Sandhya.np14 at 11:25, 7 June 2018

2018-06-07T11:25:48Z

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Jyotisolanki at 06:32, 21 November 2017

2017-11-21T06:32:37Z

Jyotisolanki at 06:48, 2 November 2017

2017-11-02T06:48:02Z

Jyotisolanki at 07:04, 5 October 2017

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Jyotisolanki at 08:38, 22 September 2017

2017-09-22T08:38:48Z

Jyotisolanki: Created page with "{| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone.Welcome to this tutorial on ‘Customizing Diagram Layout’. |- | 00:08 | In this tutorial, we w..."

2017-09-22T08:37:56Z

Created page with "{| border=1 || '''Time''' || '''Narration''' |- | 00:01 | Hello everyone.Welcome to this tutorial on ‘Customizing Diagram Layout’. |- | 00:08 | In this tutorial, we w..."

New page

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

|-
| 00:01
| Hello everyone.Welcome to this tutorial on ‘Customizing Diagram Layout’.

|-
| 00:08
| In this tutorial, we will learn how to: Change color, shape and width of a '''Reaction line'''

|-
| 00:19
|Add '''Anchor points''' to a '''Reaction line'''Align '''Components''' Show/hide '''Reaction ids'''

|-
| 00:30
| We will also learn how to: Add notes to '''Components'''Edit '''Protein'''Edit information

|-
|00:39
| And get a bird’s eye view of the diagram

|-
| 00:44
| To record this tutorial, I am using'''Ubuntu Linux OS 14.04''' '''CellDesigner version 4.3''' '''Java version 1.7'''

|-
| 01:01
| To follow this tutorial, learners should be familiar with:'''Undergraduate Biochemistry '''and
'''CellDesigner interface.'''

|-
| 01:12
| If not, for relevant '''CellDesigner '''tutorials, please visit the '''Spoken Tutorial '''website.

|-
| 01:20
| Let us begin.

|-
| 01:22
| The assignment for one of the previous tutorials was- To build a '''process diagram '''for '''Methionine Biosynthesis'''.

|-
| 01:32
| I am going to use that same diagram as the example for this tutorial.And I will demonstrate how to customize it.

|-
| 01:43
| Let me switch to '''CellDesigner''' interface.

|-
| 01:47
| What you see here is the '''process diagram '''for '''Methionine Biosynthesis.'''

|-
| 01:53
| Pause the tutorial here and open the '''Methionine Biosynthesis process diagram '''that you created.

|-
| 02:01
| If you do not have a saved file, you may open from the code file provided.

|-
| 02:08
| Now, let me start customizing the '''diagram.'''

|-
| 02:12
| Let us go back to the''' Cell designer '''interface

|-
| 02:16
| To start with, I will change the width and color of a '''Reaction line'''.

|-
| 02:22
| To do so, I am selecting the '''State Transition''' between''' Homoserine '''and '''Succinyl homoserine'''.

|-
| 02:30
| Now, go to “'''Component'''” in the main menu bar.

|-
| 02:35
| And click on “'''Change color & shape'''” option.

|-
| 02:39
| Alternately, you may right-click on a '''Reaction line''' and select “'''Change color & shape'''” option.

|-
| 02:47
| A dialog box named “'''Change color & shape”''' appears on the screen.

|-
| 02:53
| For a thicker '''Reaction line''', change the '''Line Width '''from 1.0 to a higher value.

|-
| 03:02
| I will change this to 3.0

|-
| 03:06
| To change the color of the '''Reaction line''', go to the''' Color panel.'''

|-
| 03:12
| In the''' Color panel''' we can see a color wheel, with a pointer like handle.

|-
| 03:19
| Click and hold the pointer and rotate to select the preferred color.

|-
| 03:25
| I will select a shade of blue.

|-
| 03:28
| Next, click anywhere inside the color triangle.

|-
| 03:34
| Now, Click and drop the small circle at the pointer.

