Difference between revisions of "CellDesigner/C2/Getting-Started-with-CellDesigner/English-timed"
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| 00:01 | | 00:01 | ||
− | | Welcome to the Spoken tutorial on ''' Getting started with | + | | Welcome to the '''Spoken tutorial''' on ''' Getting started with CellDesigner'''. |
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| 00:05 | | 00:05 | ||
− | | In this tutorial we will learn : | + | | In this tutorial, we will learn about: CellDesigner , '''Menu''' and '''Tool bar'''s in CellDesigner, |
|- | |- | ||
| 00:13 | | 00:13 | ||
− | | | + | |different areas in the CellDesigner '''workspace''', |
|- | |- | ||
| 00:17 | | 00:17 | ||
− | | | + | |components of CellDesigner which includes '''Species''' and '''Reactions'''. |
|- | |- | ||
|00:23 | |00:23 | ||
− | | We will also learn | + | | We will also learn how to: create a simple network, |
|- | |- | ||
| 00:27 | | 00:27 | ||
− | | | + | |'''save''' a '''network''', |
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| 00:29 | | 00:29 | ||
− | | | + | |'''export''' an '''image''', |
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| 00:30 | | 00:30 | ||
− | | | + | |how to zoom a network. |
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| 00:33 | | 00:33 | ||
− | | '''CellDesigner''' is a process diagram editor | + | | '''CellDesigner''' is a '''process diagram editor''' for drawing gene-regulatory and biochemical networks. |
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| 00:40 | | 00:40 | ||
− | | The process diagram was proposed by Kitano These diagrams are stored using the '''Systems Biology Markup Language (SBML)''' | + | | The process diagram was proposed by Kitano. These diagrams are stored using the '''Systems Biology Markup Language (SBML)'''. |
|- | |- | ||
| 00:50 | | 00:50 | ||
− | | I am using Windows XP and CellDesigner Version 4. | + | | I am using '''Windows XP''' and '''CellDesigner''' Version 4.3. CellDesigner works on '''Linux''' and '''Mac OS X''' also. |
|- | |- | ||
| 01:00 | | 01:00 | ||
− | | To open CellDesigner, double-click on the shortcut CellDesigner icon on the desktop. | + | | To open CellDesigner, double-click on the '''shortcut CellDesigner icon''' on the desktop. |
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| 01:07 | | 01:07 | ||
− | |This will open CellDesigner | + | |This will open CellDesigner. Now let's explore . |
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| 01:12 | | 01:12 | ||
− | | On the '''Menu''' bar you can see various Menu options | + | | On the '''Menu''' bar, you can see various Menu options like- '''File''', '''Edit''', '''Component''' ,'''View''', '''Database''' and others. |
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| 01:24 | | 01:24 | ||
− | | Under the '''Main Menu ''' you will see various '''Toolbars'''. | + | | Under the '''Main Menu, ''' you will see various '''Toolbars'''. |
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| 01:30 | | 01:30 | ||
− | | There are '''Toolbars '''for editing, species, reactions, compartments | + | | There are '''Toolbars '''for editing, '''species''', '''reactions''', '''compartments''' etc. |
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| 01:42 | | 01:42 | ||
− | | Let us learn about the different areas of the CellDesigner workspace. | + | | Let us learn about the different areas of the '''CellDesigner workspace'''. |
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| 01:52 | | 01:52 | ||
− | | On the right hand side is the '''Draw''' area. | + | | On the right hand side, is the '''Draw''' area. |
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| 02:14 | | 02:14 | ||
− | | One can see the list of all these symbols and their meanings from the CellDesigner website – | + | | One can see the list of all these symbols and their meanings from the CellDesigner website – that is '''www.celldesigner.org''' |
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| 02:29 | | 02:29 | ||
− | | I will click on the ''' Documents ''' | + | | I will click on the ''' Documents. ''' |
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| 02:33 | | 02:33 | ||
− | |Now let's | + | |Now let's click on the '''Startup guide'''. That is also on another tab. |
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|02:55 | |02:55 | ||
− | | Below '''Draw''' area is the '''List''' area. | + | | Below '''Draw''' area, is the '''List''' area. |
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| 03:21 | | 03:21 | ||
− | | Below that is the '''Layer''' area which displays all the layers of the model. | + | | Below that, is the '''Layer''' area which displays all the layers of the model. |
