Sandhya.np14 at 11:54, 6 June 2018

2018-06-06T11:54:08Z

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Jyotisolanki at 06:20, 21 November 2017

2017-11-21T06:20:39Z

Jyotisolanki at 11:59, 12 October 2017

2017-10-12T11:59:19Z

Jyotisolanki at 11:34, 12 October 2017

2017-10-12T11:34:27Z

Jyotisolanki: Created page with " {| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone. Welcome to this tutorial on''' Create and Edit Components''' in''' CellDesigner'''. |- | 00:08 |..."

2017-09-19T09:59:35Z

Created page with " {| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone. Welcome to this tutorial on''' Create and Edit Components''' in''' CellDesigner'''. |- | 00:08 |..."

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{| border=1
|| '''Time'''
|| '''Narration'''

|-
| 00:01
| Hello everyone. Welcome to this tutorial on''' Create and Edit Components''' in''' CellDesigner'''.

|-
| 00:08
| In this tutorial, we will learn to: Open an already saved .xml file in the draw area.

|-
| 00:15
| Change the following in a '''compartment''' :shape, size, color and thickness of the border.

|-
| 00:22
| Createmultiple files in''' CellDesigner''' Change identity of a '''Species'''

|-
| 00:28
| We will also learn how to Cut, Copy and Paste a '''Species''' About Start-point and End-point of a '''Species'''.

|-
| 00:37
|How to Activate and change color of a''' Species'''. Change properties of a ''' Reaction''' How to close a''' File'''.

|-
| 00:47
| Here I am using '''Ubuntu Linux OS version 14.04''' '''CellDesigner version 4.3''' '''Java version 1.7'''

|-
| 00:57
| To follow this tutorial, you should be familiar with undergraduate''' Biochemistry''' and '''CellDesigner '''interface.

|-
| 01:05
| If not, for relevant''' CellDesigner tutorials''', please visit our website''' www.spoken-tutorial.org'''

|-
| 01:16
| Learners please note: some of the previous tutorials in this series, were created on''' Windows OS'''.

|-
| 01:24
| However, hereon the series will be completed on''' Ubuntu Linux OS'''.

|-
|01:30
| Let's proceed to create and edit components in '''CellDesigner'''.

|-
| 01:35
| Open the '''terminal''' by pressing '''Ctrl+Alt+T''' keys simultaneously.

|-
| 01:41
| Now type '''./runCellDesigner4.3''' and press '''Enter'''.

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| 01:52
|''' CellDesigner ''' window now open on your screen.

|-
| 01:56
| Let us open the file '''Create and Edit '''that we had created earlier.

|-
| 02:02
| So, click on '''File''' and then on '''Open'''.

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| 02:07
| A dialog box named''' Open''' appears on the screen.

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| 02:11
| Here, we have to select the folder under ‘'''Folders’ '''label.

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| 02:15
| Click on the ''''Create_and_Edit.xml'''' file under the ‘'''File’''' label and then double-click on ‘'''Ok’.'''

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| 02:27
| Our file '''Create_and_Edit.xml '''is now open in the draw area.

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| 02:35
| Select the compartment. Go to the '''Component''' in the main menu bar.

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| 02:43
| Scroll down and select '''Change to OVAL'''.

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| 02:48
| On the draw area, we now have an oval compartment.

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| 02:54
| To change the color or thickness, go to “'''Component'''” in the main menu bar.

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| 03:00
| Click on “'''Change color & shape'''” option.

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| 03:05
| Alternately, right-click on the compartment boundary and select “'''Change color & shape'''” option.

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| 03:14
| A dialog box named ''''Change color & shape'''' appears on the screen.

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| 03:20
| For a thinner boundary line, change the '''Membrane Thickness''' from 12 to 8 or below.

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| 03:29
| To change the color, go to''' Color panel.'''

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| 03:34
| In the''' Color panel''' is a color wheel, with a pointer like handle.

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| 03:39
| Click and hold the pointer and rotate to select the preferred color.

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| 03:46
| After all the modifications are done, click on '''Apply'''. And then on ''''Ok''''.

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| 03:53
| Explore other options to draw various''' Compartments''' on the reaction toolbar, on your own.

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| 04:00
| We will now learn how to '''change the identity''' of ''' Species'''.

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| 04:05
| So, first we will open a new window by pressing''' CTRL+N'''.

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| 04:11
| Let us give a name to this file, say''' Change Species'''.

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| 04:16
| We will keep the default width and height. And click on '''Ok''' button.

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| 04:22
| Now, click on the icon for ''''Generic protein'''' from the toolbar. Click on the draw area.

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| 04:30
|In the dialog box, type''' Pectin''' and click on the '''Ok''' button.

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| 04:37
| Now right-click on the''' Generic protein Pectin'''.

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| 04:41
|And click on the option '''Change Identity'''.

