Difference between revisions of "CellDesigner/C3/Build-and-Modify-Process-Diagram/English-timed"
From Script | Spoken-Tutorial
Jyotisolanki (Talk | contribs) |
Sandhya.np14 (Talk | contribs) |
||
(4 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
{| border=1 | {| border=1 | ||
|| '''Time''' | || '''Time''' | ||
|| '''Narration''' | || '''Narration''' | ||
− | |||
|- | |- | ||
| 00:01 | | 00:01 | ||
− | | Hello everyone. Welcome to this tutorial on''' | + | | Hello everyone. Welcome to this tutorial on''' Build and Modify Process Diagram''' in''' CellDesigner'''. |
|- | |- | ||
| 00:08 | | 00:08 | ||
− | | In this tutorial, we will learn to: | + | | In this tutorial, we will learn to: use '''Macros''' , move '''Components''' on the '''draw area''' , connect a '''reaction line''' around a '''species''', |
|- | |- | ||
| 00:18 | | 00:18 | ||
− | | | + | | align and extend a reaction line , add a '''Product''' and a '''Reactant'''. |
|- | |- | ||
| 00:23 | | 00:23 | ||
− | | For this tutorial, I am using'''Ubuntu Linux OS 14.04''' '''CellDesigner '''version '''4.3''' '''Java version 1.7''' | + | | For this tutorial, I am using'''Ubuntu Linux OS 14.04''', '''CellDesigner '''version '''4.3''', '''Java version 1.7'''. |
|- | |- | ||
| 00:35 | | 00:35 | ||
− | | To follow this tutorial, learners should be familiar with: | + | | To follow this tutorial, learners should be familiar with: undergraduate''' Biochemistry,''' '''CellDesigner '''interface. |
|- | |- | ||
| 00:43 | | 00:43 | ||
− | |If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website | + | |If not, for relevant''' CellDesigner tutorials''', please visit the''' Spoken Tutorial '''website. |
|- | |- | ||
| 00:51 | | 00:51 | ||
− | | Let us begin | + | | Let us begin. |
|- | |- | ||
Line 45: | Line 38: | ||
|- | |- | ||
| 00:58 | | 00:58 | ||
− | | Now, we’ll use '''CellDesigner''' to create this process diagram. | + | | Now, we’ll use '''CellDesigner''' to create this '''process diagram'''. |
|- | |- | ||
Line 53: | Line 46: | ||
|- | |- | ||
| 01:09 | | 01:09 | ||
− | | Now type '''./runCellDesigner4.3''' and press '''Enter'''. | + | | Now type: '''./runCellDesigner4.3''' and press '''Enter'''. |
|- | |- | ||
| 01:20 | | 01:20 | ||
− | | CellDesigner window is now open on your terminal | + | | CellDesigner window is now open on your terminal. |
|- | |- | ||
| 01:24 | | 01:24 | ||
− | | Open a new file by pressing''' CTRL+N''' and name it '''Build | + | | Open a new file by pressing''' CTRL+N''' and name it '''Build and Modify Process Diagram'''. |
|- | |- | ||
Line 77: | Line 70: | ||
|- | |- | ||
| 01:47 | | 01:47 | ||
− | | On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the draw area. | + | | On the toolbar, click on the '''Macros''' icon for '''Catalysis '''and click on the '''draw area'''. |
|- | |- | ||
Line 89: | Line 82: | ||
|- | |- | ||
| 02:08 | | 02:08 | ||
− | | For that click on the | + | | For that, click on the '''Edit''' menu and then click on ''''Select All'.''' |
|- | |- | ||
| 02:16 | | 02:16 | ||
− | |Alternately you may press '''Ctrl + A '''keys. | + | |Alternately, you may press '''Ctrl + A '''keys. |
|- | |- | ||
Line 101: | Line 94: | ||
|- | |- | ||
| 02:24 | | 02:24 | ||
− | | Now click anywhere on the highlighted components and drag them to the desired location. | + | | Now, click anywhere on the highlighted components and drag them to the desired location. |
|- | |- | ||
| 02:30 | | 02:30 | ||
− | | | + | | Let's proceed. |
|- | |- | ||
Line 113: | Line 106: | ||
|- | |- | ||
| 02:37 | | 02:37 | ||
− | | Again on the draw area, right click on the''' Generic Protein S1.''' | + | | Again, on the draw area, right click on the''' Generic Protein S1.''' |
|- | |- | ||
Line 137: | Line 130: | ||
|- | |- | ||
| 03:10 | | 03:10 | ||
− | | However if you want to reflect the change to all components of the species, click ‘'''Yes'''’.Here, I will click''' ‘No’''' | + | | However, if you want to reflect the change to all '''components''' of the '''species''', click ‘'''Yes'''’. Here, I will click''' ‘No’'''. |
|- | |- | ||
| 03:20 | | 03:20 | ||
− | | Observe the''' Generic Protein S1 | + | | Observe the''' Generic Protein S1 '''is now a simple molecule named '''2-keto-isovalerate.''' |
|- | |- | ||
Line 149: | Line 142: | ||
|- | |- | ||
| 03:34 | | 03:34 | ||
− | | Right-click in the center of the''' end-point | + | | Right-click in the center of the''' end-point ''' '''Generic protein'''-'''S1 ''' which is a '''product'''. |
|- | |- | ||
Line 185: | Line 178: | ||
|- | |- | ||
| 04:25 | | 04:25 | ||
− | | Click in the center of the ''''end-point | + | | Click in the center of the ''''end-point species''' i.e.''' Valine '''and drag and drop at the desired location. |