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| 03:45 | | 03:45 | ||
− | | To change the position of the '''List''' & '''Notes''' area | + | | To change the position of the '''List''' & '''Notes''' area, |
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| 03:50 | | 03:50 | ||
− | | go to '''View''' option>>click on '''List''' and select '''Right'''. | + | | go to '''View''' option >> click on '''List''' and select '''Right'''. |
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| 03:56 | | 03:56 | ||
− | | It changes list to the right. Down is the default one. | + | | It changes list to the '''right'''. '''Down''' is the default one. |
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| 04:10 | | 04:10 | ||
− | | In this network Protein '''A''' undergoes state transition to Protein '''B '''under catalysis of Protein '''C'''. | + | | In this network, Protein '''A''' undergoes state transition to Protein '''B ''', under catalysis of Protein '''C'''. |
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| 04:39 | | 04:39 | ||
− | |Now | + | |Now click on '''File''' and then '''New'''. |
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| 04:48 | | 04:48 | ||
− | | This is ''' | + | | This is ''' Name ''' field. |
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| 04:50 | | 04:50 | ||
− | | I will type “'''simple network”''' | + | | I will type “'''simple network”'''. |
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| 04:53 | | 04:53 | ||
− | | Here one can change the height and width as required. However, I will keep the default height and width. | + | | Here, one can change the height and width as required. However, I will keep the default height and width. |
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| 05:12 | | 05:12 | ||
− | | Now | + | | Now go to '''Edit''' and enable '''Grid snap''' and '''Grid visible'''. |
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| 05:34 | | 05:34 | ||
− | | Before we begin to add | + | | Before we begin to add '''component'''s, let me show you some examples of '''species''' and '''reactions'''. |
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| 05:45 | | 05:45 | ||
− | | The symbols here are for '''generic protein, receptor, ion''' '''channel, truncated protein, gene,''' '''RNA''' etc. | + | | The symbols here are for '''generic protein, receptor, ion''', '''channel, truncated protein, gene,''' '''RNA''' etc. |
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| 05:58 | | 05:58 | ||
− | | Now let us see the reactions | + | | Now let us see the reactions. First is the '''State transition''', '''Heterodimer association''', '''Dissociation''', '''Catalysis, Inhibition '''etc. |
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| 06:39 | | 06:39 | ||
− | | I will name the new species as '''A''' and click on OK. | + | | I will name the new species as '''A''' and click on '''OK'''. |
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| 06:46 | | 06:46 | ||
− | |See the change in the list area too. | + | |See the change in the '''list''' area too. |
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| 06:50 | | 06:50 | ||
− | | As you can see we have added a new species | + | | As you can see, we have added a new species in the '''Draw area'''. Similarly I will add '''B'''. |
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| 07:03 | | 07:03 | ||
− | | Click on the component to select them. Make sure the select icon is on before you do so. | + | | Click on the '''component''' to select them. Make sure the select icon is on before you do so. |
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| 07:21 | | 07:21 | ||
− | | Now we will see | + | | Now we will see how to change the size of a component. |
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| 07:29 | | 07:29 | ||
− | | These are the handles to change the size. | + | | These are the '''handles''' to change the size. |
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| 07:46 | | 07:46 | ||
− | | You can “undo" the previous actions with Ctrl-Z . | + | | You can '''“undo"''' the previous actions with '''Ctrl-Z''' . |
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| 07:52 | | 07:52 | ||
− | | If you want to “re-do”, press Ctrl-Y. | + | | If you want to “re-do”, press '''Ctrl-Y'''. |
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| 07:54 | | 07:54 | ||
− | | Also you can do this directly by click on the icons for undo and redo | + | | Also you can do this directly by click on the icons for '''undo''' and '''redo'''. |
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| 08:03 | | 08:03 | ||
− | | Now let’s add | + | | Now let’s add '''reaction'''s. |
