Difference between revisions of "CellDesigner/C2/Create-and-Edit-Components/English"

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(Created page with " {| style="border-spacing:0;" | style="border:1pt solid #000000;padding:0.049cm;"| <center>'''Visual Cue'''</center> | style="border:1pt solid #000000;padding:0.049cm;"| <cent...")
 
 
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* Open an already saved .xml file in the draw area
 
* Open an already saved .xml file in the draw area
−
* Change shape, size, color and thickness of the border of a''' Compartment'''
+
* Change the following in a '''compartment''' :shape, size, color and thickness of the border
 
* Create multiple files in''' CellDesigner'''
 
* Create multiple files in''' CellDesigner'''
 
* Change identity of a '''Species'''
 
* Change identity of a '''Species'''
−
 
−
 
  
 
|-
 
|-
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* To Cut, Copy and Paste a '''Species'''
 
* To Cut, Copy and Paste a '''Species'''
 
* About Start-point and End-point of a '''Species'''
 
* About Start-point and End-point of a '''Species'''
−
* How to Activate a''' Species'''
+
* How to Activate and change color of a''' Species'''
−
* Change color of a''' Species'''
+
* Change properties of a ''' Reaction'''
−
 
+
* How to close a''' File'''
−
* Change properties of''' Reaction'''
+
−
* Close a''' File'''
+
−
 
+
−
 
+
  
 
|-
 
|-
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* '''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:1pt solid #000000;padding:0.049cm;"| To follow this tutorial, you should be familiar with undergraduate''' Biochemistry.'''
+
| style="border:1pt solid #000000;padding:0.049cm;"| To follow this tutorial, you should be familiar with  
−
 
+
*undergraduate''' Biochemistry'''
−
 
+
*and '''CellDesigner '''interface.
−
And you should be familiar with '''CellDesigner '''interface.
+
  
  
−
If not, for relevant''' CellDesigner tutorials''', please visit our website''' spoken-tutorial.org'''
+
If not, for relevant''' CellDesigner tutorials''', please visit our website''' www.spoken-tutorial.org'''
  
 
|-
 
|-
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However, hereon the series will be completed on''' Ubuntu Linux OS'''.
 
However, hereon the series will be completed on''' Ubuntu Linux OS'''.
 +
 +
|-
 +
|style="border:1pt solid #000000;padding:0.049cm;"|
 +
| style="border:1pt solid #000000;padding:0.049cm;"|Let's proceed to create and edit components in '''CellDesigner'''.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Press '''Ctrl+Alt+T''' keys
 
| style="border:1pt solid #000000;padding:0.049cm;"| Press '''Ctrl+Alt+T''' keys
−
| style="border:1pt solid #000000;padding:0.049cm;"| Open the terminal by pressing '''Ctrl+Alt+T''' keys simultaneously.
+
| style="border:1pt solid #000000;padding:0.049cm;"| Open the '''terminal''' by pressing '''Ctrl+Alt+T''' keys simultaneously.
  
 
|-
 
|-
Line 89: Line 84:
  
  
−
Recall, in the Installation tutorial it was mentioned that '''.xml '''file can be opened in '''CellDesigner''' only.
+
So, click on '''File''' and then on '''Open'''.
−
 
+
−
 
+
−
So, click on '''File''' and then on '''Open''' option.
+
  
 
|-
 
|-
Line 99: Line 91:
  
  
−
Here, we have to select the folder under ‘'''Folders’ '''label
+
Here, we have to select the folder under ‘'''Folders’ '''label.
  
