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

From Script | Spoken-Tutorial
Jump to: navigation, search
 
(2 intermediate revisions by one other user not shown)
Line 10: Line 10:
 
|-
 
|-
 
|  00:08
 
|  00:08
|  In this tutorial, we will learn to: Open an already saved .xml file in the draw area.
+
|  In this tutorial, we will learn to: open an already saved ''''.xml'''' file in the '''draw''' area,
  
 
|-
 
|-
 
|  00:15
 
|  00:15
| Change the following in a '''compartment''' :shape, size, color and thickness of the border.
+
| change the following in a '''compartment''': shape, size, color and thickness of the border,
 
   
 
   
 
|-
 
|-
 
|  00:22
 
|  00:22
| Createmultiple files in''' CellDesigner''' Change identity of a '''Species'''
+
| create multiple files in''' CellDesigner''', change identity of a '''Species'''.
  
 
|-
 
|-
 
| 00:28
 
| 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''',
  
 
|-
 
|-
 
| 00:37
 
| 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'''.
  
 
|-
 
|-
 
|  00:47
 
|  00:47
|  Here I am using '''Ubuntu Linux OS version 14.04''' '''CellDesigner version 4.3''' '''Java version 1.7'''
+
|  Here I am using '''Ubuntu Linux OS version 14.04''', '''CellDesigner version 4.3''', '''Java version 1.7'''.
  
 
|-
 
|-
Line 38: Line 38:
 
|-
 
|-
 
|  01:05
 
|  01:05
| If not, for relevant''' CellDesigner tutorials''', please visit our website''' www.spoken-tutorial.org'''
+
| If not, for relevant''' CellDesigner tutorials''', please visit our website''' www.spoken-tutorial.org'''.
  
 
|-
 
|-
Line 62: Line 62:
 
|-
 
|-
 
|  01:52
 
|  01:52
|''' CellDesigner ''' window now open on your screen.
+
|''' CellDesigner '''window now opens on your screen.
  
 
|-
 
|-
Line 86: Line 86:
 
|-
 
|-
 
|  02:27
 
|  02:27
|  Our file '''Create_and_Edit.xml '''is now open in the draw area.
+
|  Our file '''Create_and_Edit.xml '''is now open in the '''draw''' area.
  
 
|-
 
|-
 
|  02:35
 
|  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 98: Line 98:
 
|-
 
|-
 
|  02:48
 
|  02:48
| On the draw area, we now have an oval compartment.
+
| On the '''draw''' area, we now have an oval compartment.
  
 
|-
 
|-
Line 118: Line 118:
 
|-
 
|-
 
|  03:20
 
|  03:20
| 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.
  
 
|-
 
|-
 
|  03:29
 
|  03:29
|  To change the color, go to''' Color panel.'''
+
|  To change the color, go to''' Color''' panel.
  
 
|-
 
|-
 
|  03:34
 
|  03:34
| In the''' Color panel''' is a color wheel, with a pointer like handle.
+
| In the''' Color''' panel is a color wheel, with a pointer like handle.
  
 
|-
 
|-
Line 134: Line 134:
 
|-
 
|-
 
| 03:46
 
| 03:46
|  After all the modifications are done, click on '''Apply'''. And then on ''''Ok''''.
+
|  After all the modifications are done, click on '''Apply''', and then on ''''Ok''''.
  
 
|-
 
|-
Line 154: Line 154:
 
|-
 
|-
 
|  04:16
 
|  04:16
| We will keep the default width and height. And click on '''Ok''' button.
+
| We will keep the default width and height and click on '''Ok''' button.
  
 
|-
 
|-
 
|  04:22
 
|  04:22
|  Now, click on the icon for ''''Generic protein'''' from the toolbar. Click on the draw area.
+
|  Now, click on the icon for ''''Generic protein'''' from the toolbar. Click on the '''draw''' area.
  
 
|-
 
|-
Line 166: Line 166:
 
|-
 
|-
 
|  04:37
 
|  04:37
|  Now right-click on the''' Generic protein Pectin'''.
+
|  Now right-click on the''' Generic protein Pectin'''
  
 
|-
 
|-
 
|  04:41
 
|  04:41
|And click on the option '''Change Identity'''.
+
|and click on the option '''Change Identity'''.
  
