CellDesigner/C2/Installation-of-CellDesigner-on-Linux/English-timed

Time	Narration
00:01	Hello everyone. Welcome to this tutorial on Installation of CellDesigner on Linux OS.
00:08	In this tutorial, we will learn to download and install CellDesigner 4.3 on Ubuntu Linux Operating System
00:18	and create a Compartment in the draw area of CellDesigner.
00:23	Here I am using Ubuntu Operating System 14.04 ,CellDesigner version 4.3 ,Java version 1.7.
00:35	To follow this tutorial, you should be familiar with basic operations on Linux Operating System.
00:42	If not, for relevant Linux tutorials, please visit our website www.spoken-tutorial.org
00:51	To install CellDesigner, open your web browser and go to the URL as shown.
01:00	Click on Download CellDesigner button on the right hand side.
01:07	A new web-page opens.
01:09	Scroll down and locate Download.
01:13	It shows Download for Linux 64 bit and Download for Linux 32 bit.
01:20	Now, let us see how to find out the details of the OS type of our machine.
01:26	For this, click on the icon 'System Settings', located at the top right corner of your machine.
01:34	Upon clicking, the System Settings page opens up.
01:40	Under the panel 'System', double click on the icon 'Details'.
01:48	Here, a new window 'Details' opens. Check the ‘OS type’ of your machine- whether it is 64-bit or 32-bit.
02:00	I have a 64 bit machine. Now, let us close this window and go back to the browser.
02:07	In case you have a 32 bit machine, then download the 32 bit version.
02:14	I will click on Download for Linux 64 bit link.
02:19	Immediately, a new window opens up.
02:22	Since I am a new user, I will click on First Time User option.
02:26	And then click on Continue.
02:29	Now, we are prompted to fill up some personal details.
02:33	After filling these, click on Download button.
02:37	A dialog box opens. Here, click on Save File button.
02:44	This may take some time depending on the Internet speed.
02:49	Once the file is downloaded, go to the terminal by pressing Ctrl+Alt+T keys.
02:58	I have already downloaded the file in my default Downloads folder.
03:04	So, first I will go to that folder. Type-cd space Downloads and press Enter.
03:15	Type ls and press Enter.
03:20	Here is the file which we downloaded.
03:25	If you downloaded 32 bit installer, then the file name will have 32 instead of 64.
03:32	Remember to use the filename of your 32 bit installer in the terminal commands from here on.
03:39	Now, we have to change the file permission. So, type:
03:43	sudo space chmod space 777 space hyphen capital R space CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer.run
04:08	and press Enter.
04:12	Type the admin password when prompted and press Enter.
04:19	Now we will run the file by typing dot forward slash CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer dot run and press Enter.
04:39	The Setup wizard dialog box opens up.
04:43	Click on Next button.
04:47	Click on the I accept the agreement option and then click on Next.
04:54	Installation Directory dialog shows the directory where CellDesigner will be installed.
05:00	It will be displayed as /home/<your username>/CellDesigner4.3 Now, click on Next.
05:10	It says Ready to Install. Again, click on Next.
05:17	The installation will begin.
05:20	Once completed, uncheck the ‘View Readme File’ and click on the Finish button.
05:29	Now, open a new terminal by pressing Ctrl + Alt + T keys.
05:34	Type ls and press Enter.
05:39	We can see runCellDesigner4.3 file here.
05:44	We have to execute this file to open CellDesigner.
05:48	So, type: dot forward slash runCellDesigner4.3 and press Enter.
06:00	CellDesigner window is now open in our Linux machine.
06:05	Notice that we are unable to see the Main menu bar clearly. To make it visible, we have to change the system settings.
06:15	Click on the icon 'System Settings', located on top right corner of your machine.
06:23	Upon clicking, the System Settings page opens.
06:28	Under the panel 'Personal', double-click on 'Appearance'.
06:34	A window named 'Appearance' opens.