  
−
Click on the ''''Create_and_Edit.xml'''' file under the ‘'''File’''' label and then click ‘'''Ok’.'''
+
Click on the ''''Create_and_Edit.xml'''' file under the ‘'''File’''' label and then double-click on ‘'''Ok’.'''
  
 
|-
 
|-
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|-
 
|-
−
| style="border:1pt solid #000000;padding:0.049cm;"| Point to the '''compartment'''
+
| style="border:1pt solid #000000;padding:0.049cm;"| Select the compartment >> click on''' “Component”''' >> scroll down and select''' “Change to OVAL”'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| And here is our compartment named''' Cell'''.
+
  
−
|-
 
−
| style="border:1pt solid #000000;padding:0.049cm;"|
 
−
| style="border:1pt solid #000000;padding:0.049cm;"| To start with, let us change the shape of the compartment to oval.
 
  
−
|-
+
| style="border:1pt solid #000000;padding:0.049cm;"| Select the compartment.
−
| style="border:1pt solid #000000;padding:0.049cm;"| Select the compartment >> click on''' “Component”''' >> scroll down and select''' “Change to OVAL”'''
+
  
  
−
 
+
Go to the '''Component''' in the main menu bar.
−
| style="border:1pt solid #000000;padding:0.049cm;"| Select the compartment.
+
  
  
−
Go to ''''Component'''' in the main menu, scroll down and select ''''Change to OVAL''''.
+
Scroll down and select '''Change to OVAL'''.
  
  
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|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Select the compartment >> click on''' “Component”''' >> scroll down and point to''' Change color & shape'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| Select the compartment >> click on''' “Component”''' >> scroll down and point to''' Change color & shape'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| To change the color or thickness, select the compartment once again.
+
| style="border:1pt solid #000000;padding:0.049cm;"| To change the color or thickness, go to “'''Component'''” in the main menu bar.
  
  
−
Go to “'''Component'''” in the main menu and click on “'''Change color & shape'''” option.
+
Click on “'''Change color & shape'''” option.
  
 
|-
 
|-
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−
For a thinner boundary line, change the ''''Membrane Thickness'''' from 12 to 8 or below.
+
For a thinner boundary line, change the '''Membrane Thickness''' from 12 to 8 or below.
  
 
|-
 
|-
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Click and hold the pointer and rotate to select the preferred color.
 
Click and hold the pointer and rotate to select the preferred color.
−
 
−
 
−
 
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Click on Apply >> Then on Ok.
 
| style="border:1pt solid #000000;padding:0.049cm;"| Click on Apply >> Then on Ok.
−
| style="border:1pt solid #000000;padding:0.049cm;"| After all the modifications are done, click on ''''Apply'''' and then on ''''Ok''''.
+
| style="border:1pt solid #000000;padding:0.049cm;"| After all the modifications are done, click on '''Apply'''.
 +
 
 +
And then on ''''Ok''''.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"|  
 
| style="border:1pt solid #000000;padding:0.049cm;"|  
−
| style="border:1pt solid #000000;padding:0.049cm;"| Explore other options to draw various''' Compartments''' on the reaction toolbar on your own.
+
| style="border:1pt solid #000000;padding:0.049cm;"| Explore other options to draw various''' Compartments''' on the reaction toolbar, on your own.
  
  
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|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"|  
 
| style="border:1pt solid #000000;padding:0.049cm;"|  
−
| style="border:1pt solid #000000;padding:0.049cm;"| We will now learn how to '''change the identity''' of the''' Species'''.
+
| style="border:1pt solid #000000;padding:0.049cm;"| We will now learn how to '''change the identity''' of ''' Species'''.
  
 
|-
 
|-
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−
Now click on '''Ok''' button.
+
And click on '''Ok''' button.
  
 
|-
 
|-
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−
Click on the draw area, in the dialog box, type''' Pectin''' and click on ''''Ok'''' button.
+
Click on the draw area.
 +
 
 +
 
 +
In the dialog box, type''' Pectin''' and click on the '''Ok''' button.
  
 
|-
 
|-
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−
Then click on the option ''''Change Identity''''.
+
And click on the option '''Change Identity'''.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Dialog box ''''Change identity of the''' '''species'''' will be displayed.
 
| style="border:1pt solid #000000;padding:0.049cm;"| Dialog box ''''Change identity of the''' '''species'''' will be displayed.
−
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box named ''''Change identity of the species'''' appears.
+
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box named ''''Change identity of the species'''' appears on the screen.
  
 
|-
 
|-
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−
Now, give a name to this''' simple molecule''' in the''' Name''' box, let's say''' Fructose.'''
+
Now, give a name to this''' simple molecule''' in the''' Name''' box.
 +
 
 +
Let's say''' Fructose.'''
  