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| 08:09 | | 08:09 | ||
− | | This is a state transition reaction. | + | | This is a '''state transition''' reaction. |
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| 08:12 | | 08:12 | ||
− | | So I will click on the icon for '''State transition''' in the '''Reaction''' toolbar. | + | | So, I will click on the icon for '''State transition''' in the '''Reaction''' toolbar. |
+ | |||
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| 08:18 | | 08:18 | ||
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| 08:35 | | 08:35 | ||
− | | So always remember to select the reactants first. | + | | So, always remember to select the reactants first. |
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| 08:39 | | 08:39 | ||
− | | The default reaction id comes as '''re1'''. | + | | The default '''reaction id''' comes as '''re1'''. |
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| 08:43 | | 08:43 | ||
− | | Now | + | | Now, let's add '''species C''' and keep at appropriate position as shown in the earlier slide. |
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|09:00 | |09:00 | ||
− | | I will click on the edge of '''C''' | + | | I will click on the edge of '''C''' and the square symbol of the '''State transition''' reaction. |
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| 09:08 | | 09:08 | ||
− | | Now | + | | Now, I will add '''species D''' and place it besides '''B'''. |
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| 09:15 | | 09:15 | ||
− | | | + | | Let's add a '''State transition '''reaction from B to D. The default reaction-id is '''re2'''. |
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| 09:26 | | 09:26 | ||
− | | I will add species E and keep at appropriate position as shown in the earlier slide. | + | | I will add '''species E''' and keep at appropriate position as shown in the earlier slide. |
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| 09:35 | | 09:35 | ||
− | | Now I will select this icon from the '''Reaction '''toolbar | + | | Now I will select this icon from the '''Reaction '''toolbar which represents the '''Inhibition reaction'''. |
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| 09:57 | | 09:57 | ||
− | | Let us save our work. | + | | Let us '''save''' our work. |
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| 10:12 | | 10:12 | ||
− | | Now we will learn how to Export an image. To do this, Go to '''File | + | | Now we will learn how to '''Export''' an '''image'''. To do this, Go to '''File > Export Image'''. |
|- | |- | ||
| 10:22 | | 10:22 | ||
− | | You can save the image in various formats like pdf, png, jpeg etc. | + | | You can save the image in various formats like '''pdf, png, jpeg''' etc. |
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| 10:38 | | 10:38 | ||
− | | We have 4 options for zoom - ''' Zoom In, Zoom Out, Zoom Fit | + | | We have 4 options for zoom - ''' Zoom In, Zoom Out, Zoom Fit, Zoom Reset '''. |
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|11:02 | |11:02 | ||
− | | This brings us to the end of the spoken tutorial on | + | | This brings us to the end of the spoken tutorial on '''Getting started with CellDesigner'''. |
|- | |- | ||
| 11:08 | | 11:08 | ||
− | | To Summarize | + | | To Summarize : we learnt about Menu and Tool bar in CellDesigner, |
|- | |- | ||
| 11:14 | | 11:14 | ||
− | | | + | | different areas in CellDesigner, components like Species and Reactions. |
|- | |- | ||
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| 11:32 | | 11:32 | ||
− | | As an assignment | + | | As an assignment, construct a network with the help of CellDesigner 4.3 |
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| 12:01 | | 12:01 | ||
− | | Watch the video available at the following link It summarises the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it | + | | Watch the video available at the following link. It summarises the '''Spoken Tutorial''' project. If you do not have good bandwidth, you can download and watch it. |
|- | |- | ||
| 12:13 | | 12:13 | ||
− | | The Spoken Tutorial Project | + | | The Spoken Tutorial Project team: conducts workshops using spoken tutorials, gives certificates for those who pass an online test. For more details, please write to '''contact at spoken hyphen tutorial dot org'''. |
|- | |- | ||
| 12:28 | | 12:28 | ||
− | | Spoken Tutorial | + | | '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
|- | |- | ||
| 12:41 | | 12:41 | ||
− | | More information on this | + | | More information on this mission is available at '''spoken hyphen tutorial dot org slash NMEICT hyphen Intro'''. |
|- | |- | ||
| 12:53 | | 12:53 | ||
