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

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

Contributors and Content Editors

Jyotisolanki, Pratik kamble, Sakinashaikh, Sandhya.np14