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

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(Created page with " {| style="border-spacing:0;" | style="border:0.05pt solid #000000;padding:0.053cm;"| <center>'''Visual Cue'''</center> | style="border:0.05pt solid #000000;padding:0.053cm;"|...")
 
 
(One intermediate revision by the same user not shown)
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* Download and install '''CellDesigner 4.3 '''on''' Ubuntu Linux Operating System'''
 
* Download and install '''CellDesigner 4.3 '''on''' Ubuntu Linux Operating System'''
−
* and create a''' Compartment on the draw area.'''
+
* and create a''' Compartment''' in the draw area of '''CellDesigner'''.
  
 
|-
 
|-
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| style="border:0.05pt solid #000000;padding:0.053cm;"| Here I am using
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Here I am using
  
−
* '''Ubuntu Linux OS version 14.04'''
+
* '''Ubuntu Operating System 14.04'''
 
* '''CellDesigner version 4.3'''
 
* '''CellDesigner version 4.3'''
 
* '''Java version 1.7'''
 
* '''Java version 1.7'''
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'''Pre-requisites'''
 
'''Pre-requisites'''
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| To follow this tutorial, you should be familiar with basic operations on '''Linux''' '''OS.'''
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| To follow this tutorial, you should be familiar with basic operations on '''Linux Operating System.'''
  
  
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[http://celldesigner.org/features/features43.html http://celldesigner.org/features/features43.html]
 
[http://celldesigner.org/features/features43.html http://celldesigner.org/features/features43.html]
  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on '''Download''' '''CellDesigner''' button at the top right hand side.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on '''Download CellDesigner''' button on the right hand side.
  
  
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on ''''System Settings'''',
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on ''''System Settings'''',
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on the icon ''''System Settings'''', located at the top right corner of your machine.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| For this, click on the icon ''''System Settings'''', located at the top right corner of your machine.
 +
 
 +
Upon clicking, the '''System Settings''' page opens up.
  
 
|-
 
|-
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Highlight OS type field
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Highlight OS type field
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| A window named ''''Details'''' opens.  
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Here a new window ''''Details'''' opens.  
  
  
−
Here check the ‘'''OS type'''’ - whether it is '''32-bit '''or '''64-bit.'''
+
Check the ‘'''OS type'''’ of your machine- whether it is '''64-bit''' or '''32-bit'''.
  
 
|-
 
|-
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Close the window
 
Close the window
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| I have a '''64 bit''' machine. &nbsp;
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| I have a '''64 bit''' machine.  
  
  
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|-
 
|-
 
| style="background-color:#e6b8af;border:0.05pt solid #000000;padding:0.053cm;"| Point to 32 '''bit version'''
 
| style="background-color:#e6b8af;border:0.05pt solid #000000;padding:0.053cm;"| Point to 32 '''bit version'''
−
| style="background-color:#e6b8af;border:0.05pt solid #000000;padding:0.053cm;"| In case you have a 32 bit machine, then download the '''32''' '''bit version. '''
+
| style="background-color:#e6b8af;border:0.05pt solid #000000;padding:0.053cm;"| In case you have a '''32 bit''' machine, then download the '''32 bit version. '''
  
 
|-
 
|-
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−
Then click on '''Continue'''.
+
And then click on '''Continue'''.
  
 
|-
 
|-
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on '''Save File''' button
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on '''Save File''' button
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| A dialog box opens. &nbsp;
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| A dialog box opens.  
  
  
 
Here click on '''Save File''' button.
 
Here click on '''Save File''' button.
−
 
−
Click on ok button.
 
  
  
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Press '''Ctrl+Alt+T '''keys
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Press '''Ctrl+Alt+T '''keys
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Once the file is downloaded, go to the '''terminal''' by pressing '''Ctrl+Alt+T '''keys'''.'''
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Once the file is downloaded, go to the '''terminal''' by pressing '''Ctrl+Alt+T '''keys.
  
 
|-
 
|-
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So, first I will go to that folder. Type-
 
So, first I will go to that folder. Type-
  
−
'''cd Downloads '''and press '''Enter.'''
+
'''cd space Downloads '''and press '''Enter.'''
  
  
−
Now type '''ls '''and press '''Enter.'''
+
Type '''ls '''and press '''Enter.'''
  