|-
| 03:40
| After all the modifications are done, click on '''Apply''' and then on '''Ok'''.

|-
| 03:48
| Observe that the '''Reaction line '''is now thicker and in shade of blue.

|-
| 03:55
| Next we will learn how to add '''Anchor points '''on the '''Reaction line'''.

|-
| 04:01
| And why '''Anchor points '''are useful to- Turn around the '''Reaction lines'''

|-
| 04:09
|Give them a proper shape And place them in the correct position on the '''draw area.'''

|-
| 04:16
| Lets come back to the '''CellDesigner interface'''.

|-
| 04:20
| Select any '''Reaction line'''.

|-
| 04:23
| I will select the same '''State Transition reaction line''' between- '''Homoserine''' and '''Succinyl Homoserine.'''

|-
| 04:31
| On this line, using the cursor, choose the exact position where the '''Anchor point''' has to be placed.

|-
| 04:39
| Upon selection of the exact point, right-click and select '''Add Anchor Point.'''

|-
| 04:47
| You will see the newly added '''Anchor point''' at the exact chosen position on the '''Reaction line'''.

|-
| 04: 55
| Let me show you how '''Anchor Points '''can help to modify a Reaction line.

|-
| 05:03
| Let me open a new window and name it '''Anchor. '''Click''' OK'''

|-
| 05:11
| Now click on the icon for '''GTP/GDP'''

|-
| 05:18
| And click anywhere on the draw area.

|-
| 05:22
|Right-click on ''' Reaction line''' and click on ''' Add Anchor point'''

|-
| 05:29
| Drag and drop the''' Reaction line''' anywhere on the draw area.

|-
| 05:37
| Next we will see how to '''align''' the components on the '''draw area.'''

|-
| 05:44
| Let us come back to the''' Methionine '''biosynthesis process diagram window

|-
| 05:50
| Click anywhere on the draw area to uncheck the highlighted '''Reaction line.'''

|-
| 05:56
| Now, hold the ''''Shift'''' key and click on multiple '''Species''' on the '''draw area.'''

|-
| 06:04
| Go to '''Edit''' menu, scroll down select '''Alignment''' and click on the '''Alignment type'''.

|-
| 06:15
| Alternately, click on the icon for '''Alignment '''on the toolbar.

|-
| 06:21
| Explore other '''Alignment''' options on the toolbar on your own.

|-
| 06:27
| Let us undo the alignment and move ahead.

|-
| 06:31
| While working on a '''Reaction''', how can we show/hide '''Reaction ids '''on a '''process diagram'''?

|-
| 06:39
| Let’s learn that.

|-
| 06:41
| Go to ''''View'''', scroll down and uncheck the ''''Show Reaction Id''''.

|-
| 06:48
| The '''Reaction ids''' on the respective reactions on the '''draw area''' will not be visible any more.

|-
| 06:55
| In case, you wish to show the '''Reaction Id do the following.'''

|-
| 07:01
| Go to ''''View'''', scroll down and click on the ''''Show Reaction Id''''.

|-
| 07:08
| The '''Reaction ids''' will appear on the respective '''reactions''' on the '''draw area.'''

|-
| 07:15
| We can also add notes to all the '''Components''' (Compartment, Species or Reaction) on the '''draw area'''.

|-
| 07:21
| Let us learn how to do that.

|-
| 07:24
| Right-click on a '''Species''' on the '''draw area'''.

|-
| 07:28
| I will click on '''CoA.'''

|-
| 07:32
| Scroll down and click on the ‘'''Species Notes'''’.

|-
| 07:35
| A pop up menu is displayed

|-
| 07:38
| A dialog box ''''Species Notes'''' pops up. Type the text related to the '''Species'''

|-
| 07:46
| I will type the following.

|-
| 07:49
| Click ''''OK''''.

