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CentiBiN
Centralities in Biological Networks

Tutorial: A typical session with CentiBiN

Content

  1. Start CentiBiN
  2. Generate a random network
  3. Load network data
  4. Network layout
  5. Prepare network for centralities
  6. Calculate network centralities
  7. Visualise network centralities

1. Start CentiBiN

CentiBiN can be started at the following web page: http://centibin.ipk-gatersleben.de/starting.php. Please choose the version according to the main memory (RAM) available in your computer. If the Java runtime environment (JRE) is not installed yet, you might need to do so first, an instruction for this is given on the same page. Per default upon startup, CentiBiN shows a small randomly generated network.

CentiBiN directly after starting

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2. Generate a random network

If you want to create a different random network, CentiBiN offers some possibilities in the menu "Generate". It is recommended that you try at first the default values, higher values might lead to time-intensive creation- and layout procedures.

CentiBiN with a random network

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3. Loading network data

As an alternative to step 2 (the creation of a random network), you can load network data from a file. For that option, CentiBiN supports the Pajek format(*.net), DIPs tab separated files (*.tab), adjacency matrices given in text files (*mat), and the GraphML file format (*.xml). For detailed explanations on the different file formats please refer to the "Help" menu.

CentiBiNs load file dialog

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4. Network layout

Now you can improve the network visualisation by using different layout algorithms. Depending on the network structure, one or the other of the five algorithms might give the best result.

CentiBiN showing a layouted network

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5. Prepare network for centralities

Depending on the centrality measure to be applied the network has to fulfil certain preconditions. These can be simplicity, connectedness and loop-freeness. Several algorithms are implemented to clean up the network, however the easiest way to prepare the network is just to apply the function "Prepare for centralities", which is performing all cleanup procedures at once. Choose the appropriate option depending on whether you have a directed or an undirected network.

CentiBiN and the preparation menu

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6. Calculate network centralities

This step is the main part of CentiBiN. You can now calculate 17 or 15 centralities for an undirected or directed graph, respectively. A table will appear on the right side showing the nodes ranked according to the chosen centrality measure, including the correspondent value.

CentiBiNs menu of available centralities

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7. Visualise network centralities

On the table on the right side, you can now mark a number of nodes. For better visibility, the marked nodes will be coloured red in the network.

CentiBiN visualising centralities

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