open the terminal by pressing Ctrl+Alt+T keys simultaneously.
Type ./runCellDesigner4.3 >> press Enter.	Now type ./runCellDesigner4.3 and press Enter.
	CellDesigner window is now open on your terminal
Press CTRL+N>>name it Build and Modify Process Diagram.	Open a new file by pressing CTRL+N and name it Build and Modify Process Diagram.
Click Ok.	Keep the default width and height and click on the Ok button.
	Now let us learn what are ‘Macros’.
	Macros are frequently used Components sets that help in drawing the diagrams easily.
Cursor on the toolbar >> Point towards Macros for Catalysis >> click on it>>place anywhere on draw area.	On the toolbar, click on the Macros icon for Catalysis and click on the draw area. We now have a Macros-Catalysis reaction on the draw area.
	Let’s learn to move all the components to another side of the draw area.
On the main menu bar>>Click on Edit>> Scroll down and click on Select All'.	For that click on the 'Edit' menu and then click on 'Select All'. Alternately you may press Ctrl + A keys. All the Components are now highlighted.
Click on highlighted component >> without releasing the mouse button, drag the components to the desired place	Now click anywhere on the highlighted components and drag them to the desired location.
	Let’s proceed.
Click anywhere on the draw area	Click anywhere on the draw area to uncheck the highlighted components.
Right click on the Generic Protein S1	Again on the draw area, right click on the Generic Protein S1.
Click 'Change Identity'	Then click on the option 'Change Identity'.
In the dialog box 'Change identity of the species>> go to class box>> change Protein to Simple Molecule.	In the 'class' box, change the Protein to Simple Molecule.
Type Name as: 2-keto-isovalerate >> Click ‘Apply’.	Type the Name as: 2-keto-isovalerate. And then click on the ‘Apply’ button.
In the dialog box ‘The Same Species Exists’ >>Click on the option ‘No’.	In the dialog box ‘The Same Species Exists’, click ‘No’.
Point to the button "Yes"	However if you want to reflect the change to all components of the species, click ‘Yes’. Here, I will click ‘No’
Cursor on 2-keto-isovalerate.	Observe the Generic Protein S1, is now a simple molecule named 2-keto-isovalerate. I will drag the molecule to accomodate the name.
Right-click on Generic protein-S1 which is a product >> Change identity to Simple Molecule and Name it Valine.	Right-click in the center of the end-point, Generic protein-S1 which is a product. Change identity to Simple Molecule and name it Valine.
Click on the Apply button.	Click on the Apply button. You have Valine on the draw area.
Right-click and select Edit Protein. In the ‘name’ field, type Aminotransferase	Next, rename catalyst S2. Right-click on it and select Edit Protein. In the ‘name’ field, type Aminotransferase.
Click on Update>> close the dialog box. Drag the corner of the molecule to accomodate the name.	Click on Update and close the dialog box. Drag the corner of the molecule to accomodate the name.
	Next, let’s change the position of the linked reaction.
Click on Valine >> Without releasing the mouse, drag the Species.	Click in the center of the 'end-point' species i.e. Valine and drag and drop at the desired location.
	Repeat the same with Aminotransferase
	Observe that the linked reaction follows wherever the ‘end-point’ Species moves.
How to connect a reaction line around a species.	We will now learn how to connect a reaction line around a species.
	A Reaction line can be connected to any of the 16 connection points around a Species. I will show you how to do so.
Click on File >> New Type the filename as ‘Connection point of Species’.	Open a new window by pressing CTRL+N. Name this file as Connection points.
Click Ok.	Keep the default width and height and click on Ok the button.
<<PAUSE RECORDING>> On the toolbar >>Click on the Generic protein >> Click again on the draw area >> name it Protein 1 Repeat the above and name it Protein 2 <<RESUME RECORDING>>	On the draw area, draw two generic proteins and name them Protein 1 and Protein 2.
Cursor on the toolbar >>Click on the State transition>> hover the mouse on Protein 1>>	In the main menu,click on the icon for State Transition. Then, on the draw area, hover the mouse on ‘start-point' Species, Protein 1.
Mouse hovering	Observe that all 16 connection points are highlighted in grey color.
Point the cursor to one connection point.	Note that when the cursor is pointed to one of these connection points, it will change to blue color.
Click on any one of the connection points.	Let’s click on one of the connection points.
Hover the mouse on Protein 2	In the same manner, hover the mouse on the ‘end-point' Species i.e. Protein 2.
Click on any one of the connection points.	Again, as explained above, click on the required connection point.
Cursor on State Transition reaction line between the selected connection points.	A State Transition reaction line is formed between the selected connection points.
	Next, we will align the Reaction line.
Click on the State transition reaction line between Protein 1 and Protein 2	Click on the State transition reaction line between Protein 1 and Protein 2
Point the cursor on the 2 process nodes on the reaction line	Note that the 2 process nodes on the reaction line get highlighted.
One by one, hover the mouse on 2 process nodes of start point and end point of the species	If we hover the mouse on either of the 2 process nodes, a ‘plus’ sign appears.
