Flash Interactive Mode

The interactive flash mode can be selected in the view settings. The interactive mode provides also some additional features, such as automatic Layout and clustering.

In order to use the interactive network you need to have flash player installed on your computer. If you have not already installed the player you can download it from adobe.

The interactive network appears like the normal network with a small menu that you see at the top (see figure above).

Layout Top ↑

Clicking on 'Layout->Relax->Start Relaxation' you can start an an automatic force-directed layout algorithm that orders the nodes in the network. The algorithm works iteratively trying to position the nodes apart from each other with a "preferred distance" proportional to the String global score.

'Right click on a node -> fix' in order to fix the node at the current position.

Clustering Top ↑

From the 'Clustering' menu it is possible to launch 2 different clustering algorithms (KMEANS and MCL) to cluster the proteins that you are displaying in the network.

The only input to these clustering algorithms is the distance matrix obtained from the String global scores (so interacting proteins with an higher global score have more chances to end up in the same cluster).

Besides the distance matrix, both the algorithms accept 1 parameter as input:

  • KMEANS accepts a parameter to specify the number of clusters that you want to obtain.
  • MCL accepts a parameter called "inflation" that it is also indirectly related with the precision of the clustering (higher the inflation -> more clusters you obtain).

In order to launch the clustering, just click on the algorithm you want to launch (e.g. 'MCL'). A little panel with a slide-bar will appear.

You can move the slider in order to start the clustering with the right parameter value (after having moved the slider just wait few seconds for the clustering to complete). As soon as the cluster completes, you will see the following differences in the network:

  1. The color of the nodes has changed (i.e. every color corresponds to a cluster)
  2. Inter-cluster edges are represented by dashed-lines
  3. If you activate the 'Layout -> Relaxation' you will see clusters moving far away from each other (i.e. the nodes in a cluster are kept close from each other, but far away from the nodes of every other cluster)

We suggest you to use the MCL algorithm (see review paper below). Please, note that if your network is small (i.e. it contains few nodes) the MCL algorithm will produce only a single large cluster. In that case, you could simply enlarge the network (e.g. clicking the '+' button or modifying the String parameters at the bottom of the page) and relaunch the clustering.

Options Top ↑

You can click on 'Options->Background-> Add background image' in order to add a background image of your choice to the interactive network. You have to option the remove or hide proteins in the network.

References: Top ↑