  
−
And click on ''''Apply'''' button.
+
And click on '''Apply''' button.
  
 
|-
 
|-
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−
Click on the ''''Edit'''' menu, scroll down and click on ''''Cut''''.
+
Go to '''Edit''' menu, scroll down and click on '''Cut'''.
  
  
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|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Go back to the ''''Edit'''' menu, scroll down, click ''''Paste''''.
 
| style="border:1pt solid #000000;padding:0.049cm;"| Go back to the ''''Edit'''' menu, scroll down, click ''''Paste''''.
−
| style="border:1pt solid #000000;padding:0.049cm;"| To paste the species, go back to the ''''Edit'''' menu, scroll down and click on ''''Paste''''.
+
| style="border:1pt solid #000000;padding:0.049cm;"| To paste the species, go back to the ''''Edit'''' menu, scroll down and click on '''Paste'''.
  
  
Line 272: Line 262:
  
  
−
The''' Species''' reappears on the draw area.
+
The''' Species Fructose''' reappears on the draw area.
  
 
|-
 
|-
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Go to ''''Edit'''' menu, scroll down, click on''' Copy''' >> press''' Ctrl + V'''
 
Go to ''''Edit'''' menu, scroll down, click on''' Copy''' >> press''' Ctrl + V'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| To make a copy, click on the''' Species '''i.e. '''Fructose'''.
+
| style="border:1pt solid #000000;padding:0.049cm;"| To make a copy of the''' Species, go to ''' Edit''' on the main menu bar.
  
 +
Click on''' Copy'''.
  
−
On the''' Edit''' menu, click on''' Copy'''.
 
  
 +
Notice here that the shortcut key for Copy is''' Ctrl+C'''.  Click on '''Copy'''.
  
−
Notice here that the shortcut key for Copy is''' Ctrl+C'''.
+
Click on the draw area.
  
  
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|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Move the '''Fructose '''molecules to the top of the draw area >> click anywhere
 
| style="border:1pt solid #000000;padding:0.049cm;"| Move the '''Fructose '''molecules to the top of the draw area >> click anywhere
−
| style="border:1pt solid #000000;padding:0.049cm;"| Let us drag and move the''' Fructose''' '''molecules''' aside on the draw area.
+
| style="border:1pt solid #000000;padding:0.049cm;"| Let us drag and move the''' Fructose molecules''' aside on the draw area.
  
  
Line 312: Line 303:
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Click on''' Fructose''' and drag it to the top of the draw area.
 
| style="border:1pt solid #000000;padding:0.049cm;"| Click on''' Fructose''' and drag it to the top of the draw area.
−
| style="border:1pt solid #000000;padding:0.049cm;"| Next we will learn, what are '''start-point''' and '''end-point''' '''species''' and how to '''activate''' a '''species'''?
+
| style="border:1pt solid #000000;padding:0.049cm;"| Next we will learn,  
 +
*what are '''start-point''' and '''end-point''' '''species'''  
 +
*and how to '''activate''' a '''species'''?
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| In the same file, draw a''' state transition reaction''' between 2''' generic proteins.'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| In the same file, draw a''' state transition reaction''' between 2''' generic proteins.'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| Now on the draw area, I have drawn a''' state transition reaction''' between 2''' generic proteins, Protein 1 and Protien 2'''
+
| style="border:1pt solid #000000;padding:0.049cm;"| For that, I have already drawn a''' state transition reaction''' between 2''' generic proteins'''. 
−
 