Click on the process node>> Drag and place the reaction line on the required connection point.	Click on one of the process nodes. Now drag and place the pointer on the preferred connection point.
Click anywhere on the draw area to uncheck the highlighted components.	Click anywhere on the draw area to uncheck the highlighted components.
Click on the reaction line	To extend or stretch the reaction line, first click on it.
Click on either of the process nodes located on the start-point or end-point Species.	Now click on either of the process nodes located on the start-point or end-point Species.
Drag the mouse to stretch the reaction line till the preferred connection point.	Drag the mouse to stretch the reaction line till the preferred connection point.
	From here on, we will proceed with the Process diagram.
Click on the Build and Modify Process Diagram window.	Let us come back to the Build and Modify Process Diagram window.
	Let’s add a Reactant and a Product, to the existing reaction.
From the toolbar, click and place 2 simple molecules on the draw area.	From the toolbar, click and place 2 simple molecules on the draw area.
Name them Glutamate and 2-Oxoglutarate.	Name them Glutamate and 2-Oxoglutarate.
Drag and place them adjacent to the Simple molecules: 2-keto-isovalerate and Valine.	Drag and place them adjacent to the Simple molecules: 2-keto-isovalerate and Valine.
Cursor on the draw area. <<PAUSE RECORDING>>	As explained earlier, let us align the components on the draw area.
<<RESUME RECORDING>>	From what was explained earlier, I have now completed aligning the components.
On the toolbar, click on the icon for ‘Add Product’.	On the toolbar, click on the icon for ‘Add Product’.
Hover the mouse on the State Transition reaction between 2-keto-isovalerate and Valine.	Now hover the mouse on the State Transition reaction between 2-keto-isovalerate and Valine.
Click on the process node	Click on the highlighted process node.
Next, hover the mouse on 2-Oxoglutarate >> Click on any of the 16 highlighted process nodes.	Next, hover the mouse on 2-Oxoglutarate. Click on any one of the 16 highlighted process nodes.
A reaction line appears between State Transition and 2-Oxoglutarate	Observe, a reaction line appears between State Transition and 2-Oxoglutarate.
Click on ‘Add Reactant’ icon	Similarly, click on ‘Add Reactant’ icon.
On the toolbar>> click on ‘Add Reactant’ >> Hover the mouse on Glutamate>>click on any of the 16 highlighted process nodes.	Hover the mouse on Glutamate and click on one of the 16 highlighted process nodes.
Hover the mouse on the State Transition reaction >> click on the process node.	Next, hover the mouse on the State Transition reaction and click on the process node.
Cursor on reaction line between State Transition and Glutamate.	Observe, a reaction line appears between State Transition and Glutamate.
Cursor on Catalysis reaction	We now have a complete Catalysis reaction with a Reactant and a Product.
Cursor on toolbar	I will align the reaction to accommodate other components in the process diagram. From the toolbar use the icons: State Transition Simple Molecule Generic Protein and Catalysis
Cursor on completed process diagram.	This is the completed process diagram.
Go to View>> click on Zoom Fit	To view it properly, go to View on the main menu bar and click on Zoom Fit You now see the completed Process Diagram
SlideSummary	Let us summarize. In this tutorial, we will learn to: Use Macros Move Components on the draw area Connect a reaction line around a species
	We also learnt to: Align and extend a reaction line Add a Product and a Reactant
Assignment	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
Acknowledgement	About the Spoken Tutorial project- Watch the video at the following link It summarizes the Spoken Tutorial project. If you do not have a good bandwidth please download and watch it.
Acknowledgement	The Spoken Tutorial Project Team conducts- Workshops using Spoken tutorials. And gives certificates for those who pass an online test. For more details, please write to contact@spoken-tutorial.org
Acknowledgement	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.
	This is Bella Tony from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, PoojaMoolya

Difference between revisions of "CellDesigner/C2/Build-and-Modify-Process-Diagram/English"

Latest revision as of 16:38, 21 October 2015

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@@ 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
 {| style="border-spacing:0;"
@@ Line 6: / Line 12: @@
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 1'''
 '''Title Slide'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Hello everyone.
@@ Line 18: / Line 23: @@
 | style="border:0.75pt solid #000001;padding:0.071cm;"| In this tutorial, we will learn to:
-* Use Macros
+* Use '''Macros'''
 * Move Components on the draw area
 * Connect a reaction line around a species
@@ Line 26: / Line 31: @@
 '''Learning Objectives contd. ...'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We will also learn to:
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
 * Align and extend a reaction line
-* Add a Product and a Reactant
+* Add a '''Product''' and a '''Reactant'''
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 4'''
 '''System Requirement'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| For this tutorial, I am using
@@ Line 43: / Line 47: @@
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 5'''
 '''Pre-requisites'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| To follow this tutorial, learners should be familiar with:
@@ Line 57: / Line 60: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide 6'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+'''Slide 6'''
 Conventional diagram for Alanine biosynthesis
 | style="border:0.75pt solid #000001;padding:0.071cm;"| What you see here is the conventional diagram for '''Alanine Biosynthesis.'''