− | |This is Sakina Shaikh from IIT Bombay signing off. Thanks for joining. Goodbye. | + | |This is Sakina Shaikh from IIT Bombay, signing off. Thanks for joining. Goodbye. |
|} | |} |
Latest revision as of 14:57, 6 June 2018
Time | Narration |
00:01 | Welcome to the Spoken tutorial on Getting started with CellDesigner. |
00:05 | In this tutorial, we will learn about: CellDesigner , Menu and Tool bars in CellDesigner, |
00:13 | different areas in the CellDesigner workspace, |
00:17 | components of CellDesigner which includes Species and Reactions. |
00:23 | We will also learn how to: create a simple network, |
00:27 | save a network, |
00:29 | export an image, |
00:30 | how to zoom a network. |
00:33 | CellDesigner is a process diagram editor for drawing gene-regulatory and biochemical networks. |
00:40 | The process diagram was proposed by Kitano. These diagrams are stored using the Systems Biology Markup Language (SBML). |
00:50 | I am using Windows XP and CellDesigner Version 4.3. CellDesigner works on Linux and Mac OS X also. |
01:00 | To open CellDesigner, double-click on the shortcut CellDesigner icon on the desktop. |
01:07 | This will open CellDesigner. Now let's explore . |
01:12 | On the Menu bar, you can see various Menu options like- File, Edit, Component ,View, Database and others. |
01:24 | Under the Main Menu, you will see various Toolbars. |
01:30 | There are Toolbars for editing, species, reactions, compartments etc. |
01:38 | We will learn about some of them as we go along. |
01:42 | Let us learn about the different areas of the CellDesigner workspace. |
01:48 | As you can see, there are 5 areas. |
01:52 | On the right hand side, is the Draw area. |
01:55 | This is where we would be drawing the networks. |
01:58 | Any shape you see on the Draw area, for eg - rectangle, an oval or a line segment, is called a Component. |
02:08 | Component is a general term for species, reactions or a compartment. |
02:14 | One can see the list of all these symbols and their meanings from the CellDesigner website – that is www.celldesigner.org |
02:29 | I will click on the Documents. |
02:33 | Now let's click on the Startup guide. That is also on another tab. |
02:40 | I will go directly to page number 82. |
02:45 | Here you can see various symbols and their meanings. |
02:51 | Let's go back to CellDesigner window. |
02:55 | Below Draw area, is the List area. |
02:59 | Here one can display and edit the list of components and functions of a model. |
03:06 | The Notes area is used to display and edit the notes of the component. |
03:12 | On the left hand side, there is a Tree area which lists the components in a tree structure. |
03:21 | Below that, is the Layer area which displays all the layers of the model. |
03:27 | The size of the areas can be changed by dragging the borderlines. |
03:33 | I will place the cursor on the borderline . You can see a double headed arrow. Drag it to maximize or minimize the area. |
03:45 | To change the position of the List & Notes area, |
03:50 | go to View option >> click on List and select Right. |
03:56 | It changes list to the right. Down is the default one. |
04:00 | Let us go back to the slide. |
04:05 | This is the simple network which we will create. |
04:10 | In this network, Protein A undergoes state transition to Protein B , under catalysis of Protein C. |
04:21 | Protein B inturn undergoes state transition to Protein D . |
04:27 | This transition is inhibited by Protein E. |
04:32 | Let us create this network . |
04:34 | I will go back to CellDesigner window. |
04:39 | Now click on File and then New. |
04:43 | A small dialog box named as ‘New Document’ will open. |
04:48 | This is Name field. |
04:50 | I will type “simple network”. |
04:53 | Here, one can change the height and width as required. However, I will keep the default height and width. |
05:03 | Click on OK. You can see the name appearing on the top left corner of the Draw area. |
05:12 | Now go to Edit and enable Grid snap and Grid visible. |
05:21 | A grid will be visible in the Draw area. |
05:25 | Grid snap will make the components to align properly with the grid. |
05:29 | You can de-select Grid visible once the network is complete. |
05:34 | Before we begin to add components, let me show you some examples of species and reactions. |
05:42 | Let us first see the species. |
05:45 | The symbols here are for generic protein, receptor, ion, channel, truncated protein, gene, RNA etc. |
05:58 | Now let us see the reactions. First is the State transition, Heterodimer association, Dissociation, Catalysis, Inhibition etc. |
06:11 | We will select the first icon in the Species toolbar by clicking on it. This icon is for protein. |
