Sandhya.np14 at 11:19, 6 June 2018

2018-06-06T11:19:39Z

Jyotisolanki at 06:02, 21 November 2017

2017-11-21T06:02:07Z

Jyotisolanki: Created page with " {| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone. Welcome to this tutorial on '''Installation of CellDesigner on Linux OS'''. |- | 00:08 | In this..."

2017-09-19T07:02:25Z

Created page with " {| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone. Welcome to this tutorial on '''Installation of CellDesigner on Linux OS'''. |- | 00:08 | In this..."

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{| border=1
|| '''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.run ''' and press '''Enter'''.

|-
| 04:39
| The '''Setup wizard''' dialog box opens up.

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| 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 '''<nowiki>/home/<your username>/CellDesigner4.3</nowiki>''' 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, changes 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.

|}

@@ Line 18: / Line 18: @@
 |-
 | 00:23
-|  Here I am using '''Ubuntu Operating System 14.04''' '''CellDesigner version 4.3''' '''Java version 1.7'''
+|  Here I am using '''Ubuntu Operating System 14.04''' ,'''CellDesigner version 4.3''' ,'''Java version 1.7'''
 |-

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

Sandhya.np14 at 11:19, 6 June 2018

Jyotisolanki at 06:02, 21 November 2017

Jyotisolanki: Created page with " {| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone. Welcome to this tutorial on '''Installation of CellDesigner on Linux OS'''. |- | 00:08 | In this..."