+
−
 
+
  
 +
I have named them '''Protein 1''' and '''Protein 2'''.
  
 
|-
 
|-
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−
Let's proceed.
+
Let us proceed.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Point to and then to '''Protein 2'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| Point to and then to '''Protein 2'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| In this reaction, the''' ‘start point’''' is''' ‘Protein 1’''' and the''' ‘end point’''' is''' Protein 2.'''
+
| style="border:1pt solid #000000;padding:0.049cm;"| In this reaction,  
 +
*the''' ‘start point’''' is''' ‘Protein 1’'''  
 +
*and the''' ‘end point’''' is''' Protein 2.'''
  
 
|-
 
|-
Line 343: Line 337:
  
  
−
Now, press ''''a'''' on the keyboard.
+
So click on ''' Protein 2''' and press '''A''' on the keyboard.
  
 
|-
 
|-
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−
Next, on the main menu bar, go to '''Component,''' scroll down and click on''' Set Active.'''
+
Next, on the main menu bar, go to '''Component.'''  
 +
 
 +
Scroll down and click on''' Set Active.'''
  
 
|-
 
|-
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| style="border:1pt solid #000000;padding:0.049cm;"| In the color wheel >> select the preferred color >> click on 'Apply' >> 'Ok'.
 
| style="border:1pt solid #000000;padding:0.049cm;"| In the color wheel >> select the preferred color >> click on 'Apply' >> 'Ok'.
 
| style="border:1pt solid #000000;padding:0.049cm;"| As we saw earlier, in the''' Color''' panel is the color wheel.
 
| style="border:1pt solid #000000;padding:0.049cm;"| As we saw earlier, in the''' Color''' panel is the color wheel.
 +
 +
 
Click and rotate the pointer, to select the preferred color.
 
Click and rotate the pointer, to select the preferred color.
−
Then, click on ''''Apply'''' and ''''Ok''''.
+
 
 +
 
 +
Then, click on '''Apply''' and '''Ok'''.
 +
 
 +
 
 
Observe the color change in the''' species.'''
 
Observe the color change in the''' species.'''
 
'''<nowiki><<</nowiki>PAUSE>>'''
 
'''<nowiki><<</nowiki>PAUSE>>'''
Line 386: Line 388:
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Right click on the Reaction arrow between the two Species>> select ''''Change Identity'.'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| Right click on the Reaction arrow between the two Species>> select ''''Change Identity'.'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| Right click on the reaction arrow between the two species.
+
| style="border:1pt solid #000000;padding:0.049cm;"| Right-click on the '''reaction arrow''' between the two '''species'''.
−
Now select ''''Change Identity'''' option.
+
 
 +
 
 +
Now select '''Change Identity''' option.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box 'Change Properties of the Reaction' appears >> Type '''Reaction1'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box 'Change Properties of the Reaction' appears >> Type '''Reaction1'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box ''''Change Properties of the Reaction'''' appears.
+
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box '''Change Properties of the Reaction''' appears.
  
−
Type the name of the reaction in the ''''Name'''' box, say''' Reaction1.'''
+
Type the name of the reaction in the '''Name''' box, say''' Reaction1.'''
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| From the drop-down menu in the 'Type' box >> select Transport reaction >> Click on ''''Ok''''.
 
| style="border:1pt solid #000000;padding:0.049cm;"| From the drop-down menu in the 'Type' box >> select Transport reaction >> Click on ''''Ok''''.
−
| style="border:1pt solid #000000;padding:0.049cm;"| Select the required reaction from the drop-down menu in the ''''Type'''' box, say''' Transcription'''.
+
| style="border:1pt solid #000000;padding:0.049cm;"| Select the required reaction from the drop-down menu in the '''Type''' box, say''' Transcription'''.
 +
 
 +
 
 
Click on ''''Ok''''.
 
