CellDesigner/C2/Build-and-Modify-Process-Diagram/English

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. ...	We will also learn to: 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 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 dialogue box ‘The Same Species Exists’ dialog box click ‘No’.
	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
Slide Summary	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
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. 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. ... We will also learn to: 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 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 dialogue box ‘The Same Species Exists’ dialog box click ‘No’. 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 Slide Summary 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 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 link shown http://spoken-tutorial.org/NMEICT-Intro 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
	This is Bella Tony from IIT Bombay signing off. Thank you for joining.

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