Difference between revisions of "CellDesigner/C2/Build-and-Modify-Process-Diagram/English"

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| style="border:0.75pt solid #000001;padding:0.071cm;"| In this tutorial, we will learn to:
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| In this tutorial, we will learn to:
  
−
* Use Macros
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* Use '''Macros'''
 
* Move Components on the draw area
 
* Move Components on the draw area
 
* Connect a reaction line around a species
 
* Connect a reaction line around a species
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'''Learning Objectives contd. ...'''
 
'''Learning Objectives contd. ...'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"| We will also learn to:
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| style="border:0.75pt solid #000001;padding:0.071cm;"|  
  
 
* Align and extend a reaction line
 
* Align and extend a reaction line
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* Add a Product and a Reactant
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* Add a '''Product''' and a '''Reactant'''
  
 
|-
 
|-
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Click '''Ok'''.
 
Click '''Ok'''.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Keep the default width and height and click on '''Ok''' button.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Keep the default width and height and click on the '''Ok''' button.
  
 
|-
 
|-
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''' '''Click''' ‘Apply’'''.
 
''' '''Click''' ‘Apply’'''.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Type the''' Name '''as: '''2-keto-isovalerate''' and then''' '''click''' '''on the '''‘Apply’''' button.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Type the''' Name '''as: '''2-keto-isovalerate'''.
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 +
 
 +
And then click on the '''‘Apply’''' button.
  
 
|-
 
|-
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In the dialog box ‘'''The Same Species Exists'''’ >>Click on the option '''‘No’.'''
 
In the dialog box ‘'''The Same Species Exists'''’ >>Click on the option '''‘No’.'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialogue box ‘'''The Same Species Exists'''’ dialog box click '''‘No’.'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"| In the dialog box ‘'''The Same Species Exists'''’, click '''‘No’.'''
  
 
|-
 
|-
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| style="border:0.75pt solid #000001;padding:0.071cm;"|  
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Point to the button '''"Yes"'''
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.
 
Here, I will click''' ‘No’'''
 
Here, I will click''' ‘No’'''
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|-
 
|-
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' Apply '''button.
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the''' Apply '''button.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the Apply button.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the '''Apply''' button.
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 +
 
 
You have''' Valine''' on the draw area.
 
You have''' Valine''' on the draw area.
  
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, rename catalyst''' S2.'''
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| Next, rename catalyst''' S2.'''
 
Right-click on it and select '''Edit Protein.'''
 
Right-click on it and select '''Edit Protein.'''
−
In the '''‘Name’''' field, type '''Aminotransferase.'''  
+
 
 +
 
 +
In the '''‘name’''' field, type '''Aminotransferase.'''  
  
 
|-
 
|-
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In the main menu,click on the icon for '''State Transition'''.
 
In the main menu,click on the icon for '''State Transition'''.
 +
 +
 
Then, on the draw area, hover the mouse on ‘'''start-point'''' '''Species, Protein 1'''.
 
Then, on the draw area, hover the mouse on ‘'''start-point'''' '''Species, Protein 1'''.
  
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|-
 
|-
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the r'''eaction line'''
 
| style="border:0.75pt solid #000001;padding:0.071cm;"| Click on the r'''eaction line'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"| To extend or stretch the '''reaction line.'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"| To extend or stretch the '''reaction line''', first click on it.
−
 
+
−
, first click on it.
+
  
 
|-
 
|-
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Click on either of the process nodes located  
 
Click on either of the process nodes located  
  
−
on the '''start-point''' or '''end-point''' '''Species.'''
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on the '''start-point''' or '''end-point Species.'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Now click on either of the '''process nodes '''located on the '''start-point''' or '''end-point''' '''Species'''.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| Now click on either of the '''process nodes '''located on the '''start-point''' or '''end-point Species'''.
  
 
|-
 
|-
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From the toolbar use the icons:
 
From the toolbar use the icons:
  
