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Molecular Interaction Network (MINet) Viewer Frequently Asked Questions (FAQ)
- What is the MINet Viewer?
- How many views does the model currently have and how are they different?
- The view opens up empty, with nothing displayed in it. Is something wrong?
- How do I start using the viewer?
- What do the colors of the nodes in the viewer indicate?
- Is a "Zoom" functionality available?
- How do I know if I selected something in the viewer?
- How can I see the contents of a particular sub-pathway?
- How can I remove the contents of an exploded sub-pathway from the view?
- What do the arrows in the interactions indicate?
- Can I move the bio-objects around in the view?
- I am not very pleased with the placement of nodes in the Free Form Viewer. Can I do something to improve it?
- Can I get rid of the information display area at the bottom of the view?
- Sometimes when I click on a object in the view a picture pops-up in another window. What is it?
- How can I recognize hotspots in a picture and what is their use?
- How can I drag-and-drop from or into the viewer?
- How does the free-form viewer manage to have minimal crossings of the interactions?
- The arrows in the free from are drawn so well. How did you do it?
What is the MINet Viewer?
MINet Viewer (formerly ProNet Viewer) shows interactions between various bio-objects (protein, gene, plasmid, toxin, etc...) in pathways as a graph with nodes (representing bio-objects and sub-pathways) and directed links (representing the interactions).
How many views does the model currently have and how are they different?
Currently, the model has three views, Flow View, Free Form View and Linear View. All the views show the same data, but in different styles. The flow view shows nodes and links in the form of a flow chart, the free form view shows nodes and links with free placement of nodes anywhere in the 2D space of the view. The linear view has a more restricted placement, with all the nodes placed one below the other vertically.
The view opens up empty, with nothing displayed in it. Is something wrong?
No, once the view opens up, go to "Pathways" menu and then click on the Pathway you are interested in visualizing. All the sub-pathways, bio-objects, and interactions belonging to the selected pathway then appear in the view.
How do I start using the viewer?
Go to "Pathways" menu and then click on the Pathway that you are interested in visualizing. The pathway name in the menu is now checked, indicating that it's contents are being displayed in the viewer. All the bio-objects and interactions belonging to the selected pathway appear in the view. Clicking on any interaction or bio-object highlights it and displays detailed information about it in the text area at the bottom.
What do the colors of the nodes in the viewer indicate?
The background color of the nodes indicate whether it is a pathway or a bio-object. In case of a bio-object the label indicates the function of the bio-object in the interaction. The outer border color indicates the location of the bio-object in the pathogen molecule. The color index for locations and functions of bio-objects can be seen from the Colors menu in the MenuBar. The default colors can be changed by clicking on the color button in the color index and choosing the desired new color for that particular function or location.
Is a "Zoom" functionality available?
A slider present at the bottom of the viewer provides the "Zoom" functionality. Presently the "Zoom" functionality is available in two of the three viewers, that is, Flow and Free Form while the functionality is not available in Linear viewer.
How do I know if I select or highlight something in the viewer?
A simple click on the object highlights the object and a default magenta colored border appears around the object. A click in the SELECT mode (you can switch to this mode using the popup menu) on the object selects an object and a default red colored border appears around the object.
An outer outer border appears when the user selects a bio-object or clicks on it. The color of the outer outer border indicates whether it is being selected or just clicked (specified by the color index provided at the left hand side of the viewer).
How can I see the contents of a particular sub-pathway?
Sub-pathways of a pathway appear in dark yellow color while viewing the pathway. Clicking on any sub-pathway explodes it's contents in the viewer along with the original contents. The sub-pathway name in the "Pathways" menubar will appeared as checked indicating that it's contents are being displayed.
How can I remove the contents of an exploded sub-pathway from the view?
Go to "Pathways" menu, then click on the sub-pathway whose contents you want to remove from the view. The contents will disappear from the view and also the pathway name will appear un-checked in the "Pathway" menu.
What do the arrows in the interactions indicate?
The arrows indicate whether the bio-object is participating in the interaction as an input object or as as an output object. For input objects have the arrow originates from the object and is pointed away from the object. While, for output objects, the arrow terminates at the object and is pointed towards the object.
Can I move the bio-objects around in the view?
Yes. You can click on the bio-object you want to move and then drag it to the desired location. In the linear view, you can move the objects only vertically. While, in the free form view you can move the objects anywhere in the viewer window. You can even move the nodes of interactions (the black square dots where all links to a particular interaction meet).
I am not very pleased with the placement of node in the Free Form Viewer Can I do something to improve it?
The placement of the bio-objects in the free form view is done using an algorithm called Jiggle (we are very grateful to Dr. Daniel Tunkelang who let us use his code). The algorithm places nodes so that there is minimal crossings of the interactions. However, if there are still more crossovers in the placement, you can either choose to remove them by manually dragging the nodes around, or you can click on the Pathways tab and choose the pathway again which will automatically run Jiggle once more. This may result in a better placement of nodes.
Can I get rid of the information display area at the bottom of the view?
Yes, you can choose to minimize or bring back to view the information display area (as well as the graph area) at any time, simply by clicking on the arrows on the line separating the display and the information areas.
Sometimes when I click on a object in the view a picture pops-up in another window. What is it?
The picture is a biological representation of the data being visualized. The picture could contain hotspots that map portions of the pictures to the corresponding objects in the viewer.
How can I recognize hotspots in a picture and what is their use?
Move the mouse over the picture and if the mouse pointer turns to the shape of a hand, that region is a hotspot. Click on the hotspot to see the corresponding object highlighted in the view. Hotspots allow you to relate the biological picture to the graphical information displayed in the view.
How can I drag or drop from or into the viewer?
To drag or drop any object from the viewer, switch to the SELECT mode using the popup menu, and drag the object to the place you want to drop the object. Dragging simply drags the name of the bio-object or pathway and not the entire object. Dropping into the pronet viewer is currently unavailable
How does the free-form viewer manage to have minimal crossings of the interactions?
The placement of the bio-objects in the free form view is done using an algorithm called Jiggle. We are very grateful to Dr. Daniel Tunkelang who let us use his code.
The arrows in the free from are drawn so well. How did you do it?
We used an arrow drawing algorithm by Dr. F. P. Coenen. We thank him for letting us use his code.