CellDesigner/C3/Customizing-Diagram-Layout/English-timed
From Script | Spoken-Tutorial
| 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. |
