The ALMAInteraction applet will take some seconds to be loaded. Once loaded, the applet will read the files with the information about the proteins, the interaction among them and the structure of the graph. These files have a size of about 450Kb. The time spent in the reading will depend on the speed of your connection. After been loaded, the main window of the ALMAInteraction applet will popup.
The ALMAInteraction applet window is divided in three parts or panels: the main panel, on the top, in which the graph will be painted, the panel in the middle with the controls to display the graph, and the bottom panel in which the information about the proteins and interactions will be shown.
Additionally, ALMAInteraction has a menu that allows to search Entities and highlight them in the graph.
In this panel you can find several controls that affect to the drawing of the graph
- Relations score: in this section you control the interactions displayed in the graph, according to their score (a measure of their relevance based on the number of times that the interaction has been found in the literature). You can specify the score of relations with the slider or by typing it directly in the adjacent text box. Once the new score has been specified, press the button to apply the changes. Thus, just the interactions with a score greater or equal than the selected value will be shown.
- show label of relations: if you check this checkbox, all the edges will be labelled with the verb that defines the main interaction between the two entities, and its related score (e.g. Activate (45) ).
- collapse nodes: if the graph represents a great number of interactions, it could be very difficult to see anything among all the nodes and edges. By checking this option you can reduce the representation of the nodes drawing them as a black dot instead of the white box with the name inside.
- Start/stop button (relaxation of the graph): initially, the deployment of the nodes is done randomly. Instead of moving manually all the nodes, you can press the button to start an automatic process to adjust the position of the nodes. You can stop the process by pressing the button again.
The graph panel
The graph will be painted in this panel. The nodes represents proteins, and other biological entities as dna, rna, atp, etc. An edge between two nodes represents an interaction between the two biological entities. This edges vary in width depending on how many times that this interaction has been found in the literature.
If you doubleclick in a node or edge, the information available about the protein, or the interaction, will be shown in the information (bottom) panel.
You can move and change the position of the nodes by dragging them over the panel.
In this panel you can also customise the representation of the graph. If you press down the right button of the mouse over a node or interaction, a popup menu will appear with the following options:
Popup menu of a protein
- fix/free position: fixes the position of the selected node in the panel, so it will not be affected by the automatic process of relaxation of the graph. If the position of the node has been set to the center before, this option will free it back.
- center/decenter: fixes the position of the selected node in the center of the panel, so it will not be affected by the automatic process of relaxation of the graph. If the position of the node has been fixed before, this option will free it back.
- remove node: removes this node and the interactions related to it from the graph.
- change name: changes the name shown in the node.
- remove not connected nodes: remove all the nodes not connected with the selected node.
- fuse with: this option allows to fuse two nodes in one, conserving all the interactions of the two entities. After selecting this option, the cursor will change into a crosshair and you must select the second node. The resulting entity will have the name of the entity selected in first place.
- show near nodes: this option allows to show just the interactions in which an entity is involved that have been hidden because of their low score. Thus, you can inspect in detail a section of the graph in which you are specially interested. After selecting the option expand you will be prompted for the maximum score of the interactions to display on the selected node. The option restart leaves the graph just as it was before the expansion.
Popup menu of an interaction
- delete relation: removes this edge from the graph.
- reduce score: reduces the score of the interaction.
- check: checks an interaction, changing its color.
- change color: changes the color of the edge.
- color subgraph: changes the color of all the edges of the subgraph in which is included the selected interaction.
If you press the right button of the mouse over the panel (not over any node or relation) you will have the option to show all the interactions that are hidden due to its low score.
The information panel
The bottom panel shows the information available about the interactions and the biological entities. This panels has two tabs to select the information that you want to display. This information include:
Information about proteins (biological entities)
- Synonyms: synonyms of this entities founded in the literature. The associated numbers measures the likelihood that this word is a synonym of the entity.
- Dictionary entries: selection of sentences that give an insight of the function of the entity.
Information about relations (interactions)
- Name of the entities involved in the interaction.
- Types of interactions detected: shows all the types of interactions between this two entities detected in the literature, with its associated score.
- Medline entries: Selected sentences obtained from Medline that illustrates the interaction.