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Here is the file which we downloaded
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Here is the file which we downloaded.
−
 
+
−
'''CellDesigner-4.3-linux-x64-installer.run'''
+
  
 
|-
 
|-
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−
>> press '''Enter'''. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+
>> press '''Enter'''.  
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Now, we have to change the file permission.
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Now, we have to change the file permission.
  
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So, type  
 
So, type  
  
−
'''sudo chmod 777 -R CellDesigner-4.3-linux-x64 -installer.run'''
+
'''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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| style="border:0.05pt solid #000000;padding:0.053cm;"| Now we will run the file by typing
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Now we will run the file by typing
  
−
'''./CellDesigner-4.3-linux-x64-installer.run '''
+
'''dot forward slash CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer.run '''
  
 
and press '''Enter'''.
 
and press '''Enter'''.
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| style="border:0.05pt solid #000000;padding:0.053cm;"| Point to '''Ready to Install '''>> click on '''Next.'''
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Point to '''Ready to Install '''>> click on '''Next.'''
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| It says '''Ready to Install'''.  
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| It says '''Ready to Install'''.  
 +
  
 
Again, click on '''Next.'''
 
Again, click on '''Next.'''
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−
Once completed, uncheck the ‘View Read me’ File and click on '''Finish''' button.
+
Once completed, uncheck the '''‘View Readme File’'''  and click on the '''Finish''' button.
  
  
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Type '''./runCellDesigner4.3''' >> press '''Enter'''.
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Type '''./runCellDesigner4.3''' >> press '''Enter'''.
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| So type '''./runCellDesigner4.3''' and press '''Enter'''.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| So type '''dot forward slash runCellDesigner4.3''' and press '''Enter'''.
  
 
|-
 
|-
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on ''''System Settings'''',
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on ''''System Settings'''',
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on the icon ''''System Settings'''', located on top right corner of the Computer.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Click on the icon ''''System Settings'''', located on top right corner of your machine.
  
 +
 +
Upon clicking, the '''System Settings''' page opens.
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Under ''''Personal' >> '''click on ‘'''Appearance'.'''
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Under ''''Personal' >> '''click on ‘'''Appearance'.'''
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−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Under the panel ''''Personal', '''double click on the icon ''''Appearance'.'''
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Under the panel ''''Personal', '''double-click on ''''Appearance'.'''
  
−
A window named ''''Appearance'''' opens. Here, select the tab ''''Look''''.
+
A window named ''''Appearance'''' opens.  
  
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| From the drop-down menu in the ''''Theme'''' box >> select ''''Radiance'''' >> close the window.
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| From the drop-down menu in the ''''Theme'''' box >> select ''''Radiance'''' >> close the window.
  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| From the drop-down menu in the ''''Theme'''' box select ''''Radiance'''' and close the window.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Under the tab ''''Look'''',  go to '''Theme'''.
 +
 
 +
From the drop-down menu in the ''''Theme'''' box, select ''''Radiance'''' and close the window.
  
 
|-
 
|-
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−
| style="border:0.05pt solid #000000;padding:0.053cm;"| To open a new document click on '''File''' and then on '''New.'''
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| To open a new document, click on '''File''' and then on '''New.'''
  
  
Line 318: Line 321:
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Type 900 for Width , &nbsp;800 for height >> click Ok
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| Type 900 for Width , &nbsp;800 for height >> click Ok
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Set the '''Width''' to 900, '''Height''' to 800 and click on the '''Ok''' button at the bottom.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Set the '''Width''' to 900, '''Height''' to 800.
 +
 
 +
 
 +
Click on the '''Ok''' button at the bottom.
  
 
|-
 
|-
Line 325: Line 331:
  
  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| An 'Information' box opens and all spaces in the name that we gave, changes to '''underscore'''.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| An information box opens.
 +
 
 +
 
 +
And all spaces in the name that we gave, changes to '''underscore'''.
  
  
−
So, the actual name of our file will be ''''Create_and_Edit''''.
+
So, the actual name of our file will be ''''Create underscore and underscore Edit''''.
  