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* State Transition
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* '''State Transition'''
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* Simple Molecule
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* '''Simple Molecule'''
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* Generic Protein and
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* '''Generic Protein''' and
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* Catalysis
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* '''Catalysis'''
  
 
|-
 
|-
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In this tutorial, we will learn to:
 
In this tutorial, we will learn to:
  
−
* Use Macros
+
* Use '''Macros'''
 
* Move Components on the draw area
 
* Move Components on the draw area
 
* Connect a reaction line around a species
 
* Connect a reaction line around a species
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* Align and extend a reaction line
 
* Align and extend a reaction line
−
* Add a Product and a Reactant
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* Add a '''Product''' and a '''Reactant'''
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 +
|-
 +
| style="border:0.75pt solid #000001;padding:0.071cm;"|
 +
 
 +
'''Assignment'''
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| style="border:0.75pt solid #000001;padding:0.071cm;"|
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For the assignment:
 +
 
 +
* Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner'''
 +
*# Explore the '''Macros''' for '''GTP/GD'''
 +
*# Find out how to create a ’Curve’ reaction line
  
 
|-
 
|-
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It is funded by '''NMEICT, MHRD, Government of India'''.
 
It is funded by '''NMEICT, MHRD, Government of India'''.
  
−
More information on this Mission is available at the link shown
+
More information on this Mission is available at the given link.
−
 
+
−
[http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro]
+
  
 
|-
 
|-
 
| style="border:0.75pt solid #000001;padding:0.071cm;"|  
 
| style="border:0.75pt solid #000001;padding:0.071cm;"|  
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| style="border:0.75pt solid #000001;padding:0.071cm;"| This is '''Bella Tony '''from''' IIT Bombay''' signing off. Thank you for joining.
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| style="border:0.75pt solid #000001;padding:0.071cm;"| This is '''Bella Tony '''from''' IIT Bombay''' signing off.  
 +
 
 +
Thank you for joining.
  
 
|}
 
|}

Latest revision as of 16:38, 21 October 2015

Title of the Script: Build and Modify Process Diagram

Author: Bella Tony

Keywords: Process Diagram, Macros, Alanine Biosythesis, Generic Protein, Aminotransferase

Visual Cue
 Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on ‘Build and Modify Process Diagram in CellDesigner’.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to:
  • Use Macros
  • Move Components on the draw area
  • Connect a reaction line around a species
Slide Number 3

Learning Objectives contd. ...

  • Align and extend a reaction line
  • Add a Product and a Reactant
Slide Number 4

System Requirement

For this tutorial, I am using
  • Ubuntu Linux OS 14.04
  • CellDesigner version 4.3
  • Java version 1.7
Slide Number 5

Pre-requisites

To follow this tutorial, learners should be familiar with:
  • Undergraduate Biochemistry.
  • CellDesigner interface.

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

Let us begin

Slide 6 Conventional diagram for Alanine biosynthesis

What you see here is the conventional diagram for Alanine Biosynthesis.
Now, we’ll use CellDesigner to create this process diagram.

Open terminal by pressing Ctrl+Alt+T keys

Open the terminal by pressing Ctrl+Alt+T keys simultaneously.

Type ./runCellDesigner4.3 >> press Enter.

Now type ./runCellDesigner4.3 and press Enter.
CellDesigner window is now open on your terminal

Press CTRL+N>>name it Build and Modify Process Diagram.

Open a new file by pressing CTRL+N and name it Build and Modify Process Diagram.

Click Ok.

Keep the default width and height and click on the Ok button.
Now let us learn what are ‘Macros’.
Macros are frequently used Components sets that help in drawing the diagrams easily.

Cursor on the toolbar >> Point towards Macros for Catalysis >>

click on it>>place anywhere on draw area.

On the toolbar, click on the Macros icon for Catalysis and click on the draw area.

We now have a Macros-Catalysis reaction on the draw area.

Let’s learn to move all the components to another side of the draw area.

On the main menu bar>>Click on Edit>>


Scroll down and click on Select All'.

For that click on the 'Edit' menu and then click on 'Select All'.

