CellDesigner/C3/Customizing-Diagram-Layout/English-timed

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	Let's 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 andAngle 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.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14