  
−
Click ''''Ok'''' and proceed.
+
Click '''Ok''' and proceed.
  
 
|-
 
|-
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.079cm;"|  
 
| style="border:0.05pt solid #000000;padding:0.079cm;"|  
−
| style="border:0.05pt solid #000000;padding:0.079cm;"| Before we draw a component, we will ensure that '''Grid Snap''' and '''Grid Visible''' are enabled in '''CellDesigner.'''
+
| style="border:0.05pt solid #000000;padding:0.079cm;"| Before we draw a component, we will ensure that '''Grid Snap''' and '''Grid Visible''' are enabled in '''CellDesigner''' window.
  
 
|-
 
|-
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Scroll down and click on '''Grid Snap'''.
 
Scroll down and click on '''Grid Snap'''.
−
| style="border:0.05pt solid #000000;padding:0.079cm;"| Click on '''Edit''' in the main menu bar.
+
| style="border:0.05pt solid #000000;padding:0.079cm;"| For that, click on '''Edit''' in the main menu bar.
  
 
Scroll down and click on '''Grid Snap.'''
 
Scroll down and click on '''Grid Snap.'''
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.079cm;"| Click on '''Edit''' >> Scroll down and click on '''Grid Visible'''.
 
| style="border:0.05pt solid #000000;padding:0.079cm;"| Click on '''Edit''' >> Scroll down and click on '''Grid Visible'''.
−
| style="border:0.05pt solid #000000;padding:0.079cm;"| Go back to '''Edit''' again and click on '''Grid Visible.'''
+
| style="border:0.05pt solid #000000;padding:0.079cm;"| Again, go back to '''Edit''' and click on '''Grid Visible.'''
  
 
|-
 
|-
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−
Recall, we already learnt about List area, Notes area and Draw area in the previous tutorial.
+
Recall, we already learnt about '''List''' area, '''Notes''' area and Draw area in the previous tutorial.
  
  
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Place the cursor on borderline of draw area and drag.  
 
Place the cursor on borderline of draw area and drag.  
−
| style="border:0.05pt solid #000000;padding:0.079cm;"| The size of the areas can be altered by
+
| style="border:0.05pt solid #000000;padding:0.079cm;"| The size of the areas can be altered by dragging the borderlines.
−
 
+
−
dragging the borderlines.
+
  
  
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−
You can see a double headed arrow. Drag it to maximize or minimize the area.
+
You can see a double headed arrow. Drag it to maximize or minimize the draw area.
  
 
|-
 
|-
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|-
 
|-
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"|  
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"|  
−
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| Before that, we should be able to view all the icons on the menu bar of the '''CellDesigne'''r window.
+
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| Before that, we should be able to view all the icons on the '''CellDesigner''' window.
  
 
|-
 
|-
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| Cursor on '''View '''on the main menu bar toolbar>> C'''hange Toolbar Visible'''>>'''Show All'''
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| Cursor on '''View '''on the main menu bar toolbar>> C'''hange Toolbar Visible'''>>'''Show All'''
−
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| Go to '''View '''on the main menu bar, scroll down and select '''Change Toolbar Visible'''
+
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| For that, go to '''View '''on the main menu bar.
  
  
−
Now select the option''' Show All'''
+
Click on '''Change Toolbar Visible''' and select the ''' Show All''' option.
  
 
|-
 
|-
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"|  
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"|  
−
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| Observe, you are now able to see all the icons on the '''CellDesigner''' window
+
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.079cm;"| You are now able to see all the icons on the '''CellDesigner''' window. 
 +
 
 +
Let's go ahead.
  
 
|-
 
|-
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.079cm;"| Click on the ''''Square'''' icon>> Click and drag on the draw area.
 
| style="border:0.05pt solid #000000;padding:0.079cm;"| Click on the ''''Square'''' icon>> Click and drag on the draw area.
−
| style="border:0.05pt solid #000000;padding:0.079cm;"| Then click on the draw area and without releasing the mouse button, drag to draw the square.
+
| style="border:0.05pt solid #000000;padding:0.079cm;"| Then click on the draw area.
 +
 
 +
 
 +
And without releasing the mouse button, drag to draw the square.
  