Alternately you may press Ctrl + A keys. All the Components are now highlighted.

Click on highlighted component >> without releasing the mouse button,

drag the components to the desired place

Now click anywhere on the highlighted components and drag them to the desired location.
Let’s proceed.

Click anywhere on the draw area

Click anywhere on the draw area to uncheck the highlighted components.

Right click on the Generic Protein S1

Again on the draw area, right click on the Generic Protein S1.

Click 'Change Identity'

Then click on the option 'Change Identity'.

In the dialog box 'Change identity of the species>> go to class box>>

change Protein to Simple Molecule.

In the 'class' box, change the Protein to Simple Molecule.

Type Name as: 2-keto-isovalerate >>

Click ‘Apply’.

Type the Name as: 2-keto-isovalerate.


And then click on the ‘Apply’ button.

In the dialog box ‘The Same Species Exists’ >>Click on the option ‘No’.

In the dialog box ‘The Same Species Exists’, click ‘No’.
Point to the button "Yes" However if you want to reflect the change to all components of the species, click ‘Yes’.

Here, I will click ‘No’

Cursor on 2-keto-isovalerate. Observe the Generic Protein S1, is now a simple molecule named 2-keto-isovalerate.

I will drag the molecule to accomodate the name.

Right-click on Generic protein-S1 which is a product >>

Change identity to Simple Molecule and Name it Valine.

Right-click in the center of the end-point, Generic protein-S1 which is a product.

Change identity to Simple Molecule and name it Valine.

Click on the Apply button. Click on the Apply button.


You have Valine on the draw area.

Right-click and select Edit Protein.

In the ‘name’ field, type Aminotransferase

Next, rename catalyst S2.

Right-click on it and select Edit Protein.


In the ‘name’ field, type Aminotransferase.

Click on Update>> close the dialog box.

Drag the corner of the molecule to accomodate the name.

Click on Update and close the dialog box.

Drag the corner of the molecule to accomodate the name.

Next, let’s change the position of the linked reaction.

Click on Valine >> Without releasing the mouse,

drag the Species.

Click in the center of the 'end-point' species i.e. Valine and drag and drop at the desired location.
Repeat the same with Aminotransferase
Observe that the linked reaction follows wherever the ‘end-point’ Species moves.

How to connect a reaction line around a species.

We will now learn how to connect a reaction line around a species.
A Reaction line can be connected to any of the 16 connection points around a Species.

I will show you how to do so.

Click on File >> New

Type the filename as ‘Connection point of Species’.

Open a new window by pressing CTRL+N.

Name this file as Connection points.

Click Ok. Keep the default width and height and click on Ok the button.
<<PAUSE RECORDING>>

On the toolbar >>Click on the Generic protein >>

Click again on the draw area >> name it Protein 1 Repeat the above and name it Protein 2

<<RESUME RECORDING>>

On the draw area, draw two generic proteins and name them Protein 1 and Protein 2.

Cursor on the toolbar >>Click on the State transition>>

hover the mouse on Protein 1>>

In the main menu,click on the icon for State Transition.


Then, on the draw area, hover the mouse on ‘start-point' Species, Protein 1.

Mouse hovering Observe that all 16 connection points are highlighted in grey color.

Point the cursor to one connection point.

Note that when the cursor is pointed to one of these connection points, it will change to blue color.

Click on any one of the connection points.

Let’s click on one of the connection points.

Hover the mouse on Protein 2

In the same manner, hover the mouse on the ‘end-point' Species i.e. Protein 2.

Click on any one of the connection points.

Again, as explained above, click on the required connection point.

Cursor on State Transition reaction line between the selected connection points.

A State Transition reaction line is formed between the selected connection points.
Next, we will align the Reaction line.

Click on the State transition reaction line between

Protein 1 and Protein 2

Click on the State transition reaction line between Protein 1 and Protein 2

Point the cursor on the 2 process nodes on the reaction line

Note that the 2 process nodes on the reaction line get highlighted.