@@ Line 67: / Line 70: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Open terminal by pressing '''Ctrl+Alt+T''' keys
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Open terminal by pressing '''Ctrl+Alt+T''' keys
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Open the '''terminal''' by pressing '''Ctrl+Alt+T''' keys simultaneously.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Type '''./runCellDesigner4.3''' >> press '''Enter'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Type '''./runCellDesigner4.3''' >> press '''Enter'''.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Now type '''./runCellDesigner4.3''' and press '''Enter'''.
@@ Line 79: / Line 84: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Press''' CTRL+N'''>>name it '''Build''' '''and Modify Process Diagram'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Press''' CTRL+N'''>>name it '''Build''' '''and Modify Process Diagram'''.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Open a new file by pressing''' CTRL+N''' and name it '''Build''' '''and Modify Process Diagram'''.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click '''Ok'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Keep the default width and height and click on '''Ok''' button.
+Click '''Ok'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Keep the default width and height and click on the '''Ok''' button.
 |-
@@ Line 98: / Line 103: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on the toolbar >> Point towards Macros for '''Catalysis''' >> click on it>>place anywhere on draw area.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Cursor on the toolbar >> Point towards Macros for '''Catalysis''' >>
+click on it>>place anywhere on draw area.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the draw area.
 We now have a '''Macros-Catalysis reaction '''on the draw area.
@@ Line 112: / Line 116: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the main menu bar>>Click on''' Edit'''>>
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-Scroll down and click on''' Select All'.'''
+On the main menu bar>>Click on''' Edit'''>>
-| style="border:0.75pt solid #000001;padding:0.071cm;"| For that click on the ''''Edit'''' menu and then click on ''''Select All'.'''
-Alternately you may press '''Ctrl + A '''keys.
+Scroll down and click on''' Select All'.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+For that click on the ''''Edit'''' menu and then click on ''''Select All'.'''
+Alternately you may press '''Ctrl + A '''keys.
 All the '''Components''' are now highlighted.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on highlighted component >> without releasing the mouse button, drag the components to the desired place
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click on highlighted component >> without releasing the mouse button,
+drag the components to the desired place
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Now click anywhere on the highlighted components and drag them to the desired location.
@@ Line 132: / Line 142: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click anywhere on the draw area
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area to uncheck the highlighted components.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Right click on the''' Generic Protein S1'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Right click on the''' Generic Protein S1'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Again on the draw area, right click on the''' Generic Protein S1.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click ''''Change Identity''''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click ''''Change Identity''''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Then click on the option ''''Change Identity''''.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialog box ''''Change identity of the species'''>> go to '''class''' box>> change '''Protein''' to''' Simple Molecule'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+In the dialog box ''''Change identity of the species'''>> go to '''class''' box>>
+change '''Protein''' to''' Simple Molecule'''.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| In the ''''class'''' box, change the '''Protein''' to''' Simple Molecule.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Type''' Name '''as: '''2-keto-isovalerate''' >>''' '''Click''' ‘Apply’'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Type the''' Name '''as: '''2-keto-isovalerate''' and then''' '''click''' '''on the '''‘Apply’''' button.
-|-
+Type''' Name '''as: '''2-keto-isovalerate''' >>
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialog box ‘'''The Same Species Exists'''’ >>Click on the option '''‘No’.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialogue box ‘'''The Same Species Exists'''’ dialog box click '''‘No’.'''
+''' '''Click''' ‘Apply’'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Type the''' Name '''as: '''2-keto-isovalerate'''.
+And then click on the '''‘Apply’''' button.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.
+In the dialog box ‘'''The Same Species Exists'''’ >>Click on the option '''‘No’.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialog box ‘'''The Same Species Exists'''’, click '''‘No’.'''
+|-
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Point to the button '''"Yes"'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.
 Here, I will click''' ‘No’'''
@@ Line 171: / Line 192: @@
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''2-keto-isovalerate.'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Observe the''' Generic Protein S1, '''is now a '''simple molecule '''named '''2-keto-isovalerate.'''
 I will drag the molecule to accomodate the name.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Right-click on '''Generic protein'''-'''S1 '''which is a '''product '''>> Change identity to''' Simple Molecule '''and '''Name '''it '''Valine.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Right-click on '''Generic protein'''-'''S1 '''which is a '''product '''>>
+Change identity to''' Simple Molecule '''and '''Name '''it '''Valine.'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Right-click in the center of the''' end-point,''' '''Generic protein'''-'''S1 '''which is a '''product'''.
 Change identity to''' Simple Molecule '''and name''' '''it '''Valine.'''
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' Apply '''button.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the Apply button.
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''Apply''' button.
@@ Line 194: / Line 212: @@
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Right-click and select '''Edit Protein.'''
 In the ‘name’ field, type '''Aminotransferase'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Next, rename catalyst''' S2.'''
+Right-click on it and select '''Edit Protein.'''