06:38	Under the tab 'Look', go to Theme.
06:43	From the drop-down menu in the 'Theme' box, select 'Radiance' and close the window.
06:53	Notice that the Main menu bar is now clearly visible. Let’s proceed.
07:01	To open a new document, click on File and then on New.
07:07	Alternately, click on the New icon in the menu bar. Or, press Ctrl + N keys.
07:16	A dialog box New Document appears on the screen, prompting us to name the file.
07:23	Type the filename as 'Create and Edit'.
07:30	Set the Width to 900, Height to 800.
07:36	Click on the Ok button at the bottom.
07:40	An information box opens.
07:43	And, all spaces in the name that we gave, change to underscore.
07:48	So, the actual name of our file will be 'Create underscore and underscore Edit'. Click Ok and proceed.
07:58	The white area in the centre is what we call the draw area.
08:02	We will learn about the menu bars, toolbars and various panels in detail in the coming tutorials.
08:09	Before selecting any other icon from the toolbar, click on the Select Mode icon.
08:16	This acts as a selection tool. With this selection tool, we can select, draw and move the components on the draw area.
08:25	Before we draw a component, we will ensure that Grid Snap and Grid Visible are enabled in CellDesigner window.
08:35	For that, click on Edit in the main menu bar.
08:39	Scroll down and click on Grid Snap.
08:43	Again, go back to Edit and click on Grid Visible.
08:49	Grids enable us to better align the components in the draw area.
08:54	Now, let us change the position of the List & Notes area.
08:59	Recall, we already learnt about List area, Notes area and Draw area in the previous tutorial.
09:06	If you do not know, refer to the previous tutorials in this series.
09:12	Let's proceed and change the location of the List area.
09:15	Go to View option, click on List and select the option ‘Right’.
09:24	It changes ‘List’ to the right side of the draw area.
09:30	The size of the areas can be altered by dragging the borderlines.
09:35	I will place the cursor on the borderline .
09:38	You can see a double headed arrow. Drag it to maximize or minimize the draw area.
09:45	We will now proceed to work on the draw area.
09:49	Before that, we should be able to view all the icons on the CellDesigner window.
09:55	For that, go to View on the main menu bar.
10:00	Click on Change Toolbar Visible and select the Show All option.
10:09	You are now able to see all the icons on the CellDesigner window. Let's go ahead.
10:17	To represent a cell or an intracellular compartment, we will use the Square icon from the toolbar. So, first click on it.
10:28	Then click on the draw area. And without releasing the mouse button, drag to draw the square. Now release the mouse button.
10:38	In the 'Property of Compartment' dialog that opens, specify the Name as Cell and set the Size as 1.0. Click Ok.
10:52	The name appears at the bottom of the compartment.
10:57	One can change the position of the compartment name too.
11:01	To do so, select the compartment name which is Cell, in our case.
11:07	Now, drag and drop it wherever you want to place it.
11:14	Let us save this file by clicking on File and then on Save As option.
11:22	Now choose the folder where you want to save your file.
11:26	I want to save it on the Desktop.
11:28	So, I will double click on Desktop as the folder in which I want to save.
11:34	And then click on Ok button at the bottom right.
11:38	Once again, click on the OK button at the bottom right. Our file is now saved.
11:46	To close CellDesigner, click on File and then on Exit.
11:52	Let us now go to the folder where we saved our file. So, I will go to my Desktop. Here is my file.
12:00	Notice that the file is saved in .xml format. This is the default CellDesigner file format.
12:08	Also, note that this file can only be opened in CellDesigner.
12:12	Let us summarize In this tutorial, we learnt: how to download and
12:17	install CellDesigner version 4.3 on Ubuntu Linux OS , create a Compartment in CellDesigner .
12:27	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
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12:45	Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. Information on this mission is available on this link.
12:57	This is Bella Tony from IIT Bombay, signing off. Thanks for watching.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14