One by one, hover the mouse on 2 process nodes of

start point and end point of the species

If we hover the mouse on either of the 2 process nodes, a ‘plus’ sign appears.

Click on the process node>> Drag and place the

reaction line on the required connection point.

Click on one of the process nodes.

Now drag and place the pointer on the preferred connection point.

Click anywhere on the draw area to uncheck the

highlighted components.

Click anywhere on the draw area to uncheck the highlighted components.
Click on the reaction line To extend or stretch the reaction line, first click on it.

Click on either of the process nodes located

on the start-point or end-point Species.

Now click on either of the process nodes located on the start-point or end-point Species.

Drag the mouse to stretch the reaction line till the preferred connection point.

Drag the mouse to stretch the reaction line till the preferred connection point.
From here on, we will proceed with the Process diagram.

Click on the Build and Modify Process Diagram window.

Let us come back to the Build and Modify Process Diagram window.
Let’s add a Reactant and a Product, to the existing reaction.

From the toolbar, click and place 2 simple molecules on the draw area.

From the toolbar, click and place 2 simple molecules on the draw area.

Name them Glutamate and 2-Oxoglutarate.

Name them Glutamate and 2-Oxoglutarate.

Drag and place them adjacent to the Simple molecules:

2-keto-isovalerate and Valine.

Drag and place them adjacent to the Simple molecules: 2-keto-isovalerate and Valine.

Cursor on the draw area.

<<PAUSE RECORDING>>

As explained earlier, let us align the components on the draw area. 
<<RESUME RECORDING>>
From what was explained earlier, I have now completed aligning the components.

On the toolbar, click on the icon for ‘Add Product’.

On the toolbar, click on the icon for ‘Add Product’.

Hover the mouse on the State Transition reaction

between 2-keto-isovalerate and Valine.

Now hover the mouse on the State Transition reaction between 2-keto-isovalerate and Valine.
Click on the process node Click on the highlighted process node.

Next, hover the mouse on 2-Oxoglutarate >> Click on any of the 16 highlighted process nodes.

Next, hover the mouse on 2-Oxoglutarate.

Click on any one of the 16 highlighted process nodes.

A reaction line appears between State Transition

and 2-Oxoglutarate

Observe, a reaction line appears between State Transition and 2-Oxoglutarate.

Click on ‘Add Reactant’ icon

Similarly, click on ‘Add Reactant’ icon.

On the toolbar>> click on ‘Add Reactant’ >> Hover the mouse on

Glutamate>>click on any of the 16 highlighted process nodes.

Hover the mouse on Glutamate and click on one of the 16 highlighted process nodes.

Hover the mouse on the State Transition reaction >> click on the process node.

Next, hover the mouse on the State Transition reaction and click on the process node.

Cursor on reaction line between

State Transition and Glutamate.

Observe, a reaction line appears between State Transition and Glutamate.

Cursor on Catalysis reaction

We now have a complete Catalysis reaction with a Reactant and a Product.

Cursor on toolbar

I will align the reaction to accommodate other components in the process diagram.

From the toolbar use the icons:

  • State Transition
  • Simple Molecule
  • Generic Protein and
  • Catalysis

Cursor on completed process diagram.

This is the completed process diagram.

Go to View>> click on Zoom Fit

To view it properly, go to View on the main menu bar and click on Zoom Fit

You now see the completed Process Diagram

SlideSummary

Let us summarize.

In this tutorial, we will learn to:

  • Use Macros
  • Move Components on the draw area
  • Connect a reaction line around a species


We also learnt to:

  • Align and extend a reaction line
  • Add a Product and a Reactant

Assignment

For the assignment:

  • Build a process diagram for Methionine Biosynthesis using tools in CellDesigner
    1. Explore the Macros for GTP/GD
    2. Find out how to create a ’Curve’ reaction line

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.

Acknowledgement

The Spoken Tutorial Project Team conducts-

  • Workshops using Spoken tutorials.

Acknowledgement

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

Nancyvarkey, PoojaMoolya

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