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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 the button.
05:14 On the draw area, draw two generic proteins and name them Protein 1 and Protein 2.
05:23 In the main menu,click on the icon for State Transition.
05:28 Then, on the draw area, hover the mouse on ‘start-point' Species, Protein 1.
05:36 Observe that all 16 connection points are highlighted in grey color.
05:42 Note that when the cursor is pointed to one of these connection points, it will change to blue color.
05:49 Let’s click on one of the connection points.
05:53 In the same manner, hover the mouse on the ‘end-point' Species i.e. Protein 2.
06:00 Again, as explained above, click on the required connection point.
06:05 A State Transition reaction line is formed between the selected connection points.
06:12 Next, we will align the Reaction line.
06:16 Click on the State transition reaction line between Protein 1 and Protein 2
06:21 Note that the 2 process nodes on the reaction line get highlighted.
06:27 If we hover the mouse on either of the 2 process nodes, a ‘plus’ sign appears.
06:34 Click on one of the process nodes.
06:37 Now drag and place the pointer on the preferred connection point.
06:43 Click anywhere on the draw area to uncheck the highlighted components.
06:49 To extend or stretch the reaction line, first click on it.
06:54 Now click on either of the process nodes located on the start-point or end-point Species.
07:01 Drag the mouse to stretch the reaction line till the preferred connection point.
07:07 From here on, we will proceed with the Process diagram.
07:12 Let us come back to the Build and Modify Process Diagram window.
07:16 Let’s add a Reactant and a Product, to the existing reaction.
07:21 From the toolbar, click and place 2 simple molecules on the draw area.
07:27 Name them Glutamate and 2-Oxoglutarate.
07:36 Drag and place them adjacent to the Simple molecules: 2-keto-isovalerate and Valine.
07:44 As explained earlier, let us align the components on the draw area.
07:49 From what was explained earlier, I have now completed aligning the components.
07:55 On the toolbar, click on the icon for ‘Add Product’.
08:00 Now hover the mouse on the State Transition reaction between 2-keto-isovalerate and Valine.
08:07 Click on the highlighted process node.
08:10 Next, hover the mouse on 2-Oxoglutarate.
08:17 Click on any one of the 16 highlighted process nodes.
08:21 Observe, a reaction line appears between State Transition and 2-Oxoglutarate.
08:29 Similarly, click on ‘Add Reactant’ icon.
08:34 Hover the mouse on Glutamate and click on one of the 16 highlighted process nodes.
08:40 Next, hover the mouse on the State Transition reaction and click on the process node.
08:49 Observe, a reaction line appears between State Transition and Glutamate.
08:55 We now have a complete Catalysis reaction with a Reactant and a Product.
09:01 I will align the reaction to accommodate other components in the process diagram.
09:09 From the toolbar use the icons: State Transition , Simple Molecule, Generic Protein and Catalysis
09:18 This is the completed process diagram.
09:22 To view it properly, go to View on the main menu bar and click on Zoom Fit
09:32 You now see the completed Process Diagram
09:36 Let us summarize. In this tutorial, we have learnt to Use Macros.
09:42 Move Components on the draw area , Connect a reaction line around a species.
09:48 Align and extend a reaction line, Add a Product and a Reactant
09:54 For the assignment:Build a process diagram for Methionine Biosynthesis using tools in CellDesigner

Explore the Macros for GTP/GD, Find out how to create a ’Curve’ reaction line

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10:54 This is Bella Tony from IIT Bombay signing off.

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Contributors and Content Editors

Jyotisolanki, Pratik kamble, Sakinashaikh