Click on ''''Ok''''.
  
Line 405: Line 411:
  
 
We do not see the name that we gave on the reaction arrow in the draw area.
 
We do not see the name that we gave on the reaction arrow in the draw area.
 +
 +
 
Don't worry, we will learn about it in upcoming tutorials.
 
Don't worry, we will learn about it in upcoming tutorials.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Right click on the Reaction arrow >> click on''' Change Identity >>''' select''' TRUE >>''' click on ''''Ok''''.
 
| style="border:1pt solid #000000;padding:0.049cm;"| Right click on the Reaction arrow >> click on''' Change Identity >>''' select''' TRUE >>''' click on ''''Ok''''.
−
| style="border:1pt solid #000000;padding:0.049cm;"| Let's right-click once again on the reaction arrow and click on''' Change Identity'''.
+
| style="border:1pt solid #000000;padding:0.049cm;"| Let's right-click once again on the '''reaction arrow''' and click on''' Change Identity''' option.
  
−
In case it is a ''''Reversible'''' reaction, select the option''' TRUE''' and click on ''''Ok''''.
+
In case it is a '''Reversible''' reaction, select the option''' TRUE''' and click on '''Ok'''.
  
 
|-
 
|-
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| style="border:1pt solid #000000;padding:0.049cm;"| To exit''' CellDesigner''', click on''' File''' and select''' Exit''' option.
 
| style="border:1pt solid #000000;padding:0.049cm;"| To exit''' CellDesigner''', click on''' File''' and select''' Exit''' option.
  
−
Alternately, you may press''' Ctrl+Q.'''
+
 
 +
Alternately, you may press''' Ctrl Q.'''
  
 
'''<nowiki><<</nowiki>PAUSE>>'''
 
'''<nowiki><<</nowiki>PAUSE>>'''
 +
 +
 +
|-
 +
| style="border:1pt solid #000000;padding:0.049cm;"| Confirmation dialog box >> Click '''Yes'''>>double-click on '''Ok'''
 +
| style="border:1pt solid #000000;padding:0.049cm;"|A dialog box '''Confirmation''' appears on the screen asking if we wish to save the changes.
 +
 +
Click '''Yes''' and double-click on the '''Ok''' button.
 +
 +
|-
 +
| style="border:1pt solid #000000;padding:0.049cm;"|Click '''Yes'''
 +
| style="border:1pt solid #000000;padding:0.049cm;"|It says the file has been modified. 
 +
 +
 +
'''Save the changes?'''
 +
 +
Click '''Yes'''.
  
 
|-
 
|-
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* Open an already saved .xml file in the draw area
 
* Open an already saved .xml file in the draw area
−
* Change shape, size, color and thickness of the border of a''' Compartment'''  
+
* Change shape, size, color and thickness of the border of the ''' Compartment'''  
 
* Create multiple files in''' CellDesigner'''
 
* Create multiple files in''' CellDesigner'''
−
* Change identity of a '''Species'''
+
* And change identity  
 +
* And Cut, Copy and Paste a '''Species'''
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| Summary
 
| style="border:1pt solid #000000;padding:0.049cm;"| Summary
−
| style="border:1pt solid #000000;padding:0.049cm;"| We have learnt:
+
| style="border:1pt solid #000000;padding:0.049cm;"| We also learnt:
−
 
+
−
* To Cut, Copy and Paste a '''Species'''
+
 
* About Start-point and End-point of a '''Species'''
 
* About Start-point and End-point of a '''Species'''
 
* How to Activate a''' Species'''
 
* How to Activate a''' Species'''
 
* Change color of a''' Species'''
 
* Change color of a''' Species'''
−
* Change properties of''' Reaction'''
+
* Change properties of a ''' Reaction'''
−
* Close a''' File'''
+
* And close a''' File'''
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| '''Assignment'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| '''Assignment'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| Using tools in the tool bar:
+
| style="border:1pt solid #000000;padding:0.049cm;"| For your assignment:
  