-Right-click on it and select '''Edit Protein.'''
+In the '''‘name’''' field, type '''Aminotransferase.'''
-In the '''‘Name’''' field, type '''Aminotransferase.'''
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''Update>>''' close the dialog box.
 Drag the corner of the molecule to accomodate the name.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''Update''' and close the dialog box.
 Drag the corner of the molecule to accomodate the name.
 |-
@@ Line 224: / Line 230: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''Valine''' >> Without releasing the mouse, drag the '''Species.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click on '''Valine''' >> Without releasing the mouse,
+drag the '''Species.'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click in the center of the ''''end-point'''' '''species''' i.e.''' Valine '''and drag and drop at the desired location'''.'''
@@ Line 236: / Line 246: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| How to connect a reaction line around a species.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+How to connect a reaction line around a species.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| We will now learn how to connect a '''reaction line''' around a '''species'''.
@@ Line 242: / Line 254: @@
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
 | style="border:0.75pt solid #000001;padding:0.071cm;"| A '''Reaction line '''can be connected to any of the 16 connection points around a '''Species'''.
 I will show you how to do so.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click on''' File''' >> '''New'''
 Type the filename as''' ‘Connection point of Species'''’.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Open a new window by pressing''' CTRL+N'''.
 Name this file as''' Connection points.'''
@@ Line 265: / Line 268: @@
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| '''<<PAUSE RECORDING>>'''
+On the toolbar >>Click on the '''Generic protein '''>>
-On the toolbar >>Click on the '''Generic protein '''>> Click again on the draw area >> name it '''Protein 1'''
+Click again on the draw area >> name it '''Protein 1'''
 Repeat the above and name it '''Protein 2'''
 '''<<RESUME RECORDING>>'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the draw area, draw two '''generic proteins '''and name them '''Protein 1 '''and '''Protein 2.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+On the draw area, draw two '''generic proteins '''and name them '''Protein 1 '''and '''Protein 2.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on the toolbar >>Click on the '''State transition>>''' hover the mouse on''' Protein 1'''>>
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the main menu,click on the icon for '''State Transition'''.
+Cursor on the toolbar >>Click on the '''State transition>>'''
+hover the mouse on''' Protein 1'''>>
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+In the main menu,click on the icon for '''State Transition'''.
@@ Line 283: / Line 292: @@
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Mouse hovering
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Observe that all 16 connection points are highlighted in grey color.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Point the cursor to one connection point.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Point the cursor to one connection point.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Note that when the cursor is pointed to one of these connection points, it will change to blue color.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on any one of the connection points.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click on any one of the connection points.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Let’s click on one of the connection points.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on '''Protein 2'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Hover the mouse on '''Protein 2'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| In the same manner, hover the mouse on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on any one of the connection points.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click on any one of the connection points.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Again, as explained above, click on the required connection point.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''State Transition '''reaction line between the selected connection points.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Cursor on '''State Transition '''reaction line between the selected connection points.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| A '''State Transition '''reaction line is formed between the selected connection points.
@@ Line 316: / Line 329: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''State transition''' reaction line between '''Protein 1 '''and '''Protein 2'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click on the '''State transition''' reaction line between
+'''Protein 1 '''and '''Protein 2'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''State transition reaction line '''between '''Protein 1 '''and '''Protein 2'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Point the cursor on the 2 '''process nodes''' on the '''reaction line'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Point the cursor on the 2 '''process nodes''' on the '''reaction line'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Note that the 2 '''process nodes''' on the '''reaction line''' get highlighted.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| One by one, hover the mouse on 2 process nodes of '''start point '''and''' end point '''of the species
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+One by one, hover the mouse on 2 process nodes of
+'''start point '''and''' end point '''of the species
 | style="border:0.75pt solid #000001;padding:0.071cm;"| If we hover the mouse on either of the 2 '''process nodes''', a ‘'''plus’''' sign appears.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''process node'''>> Drag and place the reaction line on the required '''connection point.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on one of the '''process nodes.'''
+Click on the '''process node'''>> Drag and place the
+reaction line on the required '''connection point.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on one of the '''process nodes.'''
 Now drag and place the pointer on the preferred '''connection point.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area to uncheck the highlighted components.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click anywhere on the draw area to uncheck the
+highlighted components.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area to uncheck the highlighted components.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the r'''eaction line'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| To extend or stretch the '''reaction line.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| To extend or stretch the '''reaction line''', first click on it.
-, first click on it.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on either of the process nodes located on the '''start-point''' or '''end-point''' '''Species.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now click on either of the '''process nodes '''located on the '''start-point''' or '''end-point''' '''Species'''.
+Click on either of the process nodes located
+on the '''start-point''' or '''end-point Species.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Now click on either of the '''process nodes '''located on the '''start-point''' or '''end-point Species'''.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Drag the mouse to stretch the '''reaction line '''till the preferred connection point.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Drag the mouse to stretch the '''reaction line '''till the preferred connection point.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Drag the mouse to stretch the '''reaction line '''till the preferred connection point.