  
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|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.079cm;"| In the dialog box type '''Cell''' and and '''Size''' as 1.0 >> Click Ok
 
| style="border:0.05pt solid #000000;padding:0.079cm;"| In the dialog box type '''Cell''' and and '''Size''' as 1.0 >> Click Ok
−
| style="border:0.05pt solid #000000;padding:0.079cm;"| In the ''''Property of Compartment'''' dialog that opens, specify '''Name''' as '''Cell''' and '''Size''' as 1.0
+
| style="border:0.05pt solid #000000;padding:0.079cm;"| In the ''''Property of Compartment'''' dialog that opens, specify  
 +
* the '''Name''' as '''Cell'''  
 +
* and set the '''Size''' as 1.0
  
  
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−
The name '''Cell''' appears at the bottom of the compartment.
+
The name appears at the bottom of the compartment.
  
 
|-
 
|-
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−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Let us save this file by clicking on '''File''' and then on '''Save As'''
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Let us save this file by clicking on '''File''' and then on '''Save As''' option.
−
option.
+
  
 
|-
 
|-
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−
I wish to save it on the '''Desktop'''. So, I will double click on '''Desktop '''as the folder in which I want to save.
+
I want to save it on the '''Desktop'''.  
 +
 
 +
So, I will double click on '''Desktop '''as the folder in which I want to save.
  
  
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−
Once again, Click on the '''OK''' button on the bottom right side.
+
Once again, click on the '''OK''' button at the bottom right.
  
 
Our file is now saved.
 
Our file is now saved.
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| style="border:0.05pt solid #000000;padding:0.053cm;"| To close '''CellDesigner''', click on '''File '''and then on '''Exit'''.
 
| style="border:0.05pt solid #000000;padding:0.053cm;"| To close '''CellDesigner''', click on '''File '''and then on '''Exit'''.
  
−
|-
 
−
| style="background-color:#f4cccc;border:0.05pt solid #000000;padding:0.053cm;"| Close both the terminal windows
 
−
| style="background-color:#f4cccc;border:0.05pt solid #000000;padding:0.053cm;"| We will now close the terminal windows which we had opened earlier.
 
  
 
|-
 
|-
Line 502: Line 514:
  
  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| Let us now go to the folder where we saved our file. So, I will go to my '''Desktop'''.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| Let us now go to the folder where we saved our file.  
 +
 
 +
So, I will go to my '''Desktop'''.
  
  
Line 524: Line 538:
 
In this tutorial, we learnt to:
 
In this tutorial, we learnt to:
  
−
* Install '''CellDesigner '''on '''Ubuntu Linux OS '''
+
* Install '''CellDesigner ''' version 4.3 on '''Ubuntu Linux OS '''
−
* Create a '''Compartment''' on the draw area
+
* Create a '''Compartment''' in '''CellDesigner '''
  
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| This video summarizes the Spoken Tutorial project  
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| The video at the following link summarizes the Spoken Tutorial project.
  
−
If you do not have good bandwidth, you can download and watch it.  
+
Please download and watch it.  
  
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| '''Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates. '''
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| The '''Spoken Tutorial '''team conducts workshops and gives certificates on passing an online test.
  
−
Please contact us.  
+
For more details, please write to us.
−
 
+
−
'''contact@spoken-tutorial.org'''
+
  
 
|-
 
|-
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.053cm;"|  
 
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.053cm;"|  
−
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.053cm;"| The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.  
+
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.053cm;"| Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.  
  
−
|-
 
−
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.053cm;"|
 
−
| style="border-top:none;border-bottom:0.05pt solid #000000;border-left:0.05pt solid #000000;border-right:0.05pt solid #000000;padding:0.053cm;"| More information on this Mission is available at this link.
 
  
−
[http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.or][http://spoken-tutorial.org/NMEICT-Intro g][http://spoken-tutorial.org/NMEICT-Intro /NMEICT-Intro]
+
Information on this Mission is available on this link.
 +
 
  
 
|-
 
|-
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
 
| style="border:0.05pt solid #000000;padding:0.053cm;"|  
−
| style="border:0.05pt solid #000000;padding:0.053cm;"| This is Bella Tony from '''IIT Bombay''' signing off. Thank you for joining.
+
| style="border:0.05pt solid #000000;padding:0.053cm;"| This is Bella Tony from '''IIT Bombay''' signing off. Thanks for watching.
  
 
|}
 
|}

Latest revision as of 10:57, 16 June 2015

Visual Cue
Narration
Slide Number 1

Title

Hello everyone.


Welcome to this tutorial on Installation of CellDesigner on Linux OS.

