Difference between revisions of "CellDesigner/C3/Customizing-Diagram-Layout/English"

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I will select the same '''State Transition reaction line''' between-
 
I will select the same '''State Transition reaction line''' between-
  
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homoserine and succinyl homoserine.
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'''Homoserine''' and '''Succinyl Homoserine.'''
  
 
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| style="border:0.75pt solid #000000;padding:0.071cm;"| It is a semi-essential<sup> </sup>proteinogenic amino acid.
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| style="border:0.75pt solid #000000;padding:0.071cm;"| Type Coenzyme A
  
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| style="border:0.75pt solid #000000;padding:0.071cm;"| I will type the following-
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| style="border:0.75pt solid #000000;padding:0.071cm;"| I will type the following.
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Coenzyme A
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| style="border:0.75pt solid #000000;padding:0.071cm;"| Dialog box ''''Gene''''
 
| style="border:0.75pt solid #000000;padding:0.071cm;"| Dialog box ''''Gene''''
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| style="border:0.75pt solid #000000;padding:0.071cm;"| A dialog box named '''Protein''' appears on the screen.
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| style="border:0.75pt solid #000000;padding:0.071cm;"| A dialog box, '''Protein,''' appears on the screen.
  
 
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| style="border:0.75pt solid #000000;padding:0.071cm;"| As we do not require to add region in the '''Methionine Biosynthesis '''I will undo these changes.
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| style="border:0.75pt solid #000000;padding:0.071cm;"| As we do not require to add region in the '''Methionine Biosynthesis, '''I will undo these changes.
  
 
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| style="border:0.75pt solid #000000;padding:0.071cm;"| Cursor on '''undo '''
 
| style="border:0.75pt solid #000000;padding:0.071cm;"| Cursor on '''undo '''
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| style="border:0.75pt solid #000000;padding:0.071cm;"| I will '''undo Edit Information''' as we do not require it in '''Methionine Biosynthesis.'''
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| style="border:0.75pt solid #000000;padding:0.071cm;"| I will undo '''Edit Information,''' as we do not require it in '''Methionine Biosynthesis.'''
  
 
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Latest revision as of 14:04, 6 May 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on ‘Customizing Diagram Layout’.

Slide 2

Learning Objectives

In this tutorial, we will learn how to:
  • Change color, shape and width of a Reaction line
  • Add Anchor points to a Reaction line
  • Align Components
  • Show/hide Reaction ids
Slide 3

Learning Objectives

We will also learn how to:
  • Add notes to Components
  • Edit Protein
  • Edit information
  • And get a bird’s eye view of the diagram
Slide Number 4

System Requirement

To record this tutorial, I am using
  • Ubuntu Linux OS 14.04
  • CellDesigner version 4.3
  • Java version 1.7
Slide Number 5 To follow this tutorial, learners should be familiar with:
  • Undergraduate Biochemistry and
  • CellDesigner interface.

If not, for relevant CellDesigner tutorials, please visit the Spoken Tutorial website.

Let us begin.
Slide Number 6

Assignment for previous tutorial-

To build a Process Diagram for Methionine Biosynthesis.

The assignment for one of the previous tutorials was-

To build a process diagram for Methionine Biosynthesis.

I am going to use that same diagram as the example for this tutorial.

And I will demonstrate how to customize it.

Switch to CellDesigner interface. Let me switch to CellDesigner interface.
Show Process Diagram on CellDesigner window. What you see here is the process diagram for Methionine Biosynthesis.

Pause the tutorial here and open the Methionine Biosynthesis process diagram that you created.

If you do not have a saved file, you may open from the code file provided.
Slide 7 Now, let me start customizing the diagram.

Let us go back to the Cell designer interface

Point to a Reaction line. To start with, I will change the width and color of a Reaction line.
Select any one Reaction line. To do so, I am selecting the State Transition between Homoserine and Succinyl homoserine.
Cursor on the Reaction line Component in the main menu bar. Now, go to “Component” in the main menu bar.
Click on “Change color & shape” option And click on “Change color & shape” option.
Right-click on a Reaction line>>>Cursor on Change color & shape. Alternately, you may right-click on a Reaction line and select “Change color & shape” option.
Cursor on the dialog box A dialog box named “Change color & shape” appears on the screen.
Change color & shape >>> Cursor on Line Width >> 3.0 For a thicker Reaction line, change the Line Width from 1.0 to a higher value.