@@ Line 357: / Line 390: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' Build''' '''and Modify Process Diagram''' window.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Click on the''' Build''' '''and Modify Process Diagram''' window.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Let us come back to the '''Build''' '''and Modify Process Diagram''' window.
@@ Line 365: / Line 400: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| From the toolbar, click and place 2 '''simple molecules''' on the draw area.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+From the toolbar, click and place 2 '''simple molecules''' on the draw area.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| From the toolbar, click and place 2 '''simple molecules''' on the draw area.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Name them '''Glutamate''' and''' 2-Oxoglutarate'''.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Name them '''Glutamate''' and''' 2-Oxoglutarate'''.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Name them '''Glutamate''' and''' 2-Oxoglutarate'''.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Drag and place them adjacent to the '''Simple molecules:''' '''2-keto-isovalerate '''and '''Valine.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Drag and place them adjacent to the '''Simple molecules:
+''' '''2-keto-isovalerate '''and '''Valine.'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Drag and place them adjacent to the '''Simple molecules:''' '''2-keto-isovalerate '''and '''Valine.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on the draw area.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Cursor on the draw area.
 '''<<PAUSE RECORDING>>'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| As explained earlier, let us align the components on the draw area.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''<<RESUME RECORDING>>'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+ '''<<RESUME RECORDING>>'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| From what was explained earlier, I have now completed aligning the components.
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar, click on the icon for''' ‘Add Product’.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+On the toolbar, click on the icon for''' ‘Add Product’.'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar, click on the icon for''' ‘Add Product’.'''
+|-
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Hover the mouse on the''' State Transition '''reaction
+between''' 2-keto-isovalerate '''and '''Valine.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on the''' State Transition '''reaction between''' 2-keto-isovalerate '''and '''Valine.'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Now hover the mouse on the''' State Transition '''reaction between''' 2-keto-isovalerate '''and '''Valine.'''
@@ Line 405: / Line 451: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on '''2-Oxoglutarate >> '''Click on any of the 16 highlighted process nodes.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+Next, hover the mouse on '''2-Oxoglutarate >> '''Click on any of the 16 highlighted process nodes.
 | style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on '''2-Oxoglutarate.'''
 Click on any one of the 16 highlighted '''process nodes.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| A '''reaction line '''appears between '''State Transition '''and '''2-Oxoglutarate'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe, a '''reaction line '''appears between '''State Transition '''and '''2-Oxoglutarate.'''
-|-
+A '''reaction line '''appears between '''State Transition
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''‘Add Reactant’''' icon
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Similarly, click on '''‘Add Reactant’''' icon.
-|-
+'''and '''2-Oxoglutarate'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar>> click on '''‘Add Reactant’ >> '''Hover the mouse on '''Glutamate'''>>click on any of the 16 highlighted process nodes.
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe, a '''reaction line '''appears between '''State Transition '''and '''2-Oxoglutarate.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on '''Glutamate''' and click on one of the 16 highlighted''' process nodes.'''
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on the''' State Transition '''reaction >> click on the process node.
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on the''' State Transition '''reaction and click on the '''process node.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''reaction line '''between '''State Transition '''and''' Glutamate'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe, a '''reaction line '''appears between '''State Transition '''and''' Glutamate'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''Catalysis '''reaction
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We now have a complete '''Catalysis '''reaction with a '''Reactant''' and a '''Product'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on toolbar
-| style="border:0.75pt solid #000001;padding:0.071cm;"| I will align the '''reaction''' to accommodate other '''components''' in the process diagram.
-From the toolbar use the icons:
-* State Transition
-* Simple Molecule
-* Generic Protein and
-* Catalysis
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on completed process diagram.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| This is the completed process diagram.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Go to '''View'''>> click on '''Zoom Fit'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| To view it properly, go to '''View '''on the main menu bar and click on''' Zoom Fit'''
-You now see the completed '''Process Diagram'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide'''
-Summary
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let us summarize.
-In this tutorial, we will learn to:
-* Use Macros
-* Move Components on the draw area
-* Connect a reaction line around a species
+Click on '''‘Add Reactant’''' icon
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Similarly, click on '''‘Add Reactant’''' icon.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We also learnt to:
-* Align and extend a reaction line
-* Add a Product and a Reactant
+On the toolbar>> click on '''‘Add Reactant’ >> '''Hover the mouse on
+'''Glutamate'''>>click on any of the 16 highlighted process nodes.
-|-
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on '''Glutamate''' and click on one of the 16 highlighted''' process nodes.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Acknowledgement'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| About the Spoken Tutorial project-
-* Watch the video at the following link
-* It summarizes the Spoken Tutorial project.
-* If you do not have a good bandwidth please download and watch it.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Acknowledgement'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| The''' Spoken Tutorial Project '''Team conducts-
-* Workshops using Spoken tutorials.
-* And gives certificates for those who pass an online test.
-* For more details, please write to [mailto:contact@spoken-tutorial.org contact@spoken-tutorial.org]
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Acknowledgement'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Spoken Tutorial Project is a part of '''Talk to a Teacher project.'''