 
* Create a''' complex''' and place a''' Species''' inside the''' Complex'''
 
* Create a''' complex''' and place a''' Species''' inside the''' Complex'''
−
* Explore the toolbar and find out how to add a''' reactant''' and a''' product''' to a reaction.
+
* Assignment 2: Explore the toolbar and find out  
 +
**how to add a''' reactant''' and a''' product''' to a reaction.
 +
 
 +
 
 
Your completed assignment should look like this.
 
Your completed assignment should look like this.
 +
 +
 +
|-
 +
| style="border:1pt solid #000000;padding:0.049cm;"|Screenshots
 +
| style="border:1pt solid #000000;padding:0.049cm;"|
 +
*Your first assignment will look like this:
 +
**A complex and ''' Species''' placed inside the''' Complex'''.
 +
* Assignment 2 will look like this:
 +
**A '''state-transition reaction''' with a''' reactant''' and a''' product'''.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"| '''Acknowledgement'''
 
| style="border:1pt solid #000000;padding:0.049cm;"| '''Acknowledgement'''
−
| style="border:1pt solid #000000;padding:0.049cm;"| The video at this link summarizes the Spoken Tutorial project.
+
| style="border:1pt solid #000000;padding:0.049cm;"| About the Spoken Tutorial Project:
 +
 
 +
The video at this link summarizes the Spoken Tutorial project.
  
−
Please watch it.
+
Please download and watch it.
  
 
|-
 
|-
 
| style="border:1pt solid #000000;padding:0.049cm;"|  
 
| style="border:1pt solid #000000;padding:0.049cm;"|  
−
| style="border:1pt solid #000000;padding:0.049cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates to those who pass an on-line test.
+
| style="border:1pt solid #000000;padding:0.049cm;"| The Spoken Tutorial Project  
 +
*conducts workshops and  
 +
*gives certificates on passing an on-line test.
  
 
For more details, please write to us.
 
For more details, please write to us.
Line 471: Line 511:
 
| style="border:1pt solid #000000;padding:0.049cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
 
| style="border:1pt solid #000000;padding:0.049cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
  
−
More information on this Mission is available at this link'''.'''
+
More information on this Mission is available on this link.
  
 
|-
 
|-

Latest revision as of 17:14, 30 June 2015

Visual Cue
Narration
Slide Number 1

Title

Hello everyone.


Welcome to this tutorial on Create and Edit Components in CellDesigner.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to:
  • Open an already saved .xml file in the draw area
  • Change the following in a compartment :shape, size, color and thickness of the border
  • Create multiple files in CellDesigner
  • Change identity of a Species
Slide Number 3

Learning Objectives contd. ...

We will also learn
  • To Cut, Copy and Paste a Species
  • About Start-point and End-point of a Species
  • How to Activate and change color of a Species
  • Change properties of a Reaction
  • How to close a File
Slide Number 4

System Requirement

Here I am using
  • Ubuntu Linux OS version 14.04
  • CellDesigner version 4.3
  • Java version 1.7
Slide Number 5

Pre-requisites

To follow this tutorial, you should be familiar with
  • undergraduate Biochemistry
  • and CellDesigner interface.


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

Slide 6


Learners please note: some of the previous tutorials in this series, were created on Windows OS.


However, hereon the series will be completed on Ubuntu Linux OS.

Let's proceed to create and edit components in CellDesigner.
Press Ctrl+Alt+T keys Open the terminal by pressing Ctrl+Alt+T keys simultaneously.
Type ./runCellDesigner4.3 >> press Enter. Now type ./runCellDesigner4.3 and press Enter.
Click on File >>Open Let us open the file Create and Edit that we had created earlier.


So, click on File and then on Open.

Click on 'Create and Edit'. A dialog box named Open appears on the screen.