|- | |- | ||
| 04:33 | | 04:33 | ||
− | | Repeat the same with '''Aminotransferase''' | + | | Repeat the same with '''Aminotransferase'''. |
|- | |- | ||
Line 217: | Line 210: | ||
|- | |- | ||
| 05:08 | | 05:08 | ||
− | | Keep the default width and height and click on ''' | + | | Keep the default width and height and click on '''OK''' button. |
|- | |- | ||
Line 225: | Line 218: | ||
|- | |- | ||
| 05:23 | | 05:23 | ||
− | | In the main menu,click on the icon for '''State Transition'''. | + | | In the main menu, click on the icon for '''State Transition'''. |
|- | |- | ||
| 05:28 | | 05:28 | ||
− | |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'''. |
|- | |- | ||
Line 245: | Line 238: | ||
|- | |- | ||
| 05:53 | | 05:53 | ||
− | | In the same manner, hover the mouse on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''. | + | | In the same manner, hover the '''mouse''' on the ‘'''end-point'''' '''Species '''i.e. '''Protein 2'''. |
|- | |- | ||
Line 269: | Line 262: | ||
|- | |- | ||
| 06:27 | | 06:27 | ||
− | | If we hover the mouse on either of the 2 '''process nodes''', a | + | | If we hover the mouse on either of the 2 '''process nodes''', a plus sign appears. |
|- | |- | ||
Line 281: | Line 274: | ||
|- | |- | ||
| 06:43 | | 06:43 | ||
− | | Click anywhere on the draw area to uncheck the highlighted components. | + | | Click anywhere on the '''draw area''' to uncheck the highlighted components. |
|- | |- | ||
Line 297: | Line 290: | ||
|- | |- | ||
| 07:07 | | 07:07 | ||
− | | From here on, we will proceed with the Process diagram. | + | | From here on, we will proceed with the '''Process diagram'''. |
|- | |- | ||
| 07:12 | | 07:12 | ||
− | | Let us come back to the '''Build | + | | Let us come back to the '''Build and Modify Process Diagram''' window. |
|- | |- | ||
| 07:16 | | 07:16 | ||
− | | Let’s add a '''Reactant '''and a '''Product''' | + | | Let’s add a '''Reactant '''and a '''Product''' to the existing reaction. |
|- | |- | ||
Line 337: | Line 330: | ||
|- | |- | ||
| 08:07 | | 08:07 | ||
− | | Click on the | + | | Click on the highlighted '''process node.''' |
|- | |- | ||
Line 377: | Line 370: | ||
|- | |- | ||
| 09:09 | | 09:09 | ||
− | |From the toolbar use the icons: '''State Transition''' , '''Simple Molecule''', '''Generic Protein''' and '''Catalysis''' | + | |From the toolbar, use the icons: '''State Transition''' , '''Simple Molecule''', '''Generic Protein''' and '''Catalysis'''. |
|- | |- | ||
Line 393: | Line 386: | ||
|- | |- | ||
| 09:36 | | 09:36 | ||
− | | Let us summarize. In this tutorial, we have learnt to | + | | Let us summarize. In this tutorial, we have learnt: to use '''Macros''', |
|- | |- | ||
| 09:42 | | 09:42 | ||
− | | | + | |move '''Components''' on the '''draw area''' , connect a reaction line around a species, |
|- | |- | ||
| 09:48 | | 09:48 | ||
− | | | + | | align and extend a reaction line, add a '''Product''' and a '''Reactant'''. |
|- | |- | ||
| 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''' | + | Explore the '''Macros''' for '''GTP/GD'''. |
− | Find out how to create a ’Curve’ reaction line | + | Find out how to create a ’Curve’ reaction line. |
|- | |- | ||
| 10:11 | | 10:11 | ||
− | | About the Spoken Tutorial project- | + | | About the '''Spoken Tutorial''' project- |
|- | |- | ||
| 10:14 | | 10:14 | ||
− | |Watch the video at the following link It summarizes the Spoken Tutorial project. | + | |Watch the video at the following link. It summarizes the Spoken Tutorial project. |
|- | |- | ||
| 10:19 | | 10:19 | ||
− | | If you do not have a good bandwidth please download and watch it. | + | | If you do not have a good bandwidth, please download and watch it. |
|- | |- | ||
− | | | + | | 10:24 |
− | | The''' Spoken Tutorial Project ''' | + | | The''' Spoken Tutorial Project '''team: conducts- workshops using Spoken tutorials |
|- | |- | ||
− | | | + | | 10:29 |
− | | | + | | and gives certificates for those who pass an online test. |
|- | |- | ||
Line 435: | Line 428: | ||
|- | |- | ||
| 10:40 | | 10:40 | ||
− | | Spoken Tutorial | + | | '''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 | | 10:54 | ||
− | | This is '''Bella Tony '''from''' IIT Bombay''' signing off. | + | | This is '''Bella Tony '''from''' IIT Bombay,''' signing off. |
Thank you for joining. | Thank you for joining. | ||
|} | |} |
Latest revision as of 15:55, 7 June 2018
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 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. |
10:24 | The Spoken Tutorial Project team: conducts- workshops using Spoken tutorials |
10:29 | 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. |