CellDesigner/C2/Create-and-Edit-Components/English-timed

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Time Narration
00:01 Hello everyone. Welcome to this tutorial on Create and Edit Components in CellDesigner.
00:08 In this tutorial, we will learn to: Open an already saved .xml file in the draw area.
00:15 Change the following in a compartment :shape, size, color and thickness of the border.
00:22 Createmultiple files in CellDesigner Change identity of a Species
00:28 We will also learn how to Cut, Copy and Paste a Species, About Start-point and End-point of a Species.
00:37 How to Activate and change color of a Species. Change properties of a Reaction How to close a File.
00:47 Here I am using Ubuntu Linux OS version 14.04 CellDesigner version 4.3 Java version 1.7
00:57 To follow this tutorial, you should be familiar with undergraduate Biochemistry and CellDesigner interface.
01:05 If not, for relevant CellDesigner tutorials, please visit our website www.spoken-tutorial.org
01:16 Learners please note: some of the previous tutorials in this series, were created on Windows OS.
01:24 However, hereon the series will be completed on Ubuntu Linux OS.
01:30 Let's proceed to create and edit components in CellDesigner.
01:35 Open the terminal by pressing Ctrl+Alt+T keys simultaneously.
01:41 Now type ./runCellDesigner4.3 and press Enter.
01:52 CellDesigner window now open on your screen.
01:56 Let us open the file Create and Edit that we had created earlier.
02:02 So, click on File and then on Open.
02:07 A dialog box named Open appears on the screen.
02:11 Here, we have to select the folder under ‘Folders’ label.
02:15 Click on the 'Create_and_Edit.xml' file under the ‘File’ label and then double-click on ‘Ok’.
02:27 Our file Create_and_Edit.xml is now open in the draw area.
02:35 Select the compartment. Go to the Component in the main menu bar.
02:43 Scroll down and select Change to OVAL.
02:48 On the draw area, we now have an oval compartment.
02:54 To change the color or thickness, go to “Component” in the main menu bar.
03:00 Click on “Change color & shape” option.
03:05 Alternately, right-click on the compartment boundary and select “Change color & shape” option.
03:14 A dialog box named 'Change color & shape' appears on the screen.
03:20 For a thinner boundary line, change the Membrane Thickness from 12 to 8 or below.
03:29 To change the color, go to Color panel.
03:34 In the Color panel is a color wheel, with a pointer like handle.
03:39 Click and hold the pointer and rotate to select the preferred color.
03:46 After all the modifications are done, click on Apply. And then on 'Ok'.
03:53 Explore other options to draw various Compartments on the reaction toolbar, on your own.
04:00 We will now learn how to change the identity of Species.
04:05 So, first we will open a new window by pressing CTRL+N.
04:11 Let us give a name to this file, say Change Species.
04:16 We will keep the default width and height. And click on Ok button.
04:22 Now, click on the icon for 'Generic protein' from the toolbar. Click on the draw area.
04:30 In the dialog box, type Pectin and click on the Ok button.
04:37 Now right-click on the Generic protein Pectin.
04:41 And click on the option Change Identity.
04:46 A dialog box named 'Change identity of the species' appears on the screen.
04:53 Click on the down arrow in the Class box.
04:58 Select any option, for example, say simple molecule, from the drop-down menu.
05:05 Now, give a name to this simple molecule in the Name box.
05:10 Let's say Fructose. And click on Apply button.
05:17 Observe that our Protein Pectin is now converted to a simple molecule named Fructose.
05:25 Let us now learn to Cut, Copy and Paste.
05:29 I will use the same Fructose that is already present on the draw area.
05:34 To cut a Species, click on the Species Fructose first.
05:40 Go to Edit menu, scroll down and click on Cut.
05:47 Notice here that the shortcut key for Cut is Ctrl+X.
05:53 The Species Fructose has been cut.
05:56 To paste the species, go back to the 'Edit' menu, scroll down and click on Paste.
06:03 Notice here that the shortcut key for Paste is Ctrl+V.