-{| style="border-spacing:0;"
-| style="border:0.75pt solid #000001;padding:0.071cm;"| <center>'''Visual Cue'''</center>
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Narration'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 1'''
-'''Title Slide'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hello everyone.
-Welcome to this tutorial on''' ‘Build''' '''and Modify Process Diagram''' in''' CellDesigner’'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 2'''
-'''Learning Objectives'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In this tutorial, we will learn to:
-* Use Macros
-* Move Components on the draw area
-* Connect a reaction line around a species
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 3'''
-'''Learning Objectives contd. ...'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We will also learn to:
-* Align and extend a reaction line
-* Add a Product and a Reactant
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 4'''
-'''System Requirement'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| For this tutorial, I am using
-* '''Ubuntu Linux OS 14.04'''
-* '''CellDesigner '''version '''4.3'''
-* '''Java version 1.7'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide Number 5'''
-'''Pre-requisites'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| To follow this tutorial, learners should be familiar with:
-* Undergraduate''' Biochemistry.'''
-* '''CellDesigner '''interface.
-If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let us begin
-|-
+Hover the mouse on the''' State Transition '''reaction >> click on the process node.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide 6'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on the''' State Transition '''reaction and click on the '''process node.'''
-Conventional diagram for Alanine biosynthesis
-| style="border:0.75pt solid #000001;padding:0.071cm;"| What you see here is the conventional diagram for '''Alanine Biosynthesis.'''
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now, we’ll use '''CellDesigner''' to create this process diagram.
-|-
+Cursor on '''reaction line '''between
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
-Open terminal by pressing '''Ctrl+Alt+T''' keys
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Open the '''terminal''' by pressing '''Ctrl+Alt+T''' keys simultaneously.
-|-
+'''State Transition '''and''' Glutamate'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe, a '''reaction line '''appears between '''State Transition '''and''' Glutamate'''.
-Type '''./runCellDesigner4.3''' >> press '''Enter'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now type '''./runCellDesigner4.3''' and press '''Enter'''.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| CellDesigner window is now open on your terminal
-|-
+Cursor on '''Catalysis '''reaction
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
+| style="border:0.75pt solid #000001;padding:0.071cm;"| We now have a complete '''Catalysis '''reaction with a '''Reactant''' and a '''Product'''.
-Press''' CTRL+N'''>>name it '''Build''' '''and Modify Process Diagram'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Open a new file by pressing''' CTRL+N''' and name it '''Build''' '''and Modify Process Diagram'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click '''Ok'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Keep the default width and height and click on '''Ok''' button.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now let us learn what are ‘'''Macros’'''.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Macros''' are frequently used''' Components''' sets that help in drawing the diagrams easily.
-|-
+Cursor on toolbar
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on the toolbar >> Point towards Macros for '''Catalysis''' >> click on it>>place anywhere on draw area.
+| style="border:0.75pt solid #000001;padding:0.071cm;"| I will align the '''reaction''' to accommodate other '''components''' in the process diagram.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the draw area.
+From the toolbar use the icons:
-We now have a '''Macros-Catalysis reaction '''on the draw area.
+* '''State Transition'''
+* '''Simple Molecule'''
+* '''Generic Protein''' and
+* '''Catalysis'''
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let’s learn to move all the components to another side of the draw area.
-|-
+Cursor on completed process diagram.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the main menu bar>>Click on''' Edit'''>>
+| style="border:0.75pt solid #000001;padding:0.071cm;"| This is the completed process diagram.
-Scroll down and click on''' Select All'.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| For that click on the ''''Edit'''' menu and then click on ''''Select All'.'''
-Alternately you may press '''Ctrl + A '''keys.
-All the '''Components''' are now highlighted.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on highlighted component >> without releasing the mouse button, drag the components to the desired place
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now click anywhere on the highlighted components and drag them to the desired location.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let’s proceed.
-|-
+Go to '''View'''>> click on '''Zoom Fit'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area
+| style="border:0.75pt solid #000001;padding:0.071cm;"| To view it properly, go to '''View '''on the main menu bar and click on''' Zoom Fit'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area to uncheck the highlighted components.
+You now see the completed '''Process Diagram'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Right click on the''' Generic Protein S1'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Again on the draw area, right click on the''' Generic Protein S1.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click ''''Change Identity''''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Then click on the option ''''Change Identity''''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialog box ''''Change identity of the species'''>> go to '''class''' box>> change '''Protein''' to''' Simple Molecule'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the ''''class'''' box, change the '''Protein''' to''' Simple Molecule.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Type''' Name '''as: '''2-keto-isovalerate''' >>''' '''Click''' ‘Apply’'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Type the''' Name '''as: '''2-keto-isovalerate''' and then''' '''click''' '''on the '''‘Apply’''' button.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialog box ‘'''The Same Species Exists'''’ >>Click on the option '''‘No’.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialogue box ‘'''The Same Species Exists'''’ dialog box click '''‘No’.'''
