Difference between revisions of "CellDesigner/C3/Build-and-Modify-Process-Diagram/English-timed"
From Script | Spoken-Tutorial
Jyotisolanki (Talk | contribs) |
Jyotisolanki (Talk | contribs) |
||
| Line 405: | Line 405: | ||
|- | |- | ||
| 09:54 | | 09:54 | ||
| − | | For the assignment:Build a process diagram for '''Methionine Biosynthesis''' using tools in '''CellDesigner''' | + | | 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 | ||
|- | |- | ||
Revision as of 11:57, 21 November 2017
Title of the Script: Build and Modify Process Diagram
Author: Bella Tony
Keywords: Process Diagram, Macros, Alanine Biosythesis, Generic Protein, Aminotransferase
| Time | Narration
|
| 00:01 | Hello everyone. Welcome to this tutorial on ‘Build and Modify Process Diagram in CellDesigner’. |
| 00:08 | In this tutorial, we will learn to: Use Macros , Move Components on the draw area , Connect a reaction line around a species |
| 00:18 | Align and extend a reaction line , Add a Product and a Reactant |
| 00:23 | For this tutorial, I am usingUbuntu Linux OS 14.04 CellDesigner version 4.3 Java version 1.7 |
| 00:35 | To follow this tutorial, learners should be familiar with: Undergraduate Biochemistry. CellDesigner interface. |
| 00:43 | If not, for relevant CellDesigner tutorials, please visit the Spoken Tutorial website |
| 00:51 | Let us begin |
| 00:53 | What you see here is the conventional diagram for Alanine Biosynthesis. |
| 00:58 | Now, we’ll use CellDesigner to create this process diagram. |
| 01:02 | Open the terminal by pressing Ctrl+Alt+T keys simultaneously. |
| 01:09 | Now type ./runCellDesigner4.3 and press Enter. |
| 01:20 | CellDesigner window is now open on your terminal |
| 01:24 | Open a new file by pressing CTRL+N and name it Build and Modify Process Diagram. |
| 01:34 | Keep the default width and height and click on the Ok button. |
| 01:39 | Now let us learn what are ‘Macros’. |
| 01:42 | Macros are frequently used Components sets that help in drawing the diagrams easily. |
| 01:47 | On the toolbar, click on the Macros icon for Catalysis and click on the draw area. |
| 01:57 | We now have a Macros-Catalysis reaction on the draw area. |
| 02:02 | Let’s learn to move all the components to another side of the draw area. |
| 02:08 | For that click on the 'Edit' menu and then click on 'Select All'. |
| 02:16 | Alternately you may press Ctrl + A keys. |
| 02:21 | All the Components are now highlighted. |
| 02:24 | Now click anywhere on the highlighted components and drag them to the desired location. |
| 02:30 | Let’s proceed. |
| 02:32 | Click anywhere on the draw area to uncheck the highlighted components. |
| 02:37 | Again on the draw area, right click on the Generic Protein S1. |
| 02:43 | Then click on the option 'Change Identity'. |
| 02:47 | In the 'class' box, change the Protein to Simple Molecule. |
| 02:53 | Type the Name as: 2-keto-isovalerate. |
| 02:58 | And then click on the ‘Apply’ button. |
| 03:02 | In the dialog box ‘The Same Species Exists’, click ‘No’. |
| 03:10 | However if you want to reflect the change to all components of the species, click ‘Yes’.Here, I will click ‘No’ |
| 03:20 | Observe the Generic Protein S1, is now a simple molecule named 2-keto-isovalerate. |
| 03:30 | I will drag the molecule to accomodate the name. |
| 03:34 | Right-click in the center of the end-point, Generic protein-S1 which is a product. |
| 03:42 | Change identity to Simple Molecule and name it Valine. |
| 03:50 | Click on the Apply button. |
| 03:52 | You have Valine on the draw area. |
| 03:36 | Next, rename catalyst S2. Right-click on it and select Edit Protein. |
| 04:06 | In the ‘name’ field, type Aminotransferase. |
| 04:11 | Click on Update and close the dialog box. |
| 04:16 | Drag the corner of the molecule to accomodate the name. |
| 04:21 | Next, let’s change the position of the linked reaction. |
| 04:25 | Click in the center of the 'end-point' species i.e. Valine and drag and drop at the desired location. |
| 04:33 | Repeat the same with Aminotransferase |
| 04:37 | Observe that the linked reaction follows wherever the ‘end-point’ Species moves. |
| 04:44 | We will now learn how to connect a reaction line around a species. |
| 04:49 | A Reaction line can be connected to any of the 16 connection points around a Species. |
| 04:56 | I will show you how to do so. |
| 04:59 | Open a new window by pressing CTRL+N. |