06:08 The Species Fructose reappears on the draw area.
06:12 To make a copy of the Species, go to Edit on the main menu bar.
06:18 Click on Copy.
06:21 Notice here that the shortcut key for Copy is Ctrl+C. Click on Copy. Click on the draw area.
06:31 This time, let us press Ctrl + V to paste.
06:36 We now have a copy of Fructose on the draw area.
06:40 To undo any action press Ctrl+Z and to redo any action press Ctrl+Y.
06:51 These are however, limited in their use.
06:55 Let us drag and move the Fructose molecules aside on the draw area.
07:00 To do so, click on Fructose and drag it to the desired location.
07:07 Next we will learn, what are start-point and end-point species and how to activate a species?
07:13 For that, I have already drawn a state transition reaction between 2 generic proteins.
07:21 I have named them Protein 1 and Protein 2.
07:25 Recall, we already learnt how to draw a reaction earlier.
07:29 If you do not know, refer to the previous tutorials in this series. Let us proceed.
07:35 In this reaction, the ‘start point’ is ‘Protein 1’ and the ‘end point’ is Protein 2.
07:43 To activate a species, click on a Species which is an 'end-point' of a Reaction.
07:50 In our case, it is Protein 2.
07:53 So click on Protein 2 and press A on the keyboard.
07:59 Let me undo this change by pressing Ctrl + Z keys.
08:05 Alternately, click on Protein 2
08:09 Next, on the main menu bar, go to Component.
08:13 Scroll down and click on Set Active.
08:18 Notice that the activated species is wrapped by a dashed line.
08:24 Let us now change the color of the species, Protein 2.
08:29 So, right-click on it and then click on 'Change color and shape'.
08:35 As we saw earlier, in the Color panel is the color wheel.
08:40 Click and rotate the pointer, to select the preferred color.
08:44 Then, click on Apply and Ok.
08:49 Observe the color changes in the species ,
08:53 We will now learn how to change the properties of a Reaction.
08:57 Let us come back to our state transition reaction present on the draw area.
09:03 Right-click on the reaction arrow between the two species.
09:08 Now select Change Identity option.
09:13 A dialog box Change Properties of the Reaction appears.
09:18 Type the name of the reaction in the Name box, say Reaction1.
09:26 Select the required reaction from the drop-down menu in the Type box, say Transcription. Click on 'Ok'.
09:38 Observe that the reaction has changed on the draw area.
09:42 We do not see the name that we gave on the reaction arrow in the draw area.
09:47 Don't worry, we will learn about it in upcoming tutorials.
09:53 Let's right-click once again on the reaction arrow and click on Change Identity option.
10:00 In case it is a Reversible reaction, select the option TRUE and click on Ok.
10:09 You will now see that the reaction has reversed.
10:14 To exit CellDesigner, click on File and select Exit option.
10:20 Alternately, you may press Ctrl Q.
10:25 A dialog box Confirmation appears on the screen asking if we wish to save the changes.
10:32 Click Yes and double-click on the Ok button.
10:38 It says the file has been modified.
10:41 Save the changes? Click Yes.
10: Let us summarize: In this tutorial, we have learnt how to:
10:50 Open an already saved .xml file in the draw area
10:55 Change shape, size, color and thickness of the border of the Compartment
11:01 Create multiple files in CellDesigner And change identity
11:07 And Cut, Copy and Paste a Species
11:10 We also learnt: About Start-point and End-point of a Species
11:15 How to Activate a Species Change color of a Species Change properties of a ReactionAnd close a File
11:25 For your assignment: Create a complex and place a Species inside the Complex
11:32 Assignment 2: Explore the toolbar and find out how to add a reactant and a product to a reaction.
11:41 Your completed assignment should look like this.
11:45 Your first assignment will look like this: A complex and Species placed inside the Complex.
11:55 Assignment 2 will look like this: A state-transition reaction with a reactant and a product.
12:00 About the spoken tutorial project.
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12:35 This is Bella Tony from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14