Here, we have to select the folder under ‘Folders’ label.


Click on the 'Create_and_Edit.xml' file under the ‘File’ label and then double-click on ‘Ok’.

Our file Create_and_Edit.xml is now open in the draw area.
Select the compartment >> click on “Component” >> scroll down and select “Change to OVAL”


Select the compartment.


Go to the Component in the main menu bar.


Scroll down and select Change to OVAL.


On the draw area, we now have an oval compartment.

Select the compartment >> click on “Component” >> scroll down and point to Change color & shape To change the color or thickness, go to “Component” in the main menu bar.


Click on “Change color & shape” option.

Alternately, right-click on the compartment boundary and select “Change color & shape” option.
A dialog box appears on the screen.


Change the number to 8.

A dialog box named 'Change color & shape' appears on the screen.


For a thinner boundary line, change the Membrane Thickness from 12 to 8 or below.

Go to Color panel >> Click on the color wheel >> select any color


To change the color, go to Color panel.


In the Color panel is a color wheel, with a pointer like handle.


Click and hold the pointer and rotate to select the preferred color.

Click on Apply >> Then on Ok. After all the modifications are done, click on Apply.

And then on 'Ok'.

Explore other options to draw various Compartments on the reaction toolbar, on your own.


<<PAUSE>>

We will now learn how to change the identity of Species.
Press CTRL+N


Type Change Species.


So, first we will open a new window by pressing CTRL+N.


Let us give a name to this file, say Change Species.


We will keep the default width and height.


And click on Ok button.

Click on icon for generic protein>>Click on the draw area>> name it as Pectin>> click on Ok. Now, click on the icon for 'Generic protein' from the toolbar.


Click on the draw area.


In the dialog box, type Pectin and click on the Ok button.

Right click on Pectin >> Click 'change identity' option Now right-click on the Generic protein Pectin.


And click on the option Change Identity.

Dialog box 'Change identity of the species' will be displayed. A dialog box named 'Change identity of the species' appears on the screen.
Click on the down arrow button in the class box >> select simple molecule>> type Fructose in the Name box >> click on 'Apply'


Click on the down arrow in the Class box.


Select any option, for example, say simple molecule, from the drop-down menu.


Now, give a name to this simple molecule in the Name box.

Let's say Fructose.


And click on Apply button.

Point on the draw area. Observe that our Protein Pectin is now converted to a simple molecule named Fructose.
Let us now learn to Cut, Copy and Paste.


I will use the same Fructose that is already present on the draw area.

Click on a Species.


Go to 'Edit' menu, scroll down, click on 'Cut'.


To cut a Species, click on the Species Fructose first.


Go to Edit menu, scroll down and click on Cut.


Notice here that the shortcut key for Cut is Ctrl+X.


The Species Fructose has been cut.

Go back to the 'Edit' menu, scroll down, click 'Paste'. To paste the species, go back to the 'Edit' menu, scroll down and click on Paste.


Notice here that the shortcut key for Paste is Ctrl+V.


The Species Fructose reappears on the draw area.

Click on a Species.


Go to 'Edit' menu, scroll down, click on Copy >> press Ctrl + V

To make a copy of the Species, go to Edit on the main menu bar.

Click on Copy.


Notice here that the shortcut key for Copy is Ctrl+C. Click on Copy.

Click on the draw area.


This time, let us press Ctrl + V to paste.

We now have a copy of Fructose on the draw area.
To undo any action press Ctrl+Z and to redo any action press Ctrl+Y.


These are however, limited in their use.

<<PAUSE>>

Move the Fructose molecules to the top of the draw area >> click anywhere Let us drag and move the Fructose molecules aside on the draw area.


To do so, click on Fructose and drag it to the desired location.

Click on Fructose and drag it to the top of the draw area. Next we will learn,
  • what are start-point and end-point species
  • and how to activate a species?
In the same file, draw a state transition reaction between 2 generic proteins. For that, I have already drawn a state transition reaction between 2 generic proteins.