 
|-
 
|-
Line 190: Line 190:
 
|-
 
|-
 
|  05:10
 
|  05:10
|Let's say''' Fructose.''' And click on '''Apply''' button.
+
|Let's say''' Fructose''' and click on '''Apply''' button.
  
 
|-
 
|-
 
|  05:17
 
|  05:17
|  Observe that our''' Protein Pectin''' is now converted to a''' simple molecule''' named''' Fructose'''.
+
|  Observe that our''' Protein Pectin''' is now converted to a simple molecule named''' Fructose'''.
  
 
|-
 
|-
Line 202: Line 202:
 
|-
 
|-
 
|  05:29
 
|  05:29
|I will use the same '''Fructose''' that is already present on the draw area.  
+
|I will use the same '''Fructose''' that is already present on the '''draw''' area.  
  
 
|-
 
|-
Line 222: Line 222:
 
|-
 
|-
 
|  05:56
 
|  05:56
|  To paste the species, go back to the ''''Edit'''' menu, scroll down and click on '''Paste'''.
+
|  To '''paste''' the '''species''', go back to the ''''Edit'''' menu, scroll down and click on '''Paste'''.
  
 
|-
 
|-
Line 230: Line 230:
 
|-
 
|-
 
|  06:08
 
|  06:08
|The''' Species Fructose''' reappears on the draw area.
+
|The''' Species Fructose''' reappears on the '''draw area'''.
  
 
|-
 
|-
 
|  06:12
 
|  06:12
|  To make a copy of the''' Species, go to ''' Edit''' on the main menu bar.
+
|  To make a copy of the '''Species''', go to ''' Edit''' on the main menu bar.
  
 
|-
 
|-
Line 242: Line 242:
 
|-
 
|-
 
|  06:21
 
|  06:21
|Notice here that the shortcut key for Copy is''' Ctrl+C'''.  Click on '''Copy'''. Click on the draw area.
+
|Notice here that the shortcut key for '''Copy''' is''' Ctrl+C'''.  Click on '''Copy'''. Click on the '''draw''' area.
  
 
|-
 
|-
 
|  06:31
 
|  06:31
|This time, let us press''' Ctrl + V''' to paste.
+
|This time, let us press''' Ctrl + V''' to '''paste'''.
  
 
|-
 
|-
 
|  06:36
 
|  06:36
|  We now have a copy of '''Fructose''' on the draw area.
+
|  We now have a copy of '''Fructose''' on the '''draw''' area.
  
 
|-
 
|-
 
|  06:40
 
|  06:40
|  To undo any action press''' Ctrl+Z''' and to redo any action press''' Ctrl+Y'''.  
+
|  To '''undo''' any action, press''' Ctrl+Z''' and to '''redo''' any action, press''' Ctrl+Y'''.  
  
 
|-
 
|-
Line 262: Line 262:
 
|-
 
|-
 
|  06:55
 
|  06:55
|  Let us drag and move the''' Fructose molecules''' aside on the draw area.
+
|  Let us drag and move the''' Fructose molecules''' aside on the '''draw area'''.
  
 
|-
 
|-
Line 270: Line 270:
 
|-
 
|-
 
|  07:07
 
|  07:07
|  Next we will learn,  what are '''start-point''' and '''end-point''' '''species''' and how to '''activate''' a '''species'''?
+
|  Next we will learn,  what are '''start-point''' and '''end-point''' '''species''' and how to activate a '''species'''?
  
 
|-
 
|-
Line 302: Line 302:
 
|-
 
|-
 
|  07:53
 
|  07:53
|So click on ''' Protein 2''' and press '''A''' on the keyboard.
+
|So, click on ''' Protein 2''' and press '''A''' on the keyboard.
  
 
|-
 
|-
 
|  07:59
 
|  07:59
|  Let me undo this change by pressing''' Ctrl + Z''' keys.
+
|  Let me '''undo''' this change by pressing''' Ctrl + Z''' keys.
  
 
|-
 
|-
Line 322: Line 322:
 
|-
 
|-
 
|  08:18
 
|  08:18
|  Notice that the''' activated species''' is wrapped by a dashed line.
+
|  Notice that the activated '''species''' is wrapped by a dashed line.
  
 
|-
 
|-
Line 346: Line 346:
 
|-
 
|-
 
|  08:49
 
|  08:49
|Observe the color changes in the ''' species ''' ,
+
|Observe the color changes in the ''' species.'''  
  
