Difference between revisions of "CellDesigner/C2/Installation-of-CellDesigner-on-Linux/English-timed"

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|  In this tutorial we will learn to Download and install '''CellDesigner 4.3 '''on''' Ubuntu Linux Operating System'''
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|  In this tutorial, we will learn to download and install '''CellDesigner 4.3 '''on''' Ubuntu Linux Operating System'''
  
 
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|and create a''' Compartment''' in the draw area of '''CellDesigner'''.
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|and create a''' Compartment''' in the '''draw''' area of '''CellDesigner'''.
  
 
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|  Here I am using '''Ubuntu Operating System 14.04''' ,'''CellDesigner version 4.3''' ,'''Java version 1.7'''
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|  Here I am using '''Ubuntu Operating System 14.04''' ,'''CellDesigner version 4.3''' ,'''Java version 1.7'''.
  
 
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|  To install '''CellDesigner''', open your web browser and go to the '''URL '''as shown.
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|  To install '''CellDesigner''', open your '''web browser''' and go to the '''URL '''as shown.
  
 
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|  Now, let us see how to find out the details of the '''OS type '''of our machine.
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|  Now, let us see how to find out the details of the '''OS''' type of our machine.
  
 
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|  Here a new window  ''''Details'''' opens. Check the ‘'''OS type'''’ of your machine- whether it is '''64-bit''' or '''32-bit'''.
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|  Here, a new window  ''''Details'''' opens. Check the ‘'''OS type'''’ of your machine- whether it is '''64-bit''' or '''32-bit'''.
  
 
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|  A dialog box opens. Here click on '''Save File''' button.
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|  A dialog box opens. Here, click on '''Save File''' button.
  
 
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| Remember to use the filename of your '''32 bit installer '''in the terminal commands from here on.
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| Remember to use the filename of your '''32 bit installer '''in the terminal '''command'''s from here on.
  
 
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| Now, we have to change the file permission.So, type  
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| Now, we have to change the file permission. So, type:
  
 
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| '''sudo space chmod space 777 space hyphen capital R space CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer.run'''  
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| '''sudo space chmod space 777 space hyphen capital R space CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer.run'''  
  
 
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|  Now we will run the file by typing '''dot forward slash CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer.run ''' and press '''Enter'''.
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|  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'''.
  
 
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| We have to execute this file to open '''CellDesigner'''.
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| We have to '''execute''' this file to open '''CellDesigner'''.
  
 
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|  So type '''dot forward slash runCellDesigner4.3''' and press '''Enter'''.
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|  So, type: '''dot forward slash runCellDesigner4.3''' and press '''Enter'''.
  
 
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| Alternately, click on the '''New''' icon in the menu bar. Or, press '''Ctrl + N''' keys'''.'''
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| Alternately, click on the '''New''' icon in the menu bar. Or, press '''Ctrl + N''' keys.
  
 
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| And all spaces in the name that we gave, changes to '''underscore'''.
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| And, all spaces in the name that we gave, change to '''underscore'''.
  
 
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|  The white area in the centre is what we call the draw area.
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|  The white area in the centre is what we call the '''draw area'''.
  
 
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| This acts as a selection tool.With this selection tool, we can select, draw and move the components on the draw area.
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| This acts as a selection tool. With this selection tool, we can select, draw and move the '''component'''s on the draw area.
  
 
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|  Now let us change the position of the '''List '''& '''Notes''' area.
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|  Now, let us change the position of the '''List '''& '''Notes''' area.
  
 
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| Recall, we already learnt about '''List''' area, '''Notes''' area and Draw area in the previous tutorial.
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| Recall, we already learnt about '''List''' area, '''Notes''' area and '''Draw''' area in the previous tutorial.
  
 
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|  Let's proceed and change the location of the List area.
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|  Let's proceed and change the location of the '''List''' area.
  
 
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|We will now proceed to work on the draw area.
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|We will now proceed to work on the '''draw''' area.
  
 
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|You are now able to see all the icons on the '''CellDesigner''' window.   Let's go ahead.
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|You are now able to see all the icons on the '''CellDesigner''' window. Let's go ahead.
  
 
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|Then click on the draw area. And without releasing the mouse button, drag to draw the square. Now release the mouse button.
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|Then click on the '''draw''' area. And without releasing the '''mouse''' button, drag to draw the square. Now release the mouse button.
  
 
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|In the ''''Property of Compartment'''' dialog that opens, specify  the '''Name''' as '''Cell''' and set the '''Size''' as 1.0 Click '''Ok.'''
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|In the ''''Property of Compartment'''' dialog that opens, specify  the '''Name''' as '''Cell''' and set the '''Size''' as 1.0. Click '''Ok.'''
  
 
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|  One can change the position of the compartment name, too.
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|  One can change the position of the compartment name too.
  
 
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| To do so, select the compartment name, which is '''Cell''', in our case.
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| To do so, select the compartment name which is '''Cell''', in our case.
  
 
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|  Let us save this file by clicking on '''File''' and then on '''Save As''' option.
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|  Let us '''save''' this file by clicking on '''File''' and then on '''Save As''' option.
  
 
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| So, I will double click on '''Desktop '''as the folder in which I want to save.
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| So, I will double click on '''Desktop '''as the folder in which I want to '''save'''.
  
 
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|  Also note, that this file can only be opened in '''CellDesigner'''.
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|  Also, note that this file can only be opened in '''CellDesigner'''.
  
 
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|  Let us summarize  In this tutorial, we learnt : How to download and  
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|  Let us summarize  In this tutorial, we learnt: how to download and  
  
 
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|  Install '''CellDesigner ''' version 4.3 on '''Ubuntu Linux OS ''' Create a '''Compartment''' in '''CellDesigner '''
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|  install '''CellDesigner ''' version 4.3 on '''Ubuntu Linux OS ''', create a '''Compartment''' in '''CellDesigner '''.
  
 
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|  12:27
 
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|  The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.  
+
|  The video at the following link summarizes the '''Spoken Tutorial''' project. Please download and watch it.  
  
 
|-
 
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|  12:35
 
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|  The '''Spoken Tutorial '''team conducts workshops and gives certificates on passing an online test. For more details, please write to us.
+
|  The '''Spoken Tutorial '''team conducts workshops and gives certificates on passing an '''online''' test. For more details, please write to us.
  
 
|-
 
|-
 
| 12:45
 
| 12:45
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| Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''. Information on this Mission is available on this link.
+
| Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. Information on this mission is available on this link.
  
 
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|  12:57
 
|  12:57
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|  This is Bella Tony from '''IIT Bombay''' signing off. Thanks for watching.
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|  This is Bella Tony from '''IIT Bombay''', signing off. Thanks for watching.
  
 
|}
 
|}

Latest revision as of 16:49, 6 June 2018

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.
12:35 The Spoken Tutorial team conducts workshops and gives certificates on passing an online test. For more details, please write to us.
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

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