Start the "Simmune NetworkViewer"

Open an existing model file

Click the "File" menu and select the "Open File..." menu item. When a file dialog prompts the user to choose a model file, select the example model file and click the "Open" button.

Shortly after the network construction, the network panel on the right shows the whole network as an overview. In the tree panel, the numbers "8" and "22" enclosed in the parentheses following "Species" and "Complex" indicate that there are 8 complex species and 22 complexes in the model. The number "4" enclosed in the parentheses after the item "Receptor" indicates that 4 complexes belong to the complex species "Receptor". Similarly, the reaction rule panel shows that the model consists of "11" rules -- 3 associations, 6 dissociations, and 2 transformations.

Edge color depends on the reaction type. The default colors for complex association, complex dissociation, and complex transformation are green, orange, and purple respectively. You may set arbitrary color by configuring appearance.

An edge representing an association or a dissociation points to the mediating binding site on the complex species node. An edge representing a transformation points to the middle of the complex species node since transformations do not involve particular binding sites (except for transformations that induce intra-complex bond formations or dissociations).

Zoom in/out and panning with mouse

In the network panel, scroll mouse up/down to zoom in/out. You may also click the icon on the toolbar, for zoom in and for zoom out. Drag mouse to pan the network in any direction.

To display the whole network in the network panel, click the "View" menu and select the "Fit to screen" menu item or simply click the icon on the toolbar.

Show the network legend

Click the "View" menu and check the "Show legend" menu item to display the legend of the icons used in the network panel. Uncheck it to hide the legend. Another way to show/hide the legend is by checking/unchecking the item "Show legend" in the context menu of the network panel.

Here, three complex species are shown: "Ligand", "Receptor", and "Ligated Receptor". There are two reactions, one association and one dissociation, that involve the three complex species.

Select a complex species

Click the complex species node "Receptor" to select the complex species "Receptor". Edges are highlighted to show that 5 reaction rules, 1 association and 4 dissociations, involve complex species "Receptor".

You may also select a complex species by clicking the item "Receptor" in the tree panel.

Move nodes to adjust layout

Drag the complex species node "Receptor" in the network panel to adjust the layout. You can move all nodes, both complex species and intermediate nodes, in the network.

Select a rule

Select the rule "receptor liagation" by clicking the item "receptor liagation" in the rule panel. Expand the list of association rules by clicking the button in front of "Association" if necessary. Edges are highlighted to show which complexes as well as complex species participate in the reaction rule "receptor liagation". You may also select the rule by clicking the corresponding intermediate node or edges.

The complex species node changes to display the involved complex after changing its molecule component state(s) and binding site status. For example, the complex "Rec inactive" has an "off" component state, and a status of "don't care" and "unbound" for the first and second binding site. The second line of the text label shows the name of the complex in blue (e.g. the complex "Rec inactive" of the complex species "Receptor").

Show reaction rate of a rule

Hover over the intermediate node "receptor liagation" or one of its incident edges to show the rate through a tooltip "1e+07 liter/(mol*s)".

Select a complex

Click the item "Rec inactive" under the list of complex species "Receptor" in the tree panel. Expand the list first by clicking the button in front of "Receptor" if necessary. Edges are highlighted to show which reaction rules involve the complex "Rec inactive". In this example, two reaction rules, namely "receptor ligation" and "Ligand dissociation", involve the complex "Rec inactive".

Filter the complex species and complexes by name

Expand the filter panel. Select the radio button "By name". Put in the text field "receptor" and click the "Apply" button. The complex species and complexes that contain "receptor" in their names are marked in yellow in tree panel.

Put in the text field "gdp" and click the "Apply" button. The complex species "LigRec_Gabg" is marked in blue in the tree panel, indicating that the complex species "LigRec_Gabg" does not match the filter term "gdp" but at least one of its child complexes matches the filter term. If necessary, expand the complex list by clicking the button in front of the item "LigRec_Gabg" to find the complex "LigRec_Gabg_GDP" marked in yellow.

Click the "Clear" button to clear filtering.

Filter the complex species and complexes with regard to the constituting molecule

Select the radio button "By molecule". Select the molecule "Ligand" from the list and click the "Apply" button. All the complex species and complexes that contain the molecule "Ligand" are marked in yellow. Click the "Clear" button to clear filtering.

Find matching complexes with a set of complex-specific attributes

Complex-specific attributes are the molecule component state(s) and binding site status. You may specify a set of attributes and find matching complexes within the same complex species.

Right-click the complex species node "Receptor" and select "Find complexes of 'Receptor'" in the context menu. Starting from a set of molecule component state(s)/binding site status where all states are set to "don't care", click the icons of molecule component states/binding site status to change their states.

Change the molecule component state of "Receptor" from "don't care" to "off" to see that the complexes, "Rec inactive", "Receptor_2", and "Rec inactive unbound" match the set of states and are highlighted in tree view. The edges are highlighted to show which reaction rules involve the matching complexes.