CellDesigner/C2/Create-and-Edit-Components/English-timed
From Script | Spoken-Tutorial
| 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. |
| 12:00 | About the spoken tutorial project. |
| 12:05 | The video at this link summarizes the Spoken Tutorial project. Please download and watch it. |
| 12:13 | The Spoken Tutorial Project conducts workshops and gives certificates on passing an on-line test. For more details, please write to us. |
| 12:23 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this mission is available on this link. |
| 12:35 | This is Bella Tony from IIT Bombay, signing off. Thank you for joining. |