Slide Number 2

Learning Objectives

In this tutorial we will learn to
  • Download and install CellDesigner 4.3 on Ubuntu Linux Operating System
  • and create a Compartment in the draw area of CellDesigner.
Slide Number 3

System Requirement

Here I am using
  • Ubuntu Operating System 14.04
  • CellDesigner version 4.3
  • Java version 1.7
Slide Number 4

Pre-requisites

To follow this tutorial, you should be familiar with basic operations on Linux Operating System.


If not, for relevant Linux tutorials, please visit our website www.spoken-tutorial.org

Go to this URL http://celldesigner.org/features/features43.html To install CellDesigner, open your web browser and go to the URL as shown.
Click on Download CellDesigner button

http://celldesigner.org/features/features43.html

Click on Download CellDesigner button on the right hand side.


A new web-page opens.

Scroll down >> locate Download Scroll down and locate Download.


It shows Download for Linux 64 bit and Download for Linux 32 bit.

Now, let us see how to find out the details of the OS type of our machine.
Click on 'System Settings', For this, click on the icon 'System Settings', located at the top right corner of your machine.

Upon clicking, the System Settings page opens up.

Under 'System' >> click on ‘Details'. Under the panel 'System', double click on the icon 'Details'.
Highlight OS type field Here a new window 'Details' opens.


Check the ‘OS type’ of your machine- whether it is 64-bit or 32-bit.

Highlight OS type field


Close the window

I have a 64 bit machine.


Now, let us close this window and go back to the browser.

Point to 32 bit version In case you have a 32 bit machine, then download the 32 bit version.
Click on Download for Linux 64bit. I will click on Download for Linux 64 bit link.
Immediately, a new window opens up.
Click on First Time User >> click on Continue. Since I am a new user, I will click on First Time User option.


And then click on Continue.

Now, we are prompted to fill up some personal details.
Pause recording and fill the details.

Resume the recording.

After filling these, click on Download button.
Click on Save File button A dialog box opens.


Here click on Save File button.


This may take some time depending on the Internet speed.

Press Ctrl+Alt+T keys Once the file is downloaded, go to the terminal by pressing Ctrl+Alt+T keys.
Type cd Downloads >> press Enter. I have already downloaded the file in my default Downloads folder.


So, first I will go to that folder. Type-

cd space Downloads and press Enter.


Type ls and press Enter.

Here is the file which we downloaded.
Text on screen during editing If you downloaded 32 bit installer, then the file name will have 32 instead of 64.


Remember to use the filename of your 32 bit installer in the terminal commands from here on.

Type sudo chmod 777 -R CellDesigner-4.3-linux-x64-installer.run


>> press Enter.

Now, we have to change the file permission.


So, type

sudo space chmod space 777 space hyphen capital R space CellDesigner hyphen 4.3 hyphen linux hyphen x64 hyphen installer.run


and press Enter.

Type admin password Type the admin password when prompted and press Enter.
Type ./CellDesigner-4.3-linux-x64-installer.run >> press Enter. 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.

The Setup wizard dialog box opens up.
Click on Next Click on Next button.
Click I agree >> click on Next. Click on the I accept the agreement option and then click on Next.
Point to the directory >> click on Next.


Installation Directory dialog shows the directory where CellDesigner will be installed.


It will be displayed as

/home/<your username>/CellDesigner4.3


Now, click on Next.

Point to Ready to Install >> click on Next. It says Ready to Install.


Again, click on Next.

Click on Finish button. The installation will begin.


Once completed, uncheck the ‘View Readme File’ and click on the Finish button.


<<PAUSE>>

Open a new terminal Now, open a new terminal by pressing Ctrl + Alt + T keys.
Type ls >> press Enter. Type ls and press Enter.
Point to runCellDesigner4.3 file


We can see runCellDesigner4.3 file here.


We have to execute this file to open CellDesigner.

Type ./runCellDesigner4.3 >> press Enter. So type dot forward slash runCellDesigner4.3 and press Enter.
CellDesigner window is now open in our Linux machine.
Point to the Main Menu bar area Notice that we are unable to see the Main menu bar clearly.


To make it visible, we have to change the system settings.

Click on 'System Settings', Click on the icon 'System Settings', located on top right corner of your machine.


Upon clicking, the System Settings page opens.

Under 'Personal' >> click on ‘Appearance'.


Under the panel 'Personal', double-click on 'Appearance'.

A window named 'Appearance' opens.

From the drop-down menu in the 'Theme' box >> select 'Radiance' >> close the window. Under the tab 'Look', go to Theme.

