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| − | | Welcome to the Spoken tutorial on Getting started with '''CellDesigner'''. | + | | Welcome to the Spoken tutorial on ''' Getting started with '''CellDesigner'''. |
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Revision as of 12:05, 5 October 2017
| 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 4.2 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 lets 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 lets 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 | Lets 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 4.2 |
| 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. |
