CellDesigner/C2/Create-and-Edit-Components/English - Revision history

Nancyvarkey at 11:44, 30 June 2015

2015-06-30T11:44:49Z

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Bellatony911: Created page with " {| style="border-spacing:0;" | style="border:1pt solid #000000;padding:0.049cm;"| '''Visual Cue''' | style="border:1pt solid #000000;padding:0.049cm;"|
2015-06-30T10:42:15Z

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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{| style="border-spacing:0;"
| style="border:1pt solid #000000;padding:0.049cm;"| <center>'''Visual Cue'''</center>
| style="border:1pt solid #000000;padding:0.049cm;"| <center>'''Narration'''</center>

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Slide Number 1'''

'''Title '''
| style="border:1pt solid #000000;padding:0.049cm;"| Hello everyone.

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

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Slide Number 2'''

'''Learning Objectives'''
| style="border:1pt solid #000000;padding:0.049cm;"| In this tutorial, we will learn to:

* Open an already saved .xml file in the draw area
* Change shape, size, color and thickness of the border of a''' Compartment'''
* Create multiple files in''' CellDesigner'''
* Change identity of a '''Species'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Slide Number 3'''

'''Learning Objectives contd. ...'''
| style="border:1pt solid #000000;padding:0.049cm;"| We will also learn

* To Cut, Copy and Paste a '''Species'''
* About Start-point and End-point of a '''Species'''
* How to Activate a''' Species'''
* Change color of a''' Species'''

* Change properties of''' Reaction'''
* Close a''' File'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Slide Number 4'''

'''System Requirement'''
| style="border:1pt solid #000000;padding:0.049cm;"| Here I am using

* '''Ubuntu Linux OS version 14.04'''
* '''CellDesigner version 4.3'''
* '''Java version 1.7'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Slide Number 5'''

'''Pre-requisites'''
| style="border:1pt solid #000000;padding:0.049cm;"| To follow this tutorial, you should be familiar with undergraduate''' Biochemistry.'''

And you should be familiar with '''CellDesigner '''interface.

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

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Slide 6'''

| style="border:1pt solid #000000;padding:0.049cm;"| 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'''.

|-
| 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;"| Type '''./runCellDesigner4.3''' >> press '''Enter'''.
| style="border:1pt solid #000000;padding:0.049cm;"| Now type '''./runCellDesigner4.3''' and press '''Enter'''.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on '''File''' >>'''Open'''
| style="border:1pt solid #000000;padding:0.049cm;"| Let us open the file '''Create and Edit '''that we had created earlier.

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''' option.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on ''''Create and Edit''''.
| style="border:1pt solid #000000;padding:0.049cm;"| 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 click ‘'''Ok’.'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| Our file '''Create_and_Edit.xml '''is now open in the draw area.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Point to the '''compartment'''
| 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 >> click on''' “Component”''' >> scroll down and select''' “Change to OVAL”'''

| 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''''.

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

|-
| 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.

Go to “'''Component'''” in the main menu and click on “'''Change color & shape'''” option.

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| Alternately, right-click on the compartment boundary and select “'''Change color & shape'''” option.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| A dialog box appears on the screen.

Change the number to 8.
| style="border:1pt solid #000000;padding:0.049cm;"| 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.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Go to''' Color panel >>''' Click on the color wheel >> select any color

| style="border:1pt solid #000000;padding:0.049cm;"| 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.

|-
| 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;"|
| style="border:1pt solid #000000;padding:0.049cm;"| Explore other options to draw various''' Compartments''' on the reaction toolbar on your own.

<nowiki><<</nowiki>PAUSE>>

|-
| 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;"| Press''' CTRL+N'''

Type''' Change Species.'''

| style="border:1pt solid #000000;padding:0.049cm;"| 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.

Now click on '''Ok''' button.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on icon for generic protein>>Click on the draw area>> name it as Pectin>> click on Ok.
| style="border:1pt solid #000000;padding:0.049cm;"| 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 ''''Ok'''' button.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Right click on Pectin >> Click ''''change identity'''' option
| style="border:1pt solid #000000;padding:0.049cm;"| Now right-click on the''' Generic protein Pectin'''.