I have named them Protein 1 and Protein 2.

Recall, we already learnt how to draw a reaction earlier.


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


Let us proceed.

Point to and then to Protein 2 In this reaction,
  • the ‘start point’ is ‘Protein 1’
  • and the ‘end point’ is Protein 2.
Select Protein2 >> press “a” on keyboard. To activate a species, click on a Species which is an 'end-point' of a Reaction.


In our case, it is Protein 2.


So click on Protein 2 and press A on the keyboard.

Press Ctrl + Z Let me undo this change by pressing Ctrl + Z keys.
On the main menu bar, click on Component >> scroll down >> click on Set Active' Alternately, click on Protein 2


Next, on the main menu bar, go to Component.

Scroll down and click on Set Active.

Point to the species. Notice that the activated species is wrapped by a dashed line.
Let us now change the color of the species, Protein 2.
Click on it once >> Click on 'Change color and shape'. So, right-click on it and then click on 'Change color and shape'.
In the color wheel >> select the preferred color >> click on 'Apply' >> 'Ok'. As we saw earlier, in the Color panel is the color wheel.


Click and rotate the pointer, to select the preferred color.


Then, click on Apply and Ok.


Observe the color change in the species. <<PAUSE>>

We will now learn how to change the properties of a Reaction.
Point to the reaction. Let us come back to our state transition reaction present on the draw area.
Right click on the Reaction arrow between the two Species>> select 'Change Identity'. Right-click on the reaction arrow between the two species.


Now select Change Identity option.

A dialog box 'Change Properties of the Reaction' appears >> Type Reaction1 A dialog box Change Properties of the Reaction appears.

Type the name of the reaction in the Name box, say Reaction1.

From the drop-down menu in the 'Type' box >> select Transport reaction >> Click on 'Ok'. Select the required reaction from the drop-down menu in the Type box, say Transcription.


Click on 'Ok'.

Point to the reaction Observe that the reaction has changed on the draw area.

We do not see the name that we gave on the reaction arrow in the draw area.


Don't worry, we will learn about it in upcoming tutorials.

Right click on the Reaction arrow >> click on Change Identity >> select TRUE >> click on 'Ok'. Let's right-click once again on the reaction arrow and click on Change Identity option.

In case it is a Reversible reaction, select the option TRUE and click on Ok.

You will now see that the reaction has reversed.
To exit CellDesigner >> Click on File menu >> select Exit option To exit CellDesigner, click on File and select Exit option.


Alternately, you may press Ctrl Q.

<<PAUSE>>


Confirmation dialog box >> Click Yes>>double-click on Ok A dialog box Confirmation appears on the screen asking if we wish to save the changes.

Click Yes and double-click on the Ok button.

Click Yes It says the file has been modified.


Save the changes?

Click Yes.

Summary Let us summarize:

In this tutorial, we have learnt to:

  • Open an already saved .xml file in the draw area
  • Change shape, size, color and thickness of the border of the Compartment
  • Create multiple files in CellDesigner
  • And change identity
  • And Cut, Copy and Paste a Species
Summary We also learnt:
  • About Start-point and End-point of a Species
  • How to Activate a Species
  • Change color of a Species
  • Change properties of a Reaction
  • And close a File
Assignment For your assignment:
  • Create a complex and place a Species inside the Complex
  • Assignment 2: Explore the toolbar and find out
    • how to add a reactant and a product to a reaction.


Your completed assignment should look like this.


Screenshots
  • Your first assignment will look like this:
    • A complex and Species placed inside the Complex.
  • Assignment 2 will look like this:
    • A state-transition reaction with a reactant and a product.
Acknowledgement About the Spoken Tutorial Project:

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Please download and watch it.

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This is Bella Tony from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Bellatony911, Nancyvarkey

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