CellDesigner/C2/Installation-of-CellDesigner-on-Linux/English
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Slide Number 1
Title |
Hello everyone.
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Slide Number 2
Learning Objectives |
In this tutorial we will learn to
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Slide Number 3
System Requirement |
Here I am using
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Slide Number 4
Pre-requisites |
To follow this tutorial, you should be familiar with basic operations on Linux OS.
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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 | Click on Download CellDesigner button at the top right hand side.
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Scroll down >> locate Download | Scroll down and locate Download.
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Now, let us see how to find out the details of the OS type of our machine. | |
Click on 'System Settings', | Click on the icon 'System Settings', located at the top right corner of your machine. |
Under 'System' >> click on ‘Details'. | Under the panel 'System', double click on the icon 'Details'. |
Highlight OS type field | A window named 'Details' opens.
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Highlight OS type field
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I have a 64 bit machine.
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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.
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Now, we are prompted to fill up some personal details. | |
Pause recording and fill the details.
Resume the recording. |
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After filling these, click on Download button. | |
Click on Save File button | A dialog box opens.
Click on ok button.
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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.
cd Downloads and press Enter.
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Here is the file which we downloaded
CellDesigner-4.3-linux-x64-installer.run | |
Text on screen during editing | If you downloaded 32 bit installer, then the file name will have 32 instead of 64.
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Type sudo chmod 777 -R CellDesigner-4.3-linux-x64-installer.run
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Now, we have to change the file permission.
sudo chmod 777 -R CellDesigner-4.3-linux-x64 -installer.run
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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
./CellDesigner-4.3-linux-x64-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.
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Installation Directory dialog shows the directory where CellDesigner will be installed.
/home/<your username>/CellDesigner4.3
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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.
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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
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We can see runCellDesigner4.3 file here.
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Type ./runCellDesigner4.3 >> press Enter. | So type ./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.
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Click on 'System Settings', | Click on the icon 'System Settings', located on top right corner of the Computer. |
Under 'Personal' >> click on ‘Appearance'.
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Under the panel 'Personal', double click on the icon 'Appearance'.
A window named 'Appearance' opens. Here, select the tab 'Look'. |
From the drop-down menu in the 'Theme' box >> select 'Radiance' >> close the window. | 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
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To open a new document click on File and then on New.
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Type the filename as 'Create and Edit'. | A dialog box New Document appears on the screen, prompting us to name the file.
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Type 900 for Width , 800 for height >> click Ok | Set the Width to 900, Height to 800 and click on the Ok button at the bottom. |
Click Ok.
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An 'Information' box opens and all spaces in the name that we gave, changes to underscore.
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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.
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Before selecting any other icon from the toolbar, click on the Select Mode icon.
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Before we draw a component, we will ensure that Grid Snap and Grid Visible are enabled in CellDesigner. | |
Click on Edit in the main menu bar.
Scroll down and click on Grid Snap. |
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. | Go back to Edit again 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.
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Let's proceed and change the location of the List area. | |
Go to View >> Click on List and Select Right
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Go to View option, click on List and select the option ‘Right’.
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Change the size and position of the areas.
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The size of the areas can be altered by
dragging the borderlines.
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We will now proceed to work on the draw area. | |
Before that, we should be able to view all the icons on the menu bar of the CellDesigner window. | |
Cursor on View on the main menu bar toolbar>> Change Toolbar Visible>>Show All | Go to View on the main menu bar, scroll down and select Change Toolbar Visible
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Observe, you are now able to see all the icons on the CellDesigner window | |
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.
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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.
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In the dialog box type Cell and and Size as 1.0 >> Click Ok | In the 'Property of Compartment' dialog that opens, specify Name as Cell and Size as 1.0
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Cursor on Name of the Compartment.
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One can change the position of the compartment name, too.
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Click on File >> Save.
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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.
Our file is now saved. |
Click on File >> Exit | To close CellDesigner, click on File and then on Exit. |
Close both the terminal windows | We will now close the terminal windows which we had opened earlier. |
Go to the Desktop >> Point to the file
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Let us now go to the folder where we saved our file. So, I will go to my Desktop.
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Point to the file | Notice that the file is saved in .xml format.
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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:
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