Then 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;"| A dialog box named ''''Change identity of the species'''' appears.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on the down arrow button in the''' class''' box >> select''' simple molecule'''>> type''' Fructose''' in the''' Name''' box >> click on ''''Apply''''

| style="border:1pt solid #000000;padding:0.049cm;"| 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.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Point on the draw area.
| style="border:1pt solid #000000;padding:0.049cm;"| Observe that our''' Protein Pectin''' is now converted to a''' simple molecule''' named''' Fructose'''.

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| Let us now learn to''' Cut, Copy''' and''' Paste'''.

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

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on a''' Species'''.

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

| style="border:1pt solid #000000;padding:0.049cm;"| To cut a''' Species''', click on the''' Species Fructose''' first.

Click on the ''''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.

|-
| 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''''.

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

The''' Species''' reappears on the draw area.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on a''' Species'''.

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'''.

On the''' Edit''' menu, click on''' Copy'''.

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

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

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| We now have a copy of '''Fructose''' on the draw area.

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| To undo any action press''' Ctrl+Z''' and to redo any action press''' Ctrl+Y'''.

These are however, limited in their use.

<nowiki><<</nowiki>PAUSE>>

|-
| 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.

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

|-
| 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;"| 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;"|
| style="border:1pt solid #000000;padding:0.049cm;"| Recall, we already learnt how to draw a''' reaction''' earlier.

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

Let's proceed.

|-
| 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;"| Select''' Protein2''' >> press “'''a'''” on keyboard.
| style="border:1pt solid #000000;padding:0.049cm;"| To activate a''' species,''' click on a''' Species''' which is an''' 'end-point'''' of a''' Reaction.'''

In our case, it is''' Protein 2'''.

Now, press ''''a'''' on the keyboard.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Press Ctrl + Z
| style="border:1pt solid #000000;padding:0.049cm;"| Let me undo this change by pressing''' Ctrl + Z''' keys.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| On the main menu bar, click on''' Component >>''' scroll down >> click on''' Set Active''''
| style="border:1pt solid #000000;padding:0.049cm;"| Alternately, click on''' Protein 2'''

Next, on the main menu bar, go to '''Component,''' scroll down and click on''' Set Active.'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Point to the species.
| style="border:1pt solid #000000;padding:0.049cm;"| Notice that the''' activated species''' is wrapped by a dashed line.

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| Let us now change the color of the''' species, Protein 2.'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Click on it once >> Click on ''''Change color and shape''''.
| style="border:1pt solid #000000;padding:0.049cm;"| So, right-click on it and then click on ''''Change color and shape''''.

|-
| 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.
Click and rotate the pointer, to select the preferred color.
Then, click on ''''Apply'''' and ''''Ok''''.
Observe the color change in the''' species.'''
'''<nowiki><<</nowiki>PAUSE>>'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| We will now learn how to change the properties of a''' Reaction'''.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Point to the reaction.
| style="border:1pt solid #000000;padding:0.049cm;"| Let us come back to our''' state transition reaction '''present on the draw area.

|-
| 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.
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 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;"| Select the required reaction from the drop-down menu in the ''''Type'''' box, say''' Transcription'''.
Click on ''''Ok''''.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Point to the''' reaction'''
| style="border:1pt solid #000000;padding:0.049cm;"| 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.

|-
| 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'''.

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

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| You will now see that the reaction has reversed.

|-
| style="border:1pt solid #000000;padding:0.049cm;"| To exit CellDesigner >> Click on''' File''' menu >> 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.'''

'''<nowiki><<</nowiki>PAUSE>>'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Summary
| style="border:1pt solid #000000;padding:0.049cm;"| 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 a''' Compartment'''
* Create multiple files in''' CellDesigner'''
* Change identity of a '''Species'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| Summary
| style="border:1pt solid #000000;padding:0.049cm;"| We have learnt:

* To Cut, Copy and Paste a '''Species'''
* About Start-point and End-point of a '''Species'''
* How to Activate a''' Species'''
* Change color of a''' Species'''
* Change properties of''' Reaction'''
* Close a''' File'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"| '''Assignment'''
| style="border:1pt solid #000000;padding:0.049cm;"| Using tools in the tool bar:

* 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.
Your completed assignment should look like this.

|-
| 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.

Please watch it.

|-
| 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.

For more details, please write to us.

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| 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'''.'''

|-
| style="border:1pt solid #000000;padding:0.049cm;"|
| style="border:1pt solid #000000;padding:0.049cm;"| This is Bella Tony from''' IIT Bombay''' signing off. Thank you for joining.
|}