From the drop-down menu in the 'Theme' box, select 'Radiance' and close the window.

Notice that the Main menu bar is now clearly visible.

Let’s proceed.

Click on File >> New


Click on New icon in the menu bar.


To open a new document, click on File and then on New.


Alternately, click on the New icon in the menu bar.


Or, press Ctrl + N keys.

Type the filename as 'Create and Edit'. A dialog box New Document appears on the screen, prompting us to name the file.


Type the filename as 'Create and Edit'.

Type 900 for Width ,  800 for height >> click Ok Set the Width to 900, Height to 800.


Click on the Ok button at the bottom.

Click Ok.


An information box opens.


And all spaces in the name that we gave, changes to underscore.


So, the actual name of our file will be 'Create underscore and underscore Edit'.


Click Ok and proceed.

Point to the draw area. The white area in the centre is what we call the draw area.
Point to the menu bars and toolbars. We will learn about the menu bars, toolbars and various panels in detail in the coming tutorials.
Hover the mouse on Select Mode in the tool bar >> Click.


Before selecting any other icon from the toolbar, click on the Select Mode icon.


This acts as a selection tool.


With this selection tool, we can select, draw and move the components on the draw area.

Before we draw a component, we will ensure that Grid Snap and Grid Visible are enabled in CellDesigner window.
Click on Edit in the main menu bar.

Scroll down and click on Grid Snap.

For that, click on Edit in the main menu bar.

Scroll down and click on Grid Snap.

Click on Edit >> Scroll down and click on Grid Visible. Again, go back to Edit and click on Grid Visible.
Grids enable us to better align the components in the draw area.
Now let us change the position of the List & Notes area.


Recall, we already learnt about List area, Notes area and Draw area in the previous tutorial.


If you do not know, refer to the previous tutorials in this series.

Let's proceed and change the location of the List area.
Go to View >> Click on List and Select Right


Go to View option, click on List and select the option ‘Right’.


It changes ‘List’ to the right side of the draw area.

Change the size and position of the areas.


Place the cursor on borderline of draw area and drag.

The size of the areas can be altered by dragging the borderlines.


I will place the cursor on the borderline .


You can see a double headed arrow. Drag it to maximize or minimize the draw area.

We will now proceed to work on the draw area.
Before that, we should be able to view all the icons on the CellDesigner window.
Cursor on View on the main menu bar toolbar>> Change Toolbar Visible>>Show All For that, go to View on the main menu bar.


Click on Change Toolbar Visible and select the Show All option.

You are now able to see all the icons on the CellDesigner window.

Let's go ahead.

Cursor on the toolbar >> Point towards square icon >> and then click on it To represent a cell or an intracellular compartment, we will use the Square icon from the toolbar.


So, first click on it.

Click on the 'Square' icon>> Click and drag on the draw area. Then click on the draw area.


And without releasing the mouse button, drag to draw the square.


Now release the mouse button.

In the dialog box type Cell and and Size as 1.0 >> Click Ok In the 'Property of Compartment' dialog that opens, specify
  • the Name as Cell
  • and set the Size as 1.0


Click Ok.


The name appears at the bottom of the compartment.

Cursor on Name of the Compartment.


Drag and drop it wherever required.

One can change the position of the compartment name, too.


To do so, select the compartment name, which is Cell, in our case.


Now, drag and drop it wherever you want to place it.

Click on File >> Save.


Let us save this file by clicking on File and then on Save As option.
Choose Desktop >> click on Ok button Now choose the folder where you want to save your file.


I want to save it on the Desktop.

So, I will double click on Desktop as the folder in which I want to save.


And then click on Ok button at the bottom right.


Once again, click on the OK button at the bottom right.

Our file is now saved.

Click on File >> Exit To close CellDesigner, click on File and then on Exit.


Go to the Desktop >> Point to the file


Let us now go to the folder where we saved our file.

So, I will go to my Desktop.


Here is my file.

Point to the file Notice that the file is saved in .xml format.


This is the default CellDesigner file format.

Point to the file Also note, that this file can only be opened in CellDesigner.
Summary Let us summarize

In this tutorial, we learnt to:

  • Install CellDesigner version 4.3 on Ubuntu Linux OS
  • Create a Compartment in CellDesigner
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Contributors and Content Editors

Bellatony911, Nancyvarkey

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