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| 04:46
| A dialog box named ''''Change identity of the species'''' appears on the screen.

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| 04:53
| Click on the down arrow in the''' Class''' box.

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| 04:58
|Select any option, for example, say''' simple molecule''', from the drop-down menu.

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| 05:05
|Now, give a name to this''' simple molecule''' in the''' Name''' box.

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| 05:10
|Let's say''' Fructose.''' And click on '''Apply''' button.

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| 05:17
| Observe that our''' Protein Pectin''' is now converted to a''' simple molecule''' named''' Fructose'''.

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| 05:25
| Let us now learn to''' Cut, Copy''' and''' Paste'''.

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| 05:29
|I will use the same '''Fructose''' that is already present on the draw area.

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| 05:34
| To cut a''' Species''', click on the''' Species Fructose''' first.

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| 05:40
|Go to '''Edit''' menu, scroll down and click on '''Cut'''.

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| 05:47
|Notice here that the shortcut key for''' Cut''' is''' Ctrl+X'''.

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| 05:53
|The''' Species Fructose '''has been cut.

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| 05:56
| To paste the species, go back to the ''''Edit'''' menu, scroll down and click on '''Paste'''.

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| 06:03
|Notice here that the shortcut key for''' Paste''' is''' Ctrl+V'''.

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| 06:08
|The''' Species Fructose''' reappears on the draw area.

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| 06:12
| To make a copy of the''' Species, go to ''' Edit''' on the main menu bar.

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| 06:18
|Click on''' Copy'''.

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| 06:21
|Notice here that the shortcut key for Copy is''' Ctrl+C'''. Click on '''Copy'''. Click on the draw area.

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| 06:31
|This time, let us press''' Ctrl + V''' to paste.

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| 06:36
| We now have a copy of '''Fructose''' on the draw area.

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| 06:40
| To undo any action press''' Ctrl+Z''' and to redo any action press''' Ctrl+Y'''.

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| 06:51
|These are however, limited in their use.

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| 06:55
| Let us drag and move the''' Fructose molecules''' aside on the draw area.

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| 07:00
|To do so, click on''' Fructose''' and drag it to the desired location.

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| 07:07
| Next we will learn, what are '''start-point''' and '''end-point''' '''species''' and how to '''activate''' a '''species'''?

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| 07:13
| For that, I have already drawn a''' state transition reaction''' between 2''' generic proteins'''.

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| 07:21
|I have named them '''Protein 1''' and '''Protein 2'''.

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| 07:25
| Recall, we already learnt how to draw a''' reaction''' earlier.

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| 07:29
|If you do not know, refer to the previous tutorials in this series. Let us proceed.

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| 07:35
| In this reaction, the''' ‘start point’''' is''' ‘Protein 1’''' and the''' ‘end point’''' is''' Protein 2.'''

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| 07:43
| To activate a''' species,''' click on a''' Species''' which is an''' 'end-point'''' of a''' Reaction.'''

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| 07:50
|In our case, it is''' Protein 2'''.

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| 07:53
|So click on ''' Protein 2''' and press '''A''' on the keyboard.

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| 07:59
| Let me undo this change by pressing''' Ctrl + Z''' keys.

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| 08:05
| Alternately, click on''' Protein 2'''

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| 08:09
|Next, on the main menu bar, go to '''Component.'''

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| 08:13
|Scroll down and click on''' Set Active.'''

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| 08:18
| Notice that the''' activated species''' is wrapped by a dashed line.

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| 08:24
| Let us now change the color of the''' species, Protein 2.'''

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| 08:29
| So, right-click on it and then click on ''''Change color and shape''''.

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| 08:35
| As we saw earlier, in the''' Color''' panel is the color wheel.

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| 08:40
|Click and rotate the pointer, to select the preferred color.

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| 08:44
|Then, click on '''Apply''' and '''Ok'''.

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| 08:49
|Observe the color changes in the ''' species ''' ,

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| 08:53
| We will now learn how to change the properties of a''' Reaction'''.

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| 08:57
| Let us come back to our''' state transition reaction '''present on the draw area.

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| 09:03
| Right-click on the '''reaction arrow''' between the two '''species'''.

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| 09:08
|Now select '''Change Identity''' option.

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| 09:13
| A dialog box '''Change Properties of the Reaction''' appears.

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| 09:18
|Type the name of the reaction in the '''Name''' box, say''' Reaction1.'''

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| 09:26
| Select the required reaction from the drop-down menu in the '''Type''' box, say''' Transcription'''. Click on ''''Ok''''.

|-
| 09:38
| Observe that the''' reaction''' has changed on the draw area.

|-
| 09:42
|We do not see the name that we gave on the reaction arrow in the draw area.

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| 09:47
|Don't worry, we will learn about it in upcoming tutorials.

|-
| 09:53
| Let's right-click once again on the '''reaction arrow''' and click on''' Change Identity''' option.