 
|-
 
|-
Line 362: Line 362:
 
|-
 
|-
 
|  09:08
 
|  09:08
|Now select '''Change Identity''' option.
+
|Now, select '''Change Identity''' option.
  
 
|-
 
|-
Line 374: Line 374:
 
|-
 
|-
 
|  09:26
 
|  09:26
|  Select the required reaction from the drop-down menu in the '''Type''' box, say''' Transcription'''. Click on ''''Ok''''.
+
|  Select the required reaction from the drop-down menu in the '''Type''' box, say''' Transcription''', Click on ''''Ok''''.
  
 
|-
 
|-
 
|  09:38
 
|  09:38
|  Observe that the''' reaction''' has changed on the draw area.
+
|  Observe that the''' reaction''' has changed on the '''draw''' area.
  
 
|-
 
|-
 
|  09:42
 
|  09:42
|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.
  
 
|-
 
|-
Line 410: Line 410:
 
|-
 
|-
 
| 10:25
 
| 10:25
| A dialog box '''Confirmation''' appears on the screen asking if we wish to save the changes.
+
| A dialog box '''Confirmation''' appears on the screen asking if we wish to '''save''' the changes.
  
 
|-
 
|-
Line 430: Line 430:
 
|-
 
|-
 
|  10:50
 
|  10:50
|Open an already saved .xml file in the draw area
+
|open an already saved '''.xml''' file in the draw area,
 
   
 
   
 
|-
 
|-
 
|  10:55
 
|  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
 
|  11:01
| Create multiple files in''' CellDesigner''' And change identity  
+
| create multiple files in''' CellDesigner''' and change identity,
  
 
|-
 
|-
 
|  11:07
 
|  11:07
| And Cut, Copy and Paste a '''Species'''
+
| and, '''Cut, Copy''' and '''Paste''' a '''Species'''.
  
 
|-
 
|-
 
| 11:10
 
| 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
 
|  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'''.
  
 
|-
 
|-
 
| 11:25
 
| 11:25
|  For your assignment: Create a''' complex''' and place a''' Species''' inside the''' Complex'''
+
|  For your assignment: create a''' complex''' and place a''' Species''' inside the''' Complex'''.
 
   
 
   
 
|-
 
|-
Line 474: Line 474:
 
|-
 
|-
 
|  12:00
 
|  12:00
|About the spoken tutorial project.
+
|About the '''spoken tutorial''' project.
  
 
|-
 
|-
 
|  12:05
 
|  12:05
| The video at this link summarizes the Spoken Tutorial project.Please download and watch it.
+
| The video at this link summarizes the Spoken Tutorial project. Please download and watch it.
  
 
|-
 
|-
 
|  12:13
 
|  12:13
|  The Spoken Tutorial Project  conducts workshops and gives certificates on passing an on-line test.For more details, please write to us.
+
|  The Spoken Tutorial Project  conducts workshops and gives certificates on passing an on-line test. For more details, please write to us.
  
 
|-
 
|-
 
|  12:23
 
|  12:23
|  Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available on this link.
+
|  Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this mission is available on this link.
  
 
|-
 
|-
 
|  12:35
 
|  12:35
|  This is Bella Tony from''' IIT Bombay''' signing off. Thank you for joining.
+
|  This is Bella Tony from''' IIT Bombay''', signing off. Thank you for joining.
 
