CellDesigner/C2/Installation-of-CellDesigner-on-Linux/English-timed
From Script | Spoken-Tutorial
| 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. |