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.
-Here, I will click''' ‘No’'''
-|-
+'''Slide'''Summary
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''2-keto-isovalerate.'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"| Let us summarize.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe the''' Generic Protein S1, '''is now a '''simple molecule '''named '''2-keto-isovalerate.'''
-I will drag the molecule to accomodate the name.
-|-
+In this tutorial, we will learn to:
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Right-click on '''Generic protein'''-'''S1 '''which is a '''product '''>> Change identity to''' Simple Molecule '''and '''Name '''it '''Valine.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Right-click in the center of the''' end-point,''' '''Generic protein'''-'''S1 '''which is a '''product'''.
-Change identity to''' Simple Molecule '''and name''' '''it '''Valine.'''
-|-
+* Use '''Macros'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' Apply '''button.
+* Move Components on the draw area
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the Apply button.
+* Connect a reaction line around a species
-You have''' Valine''' on the draw area.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Right-click and select '''Edit Protein.'''
-In the ‘name’ field, type '''Aminotransferase'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, rename catalyst''' S2.'''
-Right-click on it and select '''Edit Protein.'''
-In the '''‘Name’''' field, type '''Aminotransferase.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''Update>>''' close the dialog box.
-Drag the corner of the molecule to accomodate the name.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''Update''' and close the dialog box.
-Drag the corner of the molecule to accomodate the name.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, let’s change the position of the linked reaction.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''Valine''' >> Without releasing the mouse, drag the '''Species.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click in the center of the ''''end-point'''' '''species''' i.e.''' Valine '''and drag and drop at the desired location'''.'''
-|-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Repeat the same with '''Aminotransferase'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe that the linked reaction follows wherever the ‘'''end-point’ Species '''moves.
-|-
+We also learnt to:
-| style="border:0.75pt solid #000001;padding:0.071cm;"| How to connect a reaction line around a species.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We will now learn how to connect a '''reaction line''' around a '''species'''.
-|-
+* Align and extend a reaction line
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
+* Add a '''Product''' and a '''Reactant'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| A '''Reaction line '''can be connected to any of the 16 connection points around a '''Species'''.
-I will show you how to do so.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on''' File''' >> '''New'''
-Type the filename as''' ‘Connection point of Species'''’.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Open a new window by pressing''' CTRL+N'''.
-Name this file as''' Connection points.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click '''Ok'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Keep the default width and height and click on '''Ok''' the button.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''<<PAUSE RECORDING>>'''
-On the toolbar >>Click on the '''Generic protein '''>> Click again on the draw area >> name it '''Protein 1'''
-Repeat the above and name it '''Protein 2'''
-'''<<RESUME RECORDING>>'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the draw area, draw two '''generic proteins '''and name them '''Protein 1 '''and '''Protein 2.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on the toolbar >>Click on the '''State transition>>''' hover the mouse on''' Protein 1'''>>
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the main menu,click on the icon for '''State Transition'''.
-Then, on the draw area, hover the mouse on ‘'''start-point'''' '''Species, Protein 1'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Mouse hovering
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe that all 16 connection points are highlighted in grey color.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Point the cursor to one connection point.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Note that when the cursor is pointed to one of these connection points, it will change to blue color.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on any one of the connection points.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let’s click on one of the connection points.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on '''Protein 2'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| In the same manner, hover the mouse on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on any one of the connection points.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Again, as explained above, click on the required connection point.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''State Transition '''reaction line between the selected connection points.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| A '''State Transition '''reaction line is formed between the selected connection points.
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, we will align the '''Reaction line.'''
-|-
+'''Assignment'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''State transition''' reaction line between '''Protein 1 '''and '''Protein 2'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''State transition reaction line '''between '''Protein 1 '''and '''Protein 2'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Point the cursor on the 2 '''process nodes''' on the '''reaction line'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Note that the 2 '''process nodes''' on the '''reaction line''' get highlighted.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| One by one, hover the mouse on 2 process nodes of '''start point '''and''' end point '''of the species
-| style="border:0.75pt solid #000001;padding:0.071cm;"| If we hover the mouse on either of the 2 '''process nodes''', a ‘'''plus’''' sign appears.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''process node'''>> Drag and place the reaction line on the required '''connection point.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on one of the '''process nodes.'''
-Now drag and place the pointer on the preferred '''connection point.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area to uncheck the highlighted components.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click anywhere on the draw area to uncheck the highlighted components.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the r'''eaction line'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| To extend or stretch the '''reaction line.'''
-, first click on it.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on either of the process nodes located on the '''start-point''' or '''end-point''' '''Species.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now click on either of the '''process nodes '''located on the '''start-point''' or '''end-point''' '''Species'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Drag the mouse to stretch the '''reaction line '''till the preferred connection point.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Drag the mouse to stretch the '''reaction line '''till the preferred connection point.
-|-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| From here on, we will proceed with the Process diagram.
+For the assignment:
-|-
+* Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' Build''' '''and Modify Process Diagram''' window.