|-
| 07:51
| Observe that the notes information is displayed in the '''Notes Area'''.

|-
| 07:58
| Alternately, to add notes to a '''Species''', click on a '''Species''' on the '''draw area.'''

|-
| 08:06
| I will click on''' Succinate.'''

|-
| 08:09
| Then, click on '''Edit Notes''' tab, located at the bottom right corner of the '''CellDesigner '''window.

|-
| 08:18
| A pop up window will appear.

|-
| 08:21
| Type the text related to the '''Species'''-

|-
| 08:25
| I will type and click ''''OK''''.

|-
| 08:30
| In the same manner we can edit a '''Protein'''.

|-
| 08:35
| To do so, right-click on a component on the '''draw area.'''

|-
| 08:40
| I will click on '''Homoserine succinyl transferase.'''

|-
| 08:46
| Scroll down and click on '''Edit Protein'''.

|-
| 08:51
| A dialog box named '''Protein''' appears on the screen.

|-
| 08:55
| Enter the name of the '''Protein '''in the name box.

|-
| 09:00
| I will type '''O-succinyltransferase '''in the name box.

|-
| 09:06
| Click on '''‘Update’''' and close the dialog box.

|-
| 09:11
| We can also add regions to a '''Protein'''.

|-
| 09:15
| Right-click on a '''Protein''' on the '''draw area'''.

|-
| 09:19
| I will right click on '''O-succinyltransferase.'''

|-
| 09:24
| Scroll down and click on '''Edit Protein'''.

|-
| 09:29
| A dialog box, '''Protein,''' appears on the screen.

|-
| 09:33
| Under the tab ‘'''residues/regions'''’, click on the ''''Add'''' button.

|-
| 09:40
| In the dialog box -''' ModificationResidue/Bindingregion''':

|-
| 09:46
| Select the '''‘Type’''' from the drop down menu as ‘'''Binding region'''.

|-
| 09:52
| Change the size and angle by moving the cursor at the required value.

|-
| 09:59
| For this demo, I will select- '''Size '''as 15 and'''Angle''' 38

|-
| 10:09
| Then click on ‘'''Close'''’.

|-
| 10:12
| Click on the '''Update'''

|-
| 10:14
| And close the box.

|-
| 10:17
| As we do not require to add region in the '''Methionine Biosynthesis, '''I will undo these changes.

|-
| 10:25
| Next, let us learn to edit information.

|-
| 10:30
| Right-click on the '''component '''on the '''draw area'''.

|-
| 10:33
| I will click on Homoserine.

|-
| 10:37
| Scroll down and click on ‘'''Edit Information’.'''

|-
| 10:41
| A dialog box '''‘Edit Information’''' appears on screen

|-
| 10:46
| In the dialog box do the following'''- ''' Under the tab ‘'''state'''’ select '''Open. '''

|-
| 10:54
| Under the tab ‘'''prefix'''’ select '''mt. '''

|-
| 10:59
| Under the tab '''‘label’ '''select '''dna.'''

|-
| 11:04
| Click''' '''on '''‘Ok’.'''

|-
| 11:07
| You can see the information '''mt:dna''' displayed on the draw area

|-
| 11:15
| I will undo '''Edit Information,''' as we do not require it in '''Methionine Biosynthesis.'''

|-
| 11:23
| In some cases, the '''process diagram''' can be a complicated one.

|-
| 11:28
| In such cases, '''Bird's eye view''' can help as it is convenient to navigate inside a big model.

|-
| 11:37
| Click the '''Bird's eye''' '''view '''icon.

|-
| 11:41
| Drag the red square in the '''Bird’s Eye View'''.

|-
| 11:46
| Observe that the view on the '''draw area''' moves accordingly.

|-
| 11:52
| This brings us to the end of this tutorial.

