CellDesigner/C2/Getting-Started-with-CellDesigner/English-timed

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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.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya, Sandhya.np14