+*# Explore the '''Macros''' for '''GTP/GD'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let us come back to the '''Build''' '''and Modify Process Diagram''' window.
+*# Find out how to create a ’Curve’ reaction line
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let’s add a '''Reactant '''and a '''Product''', to the existing reaction.
-|-
+'''Acknowledgement'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| From the toolbar, click and place 2 '''simple molecules''' on the draw area.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| From the toolbar, click and place 2 '''simple molecules''' on the draw area.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Name them '''Glutamate''' and''' 2-Oxoglutarate'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Name them '''Glutamate''' and''' 2-Oxoglutarate'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Drag and place them adjacent to the '''Simple molecules:''' '''2-keto-isovalerate '''and '''Valine.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Drag and place them adjacent to the '''Simple molecules:''' '''2-keto-isovalerate '''and '''Valine.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on the draw area.
-'''<<PAUSE RECORDING>>'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| As explained earlier, let us align the components on the draw area.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''<<RESUME RECORDING>>'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| From what was explained earlier, I have now completed aligning the components.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar, click on the icon for''' ‘Add Product’.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar, click on the icon for''' ‘Add Product’.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on the''' State Transition '''reaction between''' 2-keto-isovalerate '''and '''Valine.'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Now hover the mouse on the''' State Transition '''reaction between''' 2-keto-isovalerate '''and '''Valine.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''process node'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' '''highlighted '''process node.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on '''2-Oxoglutarate >> '''Click on any of the 16 highlighted process nodes.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on '''2-Oxoglutarate.'''
-Click on any one of the 16 highlighted '''process nodes.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| A '''reaction line '''appears between '''State Transition '''and '''2-Oxoglutarate'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe, a '''reaction line '''appears between '''State Transition '''and '''2-Oxoglutarate.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on '''‘Add Reactant’''' icon
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Similarly, click on '''‘Add Reactant’''' icon.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| On the toolbar>> click on '''‘Add Reactant’ >> '''Hover the mouse on '''Glutamate'''>>click on any of the 16 highlighted process nodes.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on '''Glutamate''' and click on one of the 16 highlighted''' process nodes.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Hover the mouse on the''' State Transition '''reaction >> click on the process node.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, hover the mouse on the''' State Transition '''reaction and click on the '''process node.'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''reaction line '''between '''State Transition '''and''' Glutamate'''.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Observe, a '''reaction line '''appears between '''State Transition '''and''' Glutamate'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on '''Catalysis '''reaction
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We now have a complete '''Catalysis '''reaction with a '''Reactant''' and a '''Product'''.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on toolbar
-| style="border:0.75pt solid #000001;padding:0.071cm;"| I will align the '''reaction''' to accommodate other '''components''' in the process diagram.
-From the toolbar use the icons:
-* State Transition
-* Simple Molecule
-* Generic Protein and
-* Catalysis
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Cursor on completed process diagram.
-| style="border:0.75pt solid #000001;padding:0.071cm;"| This is the completed process diagram.
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Go to '''View'''>> click on '''Zoom Fit'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| To view it properly, go to '''View '''on the main menu bar and click on''' Zoom Fit'''
-You now see the completed '''Process Diagram'''
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Slide'''
-Summary
-| style="border:0.75pt solid #000001;padding:0.071cm;"| Let us summarize.
-In this tutorial, we will learn to:
-* Use Macros
-* Move Components on the draw area
-* Connect a reaction line around a species
-|-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| We also learnt to:
-* Align and extend a reaction line
+About the Spoken Tutorial project-
-* Add a Product and a Reactant
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Acknowledgement'''
-| style="border:0.75pt solid #000001;padding:0.071cm;"| About the Spoken Tutorial project-
 * Watch the video at the following link
@@ Line 925: / Line 571: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Acknowledgement'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| The''' Spoken Tutorial Project '''Team conducts-
+'''Acknowledgement'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+The''' Spoken Tutorial Project '''Team conducts-
 * Workshops using Spoken tutorials.
@@ Line 934: / Line 584: @@
 |-
-| style="border:0.75pt solid #000001;padding:0.071cm;"| '''Acknowledgement'''
+| style="border:0.75pt solid #000001;padding:0.071cm;"|
+'''Acknowledgement'''
 | style="border:0.75pt solid #000001;padding:0.071cm;"| 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 link shown
+More information on this Mission is available at the given link.
-[http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro]
 |-
 | style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| This is '''Bella Tony '''from''' IIT Bombay''' signing off. Thank you for joining.
+| style="border:0.75pt solid #000001;padding:0.071cm;"| This is '''Bella Tony '''from''' IIT Bombay''' signing off.
-|}
+Thank you for joining.
-It is funded by '''NMEICT, MHRD, Government of India'''.
-More information on this Mission is available at the link shown
-[http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro]
-|-
-| style="border:0.75pt solid #000001;padding:0.071cm;"|
-| style="border:0.75pt solid #000001;padding:0.071cm;"| This is '''Bella Tony '''from''' IIT Bombay''' signing off. Thank you for joining.
 |}