|-
| 11:56
| Let us summarize. In this tutorial, we have learnt how to: Change- color, shape and width of a '''Reaction line'''

|-
| 12:07
| Add '''Anchor points''' to a '''Reaction line''' Align '''Components''' And show/hide '''Reaction id’s'''

|-
| 12:18
| We have also learnt how to- Add notes to '''Components'''

|-
| 12:23
| Edit '''Protein/Gene''' Edit Information

|-
| 12:27
| And get the '''Bird’s Eye View '''of the diagram

|-
| 12:32
| For Assignment Create a Glycolysis Process Diagram using tools in CellDesigner.

|-
| 12:41
| Explore different shapes of '''Reaction line'''

|-
| 12:47
| Watch the video at the following link It summarizes the Spoken Tutorial project.

|-
| 12:52
| If you do not have a good bandwidth please download and watch it.

|-
| 12:57
| The''' Spoken Tutorial Project '''Team - Conducts Workshops And gives certificates for those who pass an online test.

|-
| 13:06
| For more details, please write to contact@spoken-tutorial.org

|-
| 13:13
| Spoken Tutorial Project is a part of '''Talk to a Teacher project.''' It is funded by '''NMEICT, MHRD, Government of India'''. More information on this Mission is available at the given link.

|-
| 13:29
| This is Bella Tony''' '''from''' IIT Bombay''' signing off.

Thank you for joining.

|}

@@ Line 13: / Line 13: @@
 |-
 |  00:19
-|Add '''Anchor points''' to a '''Reaction line'''Align '''Components''' Show/hide '''Reaction ids'''
+|Add '''Anchor points''' to a '''Reaction line , '''Align '''Components''' , Show/hide '''Reaction ids'''
 |-
 | 00:30
-|  We will also learn how to: Add notes to '''Components'''Edit '''Protein'''Edit information
+|  We will also learn how to: Add notes to '''Components''' , Edit '''Protein''' , Edit information ,
 |-
 |00:39
-| And get a '''bird’s eye view''' of the diagram
+| And get a '''bird’s eye view''' of the diagram.
 |-
@@ Line 142: / Line 142: @@
 |-
 |  04:01
-|  And why '''Anchor points '''are useful to- Turn around the '''Reaction lines'''
+|  And why '''Anchor points '''are useful to- Turn around the '''Reaction lines''' ,
 |-
 |  04:09
-|Give them a proper shape And place them in the correct position on the '''draw area.'''
+|Give them a proper shape And place them in the correct position on the '''draw area.'''.
 |-
@@ Line 478: / Line 478: @@
 |-
 |  11:56
-|  Let us summarize. In this tutorial, we have learnt how to: Change- color, shape and width of a '''Reaction line'''
+|  Let us summarize. In this tutorial, we have learnt how to: Change- color, shape and width of a '''Reaction line''',
 |-
 |  12:07
-| Add '''Anchor points''' to a '''Reaction line'''  Align '''Components'''  And show/hide '''Reaction id’s'''
+| Add '''Anchor points''' to a '''Reaction line''' , Align '''Components'''  And show/hide '''Reaction id’s'''
 |-
 |  12:18
-|  We have also learnt how to- Add notes to '''Components'''
+|  We have also learnt how to- Add notes to '''Components''',
 |-
 |  12:23
-| Edit '''Protein/Gene''' Edit Information
+| Edit '''Protein/Gene''' Edit Information,
 |-
 |  12:27
-| And get the '''Bird’s Eye View '''of the diagram
+| And get the '''Bird’s Eye View '''of the diagram.
 |-

@@ Line 21: / Line 21: @@
 |-
 |00:39
-| And get a bird’s eye view of the diagram
+| And get a '''bird’s eye view''' of the diagram
 |-

@@ Line 5: / Line 5: @@
 |-
 | 00:01
-|  Hello everyone.Welcome to this tutorial on ‘Customizing Diagram Layout’.
+|  Hello everyone.Welcome to this tutorial on '''‘Customizing Diagram Layout’'''.
 |-