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

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	create multiple 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 opens 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 Reaction and 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.
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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