|}
 
|}

Latest revision as of 17:24, 6 June 2018

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 create multiple 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.
01:52 CellDesigner window now opens 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.
02:07 A dialog box named Open appears on the screen.
02:11 Here, we have to select the folder under ‘Folders’ label.
02:15 Click on the 'Create_and_Edit.xml' file under the ‘File’ label and then double-click on ‘Ok’.
02:27 Our file Create_and_Edit.xml is now open in the draw area.
02:35 Select the compartment. Go to the Component in the main menu bar.
02:43 Scroll down and select Change to OVAL.
02:48 On the draw area, we now have an oval compartment.
02:54 To change the color or thickness, go to “Component” in the main menu bar.
03:00 Click on “Change color & shape” option.
03:05 Alternately, right-click on the compartment boundary and select “Change color & shape” option.
03:14 A dialog box named 'Change color & shape' appears on the screen.
03:20 For a thinner boundary line, change the Membrane Thickness from 12 to 8 or below.
03:29 To change the color, go to Color panel.
03:34 In the Color panel is a color wheel, with a pointer like handle.
03:39 Click and hold the pointer and rotate to select the preferred color.
03:46 After all the modifications are done, click on Apply, and then on 'Ok'.
03:53 Explore other options to draw various Compartments on the reaction toolbar, on your own.
04:00 We will now learn how to change the identity of Species.
04:05 So, first we will open a new window by pressing CTRL+N.
04:11 Let us give a name to this file, say Change Species.
04:16 We will keep the default width and height and click on Ok button.
04:22 Now, click on the icon for 'Generic protein' from the toolbar. Click on the draw area.
04:30 In the dialog box, type Pectin and click on the Ok button.
04:37 Now right-click on the Generic protein Pectin
04:41 and click on the option Change Identity.
04:46 A dialog box named 'Change identity of the species' appears on the screen.
04:53 Click on the down arrow in the Class box.
04:58 Select any option, for example, say simple molecule, from the drop-down menu.
05:05 Now, give a name to this simple molecule in the Name box.
05:10 Let's say Fructose and click on Apply button.
05:17 Observe that our Protein Pectin is now converted to a simple molecule named Fructose.
05:25 Let us now learn to Cut, Copy and Paste.
05:29 I will use the same Fructose that is already present on the draw area.
05:34 To cut a Species, click on the Species Fructose first.
05:40 Go to Edit menu, scroll down and click on Cut.
05:47 Notice here that the shortcut key for Cut is Ctrl+X.
05:53 The Species Fructose has been cut.
05:56 To paste the species, go back to the 'Edit' menu, scroll down and click on Paste.
06:03 Notice here that the shortcut key for Paste is Ctrl+V.
06:08 The Species Fructose reappears on the draw area.
06:12 To make a copy of the Species, go to Edit on the main menu bar.
06:18 Click on Copy.
06:21 Notice here that the shortcut key for Copy is Ctrl+C. Click on Copy. Click on the draw area.
06:31 This time, let us press Ctrl + V to paste.
06:36 We now have a copy of Fructose on the draw area.
06:40 To undo any action, press Ctrl+Z and to redo any action, press Ctrl+Y.
06:51 These are however, limited in their use.
06:55 Let us drag and move the Fructose molecules aside on the draw area.
07:00 To do so, click on Fructose and drag it to the desired location.
07:07 Next we will learn, what are start-point and end-point species and how to activate a species?
07:13 For that, I have already drawn a state transition reaction between 2 generic proteins.
07:21 I have named them Protein 1 and Protein 2.
07:25 Recall, we already learnt how to draw a reaction earlier.
07:29 If you do not know, refer to the previous tutorials in this series. Let us proceed.
07:35 In this reaction, the ‘start point’ is ‘Protein 1’ and the ‘end point’ is Protein 2.
07:43 To activate a species, click on a Species which is an 'end-point' of a Reaction.
07:50 In our case, it is Protein 2.
07:53 So, click on Protein 2 and press A on the keyboard.
07:59 Let me undo this change by pressing Ctrl + Z keys.
08:05 Alternately, click on Protein 2
08:09 Next, on the main menu bar, go to Component.
08:13 Scroll down and click on Set Active.
08:18 Notice that the activated species is wrapped by a dashed line.
08:24 Let us now change the color of the species, Protein 2.
08:29 So, right-click on it and then click on 'Change color and shape'.
08:35 As we saw earlier, in the Color panel is the color wheel.
08:40 Click and rotate the pointer, to select the preferred color.
08:44 Then, click on Apply and Ok.
08:49 Observe the color changes in the species.
08:53 We will now learn how to change the properties of a Reaction.
08:57 Let us come back to our state transition reaction present on the draw area.
09:03 Right-click on the reaction arrow between the two species.
09:08 Now, select Change Identity option.
09:13 A dialog box Change Properties of the Reaction appears.
09:18 Type the name of the reaction in the Name box, say Reaction1.
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.
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.
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.
10:32 Click Yes and double-click on the Ok button.
10:38 It says the file has been modified.
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.
11:32 Assignment 2: Explore the toolbar and find out how to add a reactant and a product to a reaction.
11:41 Your completed assignment should look like this.
11:45 Your first assignment will look like this: A complex and Species placed inside the Complex.
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.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14