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| 10:00
|In case it is a '''Reversible''' reaction, select the option''' TRUE''' and click on '''Ok'''.

|-
| 10:09
| You will now see that the reaction has reversed.

|-
| 10:14
| To exit''' CellDesigner''', click on''' File''' and select''' Exit''' option.

|-
| 10:20
|Alternately, you may press''' Ctrl Q.'''

|-
| 10:25
| A dialog box '''Confirmation''' appears on the screen asking if we wish to save the changes.

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| 10:32
|Click '''Yes''' and double-click on the '''Ok''' button.

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| 10:38
| It says the file has been modified.

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| 10:41
|'''Save the changes?''' Click '''Yes'''.

|-
| 10:
| Let us summarize: In this tutorial, we have learnt how to:

|-
| 10:50
|Open an already saved .xml file in the draw area

|-
| 10:55
|Change shape, size, color and thickness of the border of the ''' Compartment'''

|-
| 11:01
| Create multiple files in''' CellDesigner''' And change identity

|-
| 11:07
| And Cut, Copy and Paste a '''Species'''

|-
| 11:10
| We also learnt: About Start-point and End-point of a '''Species'''

|-
| 11:15
| How to Activate a''' Species''' Change color of a''' Species''' Change properties of a ''' Reaction'''And close a''' File'''

|-
| 11:25
| For your assignment: Create a''' complex''' and place a''' Species''' inside the''' Complex'''

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| 11:32
|Assignment 2: Explore the toolbar and find out how to add a''' reactant''' and a''' product''' to a reaction.

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| 11:41
|Your completed assignment should look like this.

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| 11:45
| Your first assignment will look like this: A complex and ''' Species''' placed inside the''' Complex'''.

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| 11:55
|Assignment 2 will look like this: A '''state-transition reaction''' with a''' reactant''' and a''' product'''.

|-
| 12:00
|About the spoken tutorial project.

|-
| 12:05
| The video at this link summarizes the Spoken Tutorial project.Please download and watch it.

|-
| 12:13
| The Spoken Tutorial Project conducts workshops and gives certificates on passing an on-line test.For more details, please write to us.

|-
| 12:23
| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available on this link.

|-
| 12:35
| This is Bella Tony from''' IIT Bombay''' signing off. Thank you for joining.
|}

@@ Line 18: / Line 18: @@
 |-
 |  00:22
-| Createmultiple files in''' CellDesigner''' Change identity of a '''Species'''
+| Create multiple files in''' CellDesigner''', Change identity of a '''Species'''
 |-
@@ Line 26: / Line 26: @@
 |-
 | 00:37
-|How to Activate and change color of a''' Species'''. Change properties of a ''' Reaction''' How to close a''' File'''.
+|How to Activate and change color of a''' Species''', Change properties of a ''' Reaction''' , How to close a''' File'''.
 |-
@@ Line 430: / Line 430: @@
 |-
 |  10:50
-|Open an already saved .xml file in the draw area
+|Open an already saved .xml file in the draw area.
 |-
 |  10:55
-|Change shape, size, color and thickness of the border of the ''' Compartment'''
+|Change shape, size, color and thickness of the border of the ''' Compartment'''.
 |-
 |  11:01
-| Create multiple files in''' CellDesigner''' And change identity
+| Create multiple files in''' CellDesigner''' And change identity.
 |-
 |  11:07
-| And Cut, Copy and Paste a '''Species'''
+| And Cut, Copy and Paste a '''Species'''.
 |-
 | 11:10
-|  We also learnt: About Start-point and End-point of a '''Species'''
+|  We also learnt: About Start-point and End-point of a '''Species'''.
 |-
 |  11:15
-| How to Activate a''' Species''' Change color of a''' Species''' Change properties of a ''' Reaction'''And close a''' File'''
+| How to Activate a''' Species''' , Change color of a''' Species''' , Change properties of a ''' Reaction'''And close a''' File'''
 |-

@@ Line 90: / Line 90: @@
 |-
 |  02:35
-|  Select the compartment. Go to the '''Component''' in the main menu bar.
+|  Select the compartment. Go to the '''Component''' in the ''' main menu ''' bar.
 |-

@@ Line 22: / Line 22: @@
 |-
 | 00:28
-|  We will also learn how to Cut, Copy and Paste a '''Species''' About Start-point and End-point of a '''Species'''.
+|  We will also learn how to Cut, Copy and Paste a '''Species''', About Start-point and End-point of a '''Species'''.
 |-

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

Sandhya.np14 at 11:54, 6 June 2018

Jyotisolanki at 06:20, 21 November 2017

Jyotisolanki at 11:59, 12 October 2017

Jyotisolanki at 11:34, 12 October 2017

Jyotisolanki: Created page with " {| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone. Welcome to this tutorial on''' Create and Edit Components''' in''' CellDesigner'''. |- | 00:08 |..."