| 05:04 | Name this file as Connection points. |
| 05:08 | Keep the default width and height and click on Ok the button. |
| 05:14 | On the draw area, draw two generic proteins and name them Protein 1 and Protein 2. |
| 05:23 | In the main menu,click on the icon for State Transition. |
| 05:28 | Then, on the draw area, hover the mouse on ‘start-point' Species, Protein 1. |
| 05:36 | Observe that all 16 connection points are highlighted in grey color. |
| 05:42 | Note that when the cursor is pointed to one of these connection points, it will change to blue color. |
| 05:49 | Let’s click on one of the connection points. |
| 05:53 | In the same manner, hover the mouse on the ‘end-point' Species i.e. Protein 2. |
| 06:00 | Again, as explained above, click on the required connection point. |
| 06:05 | A State Transition reaction line is formed between the selected connection points. |
| 06:12 | Next, we will align the Reaction line. |
| 06:16 | Click on the State transition reaction line between Protein 1 and Protein 2 |
| 06:21 | Note that the 2 process nodes on the reaction line get highlighted. |
| 06:27 | If we hover the mouse on either of the 2 process nodes, a ‘plus’ sign appears. |
| 06:34 | Click on one of the process nodes. |
| 06:37 | Now drag and place the pointer on the preferred connection point. |
| 06:43 | Click anywhere on the draw area to uncheck the highlighted components. |
| 06:49 | To extend or stretch the reaction line, first click on it. |
| 06:54 | Now click on either of the process nodes located on the start-point or end-point Species. |
| 07:01 | Drag the mouse to stretch the reaction line till the preferred connection point. |
| 07:07 | From here on, we will proceed with the Process diagram. |
| 07:12 | Let us come back to the Build and Modify Process Diagram window. |
| 07:16 | Let’s add a Reactant and a Product, to the existing reaction. |
| 07:21 | From the toolbar, click and place 2 simple molecules on the draw area. |
| 07:27 | Name them Glutamate and 2-Oxoglutarate. |
| 07:36 | Drag and place them adjacent to the Simple molecules: 2-keto-isovalerate and Valine. |
| 07:44 | As explained earlier, let us align the components on the draw area. |
| 07:49 | From what was explained earlier, I have now completed aligning the components. |
| 07:55 | On the toolbar, click on the icon for ‘Add Product’. |
| 08:00 | Now hover the mouse on the State Transition reaction between 2-keto-isovalerate and Valine. |
| 08:07 | Click on the highlighted process node. |
| 08:10 | Next, hover the mouse on 2-Oxoglutarate. |
| 08:17 | Click on any one of the 16 highlighted process nodes. |
| 08:21 | Observe, a reaction line appears between State Transition and 2-Oxoglutarate. |
| 08:29 | Similarly, click on ‘Add Reactant’ icon. |
| 08:34 | Hover the mouse on Glutamate and click on one of the 16 highlighted process nodes. |
| 08:40 | Next, hover the mouse on the State Transition reaction and click on the process node. |
| 08:49 | Observe, a reaction line appears between State Transition and Glutamate. |
| 08:55 | We now have a complete Catalysis reaction with a Reactant and a Product. |
| 09:01 | I will align the reaction to accommodate other components in the process diagram. |
| 09:09 | From the toolbar use the icons: State Transition , Simple Molecule, Generic Protein and Catalysis |
| 09:18 | This is the completed process diagram. |
| 09:22 | To view it properly, go to View on the main menu bar and click on Zoom Fit |
| 09:32 | You now see the completed Process Diagram |
| 09:36 | Let us summarize. In this tutorial, we have learnt to Use Macros. |
| 09:42 | Move Components on the draw area , Connect a reaction line around a species. |
| 09:48 | Align and extend a reaction line, Add a Product and a Reactant |
| 09:54 | 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 |
| 10:11 | About the Spoken Tutorial project- |
| 10:14 | Watch the video at the following link It summarizes the Spoken Tutorial project. |
| 10:19 | If you do not have a good bandwidth please download and watch it. |
| 09:24 | The Spoken Tutorial Project Team conducts- Workshops using Spoken tutorials. |
| 09:29 | And gives certificates for those who pass an online test. |
| 10:34 | For more details, please write to contact@spoken-tutorial.org |
| 10:40 | 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. |
| 10:54 | This is Bella Tony from IIT Bombay signing off.
Thank you for joining. |