I will change this to 3.0

Cursor on Color panel. To change the color of the Reaction line, go to the Color panel.
Point to the color wheel. In the Color panel we can see a color wheel, with a pointer like handle.
Click and hold the pointer and rotate to select the color Click and hold the pointer and rotate to select the preferred color.

I will select a shade of blue.

Next, click anywhere inside the color triangle.

Now, Click and drop the small circle at the pointer.

Click on Apply >>> 'Ok'. After all the modifications are done, click on Apply and then on Ok.
Point to the Reaction line Observe that the Reaction line is now thicker and in shade of blue.

<<PAUSE>>

Slide Number 8

How to add Anchor points on the Reaction line.

Next we will learn how to add Anchor points on the Reaction line.
Slide Number 9

And why Anchor points are useful

And why Anchor points are useful to-
  • Turn around the Reaction lines
  • Give them a proper shape
  • And place them in the correct position on the draw area.
Switch to CellDesigner interface. Lets come back to the CellDesigner interface.
Select any Reaction line. Select any Reaction line.

I will select the same State Transition reaction line between-

Homoserine and Succinyl Homoserine.

Cursor on Reaction line On this line, using the cursor, choose the exact position where the Anchor point has to be placed.
Right-click on exact position for the Anchor point to be placed. Upon selection of the exact point, right-click and select Add Anchor Point.
Cursor at the Anchor point You will see the newly added Anchor point at the exact chosen position on the Reaction line.

<<PAUSE>>

Let me show you how Anchor Points can help to modify a Reaction line.

Let me open a new window and name it Anchor. Click OK

Now click on the icon for GTP/GDP

And click anywhere on the draw area.

Right click on the Reaction line and click on Add Anchor Point

Drag and drop the Reaction line anywhere on the draw area.

Next we will see how to align the components on the draw area.
Let us come back to the Methionine biosynthesis process diagram window
Click anywhere on the draw area to uncheck the highlighted Reaction line.
Click on the multiple Species to be adjusted. Now, hold the 'Shift' key and click on multiple Species on the draw area.
Go to Edit menu >> point to Alignment >> select an Alignment type. Go to Edit menu, scroll down select Alignment and click on the Alignment type.
Cursor on icons for Alignment Alternately, click on the icon for Alignment on the toolbar.
Explore other Alignment options on the toolbar on your own.

<<PAUSE>>

Let us undo the alignment and move ahead.
How can we show/hide Reaction ids on a process diagram? While working on a Reaction, how can we show/hide Reaction ids on a process diagram?

Let’s learn that.

Cursor on View->uncheck Show Reaction Id Go to 'View', scroll down and uncheck the 'Show Reaction Id'.

The Reaction ids on the respective reactions on the draw area will not be visible any more.

Cursor on View->check Show Reaction Id In case, you wish to show the Reaction Id do the following.

Go to 'View', scroll down and click on the 'Show Reaction Id'.

The Reaction ids will appear on the respective reactions on the draw area.

We can also add notes to all the Components (Compartment, Species or Reaction) on the draw area.

Let us learn how to do that.

<<PAUSE>>

Show cursor on a Species on the draw area. Right-click on a Species on the draw area.

I will click on CoA.

Right-click >> display a pop-up menu >> select Species Notes. Scroll down and click on the ‘Species Notes’.

A pop up menu is displayed

In the dialog box type the text - A dialog box 'Species Notes' pops up.

Type the text related to the Species

Type Coenzyme A I will type the following.
Click 'OK'. Click 'OK'.
Observe that the notes information is displayed in the Notes Area.
Click on a Species >>Click on 'Edit Notes' at the bottom right corner of the CellDesigner Window. Alternately, to add notes to a Species, click on a Species on the draw area.

I will click on Succinate.