06:22 | Click anywhere on the Draw Area where you want to place this species. |
06:28 | I will place it on left side of the Draw area. |
06:33 | A small dialog box will open and ask for the species name. |
06:39 | I will name the new species as A and click on OK. |
06:46 | See the change in the list area too. |
06:50 | As you can see, we have added a new species in the Draw area. Similarly I will add B. |
06:58 | You are required to select a component before you edit or move it. |
07:03 | Click on the component to select them. Make sure the select icon is on before you do so. |
07:12 | I want to place B besides A. So click on B and select it. |
07:17 | Drag and keep it next to A. |
07:21 | Now we will see how to change the size of a component. |
07:24 | I will click on A. We see small squares on it. |
07:29 | These are the handles to change the size. |
07:32 | I will keep the cursor on this edge and drag. |
07:36 | We see the size of A has changed. |
07:39 | There is another way of changing the size of component which we will learn in later tutorial. |
07:46 | You can “undo" the previous actions with Ctrl-Z . |
07:52 | If you want to “re-do”, press Ctrl-Y. |
07:54 | Also you can do this directly by click on the icons for undo and redo. |
08:03 | Now let’s add reactions. |
08:06 | A reaction is the interaction between two objects. |
08:09 | This is a state transition reaction. |
08:12 | So, I will click on the icon for State transition in the Reaction toolbar. |
08:18 | Click on any edge of A and then on B. |
08:23 | Thus, you can see the reaction arrow now joins A and B. |
08:30 | The component selected first is considered as the reactant. |
08:35 | So, always remember to select the reactants first. |
08:39 | The default reaction id comes as re1. |
08:43 | Now, let's add species C and keep at appropriate position as shown in the earlier slide. |
08:54 | I am selecting this icon from the Reaction toolbar. It is for Catalysis . |
09:00 | I will click on the edge of C and the square symbol of the State transition reaction. |
09:08 | Now, I will add species D and place it besides B. |
09:15 | Let's add a State transition reaction from B to D. The default reaction-id is re2. |
09:26 | I will add species E and keep at appropriate position as shown in the earlier slide. |
09:35 | Now I will select this icon from the Reaction toolbar which represents the Inhibition reaction. |
09:44 | I will click on the edge of E and this square symbol of the State transition reaction. This will join the two points. |
09:54 | We can see the simple network now. |
09:57 | Let us save our work. |
10:00 | Go to File. Click on Save as. |
10:04 | I will name it as “Simple Network” . |
10:06 | This will save our work in .xml format. Click on Save. |
10:12 | Now we will learn how to Export an image. To do this, Go to File > Export Image. |
10:22 | You can save the image in various formats like pdf, png, jpeg etc. |
10:29 | I will save it as a jpeg image. Click on Save. |
10:35 | Let us see how to zoom the network. |
10:38 | We have 4 options for zoom - Zoom In, Zoom Out, Zoom Fit, Zoom Reset . |
10:47 | I will click on the Zoom In icon twice. We can see the magnified image. |
10:54 | Now I will click on Zoom Reset. The network comes back to the original size. |
11:02 | This brings us to the end of the spoken tutorial on Getting started with CellDesigner. |
11:08 | To Summarize : we learnt about Menu and Tool bar in CellDesigner, |
11:14 | different areas in CellDesigner, components like Species and Reactions. |
11:20 | We created a simple network using the species and reaction components. |
11:26 | Also we learnt how to zoom, save a network and exporting an image. |
11:32 | As an assignment, construct a network with the help of CellDesigner 4.3 |
11:39 | In this network, A and B protein associates to form a complex(Complex1) in presence of catalyst protein C. |
11:51 | This complex gets degraded when catalyst protein D is present. |
11:58 | You should get a network like this. |
12:01 | Watch the video available at the following link. It summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
12:13 | The Spoken Tutorial Project team: conducts workshops using spoken tutorials, gives certificates for those who pass an online test. For more details, please write to contact at spoken hyphen tutorial dot org. |
12:28 | Spoken Tutorial project is a part of the Talk to a Teacher project. It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
12:41 | More information on this mission is available at spoken hyphen tutorial dot org slash NMEICT hyphen Intro. |
12:53 | This is Sakina Shaikh from IIT Bombay, signing off. Thanks for joining. Goodbye. |