Then, click on Edit Notes tab, located at the bottom right corner of the CellDesigner window.

Type the text and then click 'OK' A pop up window will appear.

Type the text related to the Species-

I will type and click 'OK'.

In the same manner we can edit a Protein.
Right click on a component To do so, right-click on a component on the draw area.

I will click on Homoserine succinyl transferase.

Scroll down >>>click on Edit Protein Scroll down and click on Edit Protein.
On window ‘Protein’ >>> Enter the name Hexokinase A dialog box named Protein appears on the screen.

Enter the name of the Protein in the name box.

I will type O-succinyltransferase in the name box.

Click on ‘Update’ >> close the dialog box. Click on ‘Update’ and close the dialog box.

<<PAUSE>>

We can also add regions to a Protein.
Right-click on a Gene Right-click on a Protein on the draw area.

I will right click on O-succinyltransferase.

Scroll down >> click on Edit Gene. Scroll down and click on Edit Protein.
Dialog box 'Gene' A dialog box, Protein, appears on the screen.
Point to ‘Regions’ tab >> click on the 'Add' button. Under the tab ‘residues/regions’, click on the 'Add' button.
In ModificationRegion/BindingRegion dialog box >> Select ‘Type’ as ‘Binding region’. In the dialog box - ModificationResidue/Bindingregion:

Select the ‘Type’ from the drop down menu as ‘Binding region.

Change the size and angle by moving the cursor at the required value.
Select >> Size as 15 >>

Angle 38

For this demo, I will select-

Size as 15 and

Angle 38

Click on ‘Close’ Then click on ‘Close’.
Click on the ‘Update’ button Click on the Update
Close the dialog box. And close the box.
As we do not require to add region in the Methionine Biosynthesis, I will undo these changes.
Next, let us learn to edit information.
Right click on the Component. Right-click on the component on the draw area.


I will click on Homoserine.

Scroll down>>>click on ‘Edit Information’ >> dialog box- ‘Edit Information opens Scroll down and click on ‘Edit Information’.


A dialog box ‘Edit Information’ appears on screen

In the dialog box do the following-
  • Under the tab ‘state’ select Open.
  • Under the tab ‘prefix’ select pc.
  • Under the tab ‘label’ select pH.
In the dialog box do the following-
  • Under the tab ‘state’ select Open.
  • Under the tab ‘prefix’ select mt.
  • Under the tab ‘label’ select dna.
Click ‘OK Click on ‘Ok’.

You can see the information mt:dna displayed on the draw area

Cursor on undo I will undo Edit Information, as we do not require it in Methionine Biosynthesis.
Point to Bird's eye view In some cases, the process diagram can be a complicated one.

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

Cursor on Bird’s Eye View in the Toolbar Click the Bird's eye view icon.
Drag the red square in the Bird’s Eye View Drag the red square in the Bird’s Eye View.

Observe that the view on the draw area moves accordingly.

This brings us to the end of this tutorial.
Slide 10

Summary

Let us summarize.

In this tutorial, we have learnt how to:

  • Change- color, shape and width of a Reaction line
  • Add Anchor points to a Reaction line
  • Align Components
  • And show/hide Reaction id’s
Slide 11

Summary

We have also learnt how to-
  • Add notes to Components
  • Edit Protein/Gene
  • Edit Information
  • And get the Bird’s Eye View of the diagram
Slide 12

Assignment

  • Create a Glycolysis Process Diagram using tools in CellDesigner.
  • Explore different shapes of Reaction line

Hint: Orthogonal and Polyline

Slide 13

Acknowledgement

About the Spoken Tutorial project-
  • Watch the video at the following link
  • It summarizes the Spoken Tutorial project.
  • If you do not have a good bandwidth please download and watch it.
Slide 14 The Spoken Tutorial Project Team -
  • Conducts Workshops
  • And gives certificates for those who pass an online test.
  • For more details, please write to contact@spoken-tutorial.org
Slide 15 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.

This is Bella Tony from IIT Bombay signing off.

Thank you for joining.

Contributors and Content Editors

Bellatony911, Nancyvarkey

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