Biograph

Introduction

The biograph tool can be found in the biograph directory of Biorithm. biograph performs topological analysis of undirected interaction networks. For example, to compute the node betweenness centrality of all nodes in a network, issue the following command:

 biograph -n <network-file> --node-betweenness

Alternately, to compute the subgraphs induced by different subsets of nodes, issue the following command:

 biograph -n <network-file> -S <node-sets-file> --i

A full description of all Command Line Options for biograph are available below.

Installing Biograph

Download the Biorithm package and follow the installation instructions for Biorithm. The executable files will be available as biograph/biograph

Command Line Options

The following options are available for biograph:

	Flag	Long	Description
REQUIRED INPUTS	n	network	Name of file containing the network.
GENERAL OPTIONS	-	summary	Turn on all of the following options: --all-pairs-shortest-paths, --betweenness, --components, --degree-distribution
	-	summary-with-sets	Turn on all of the following options: --summary, --comps-after-removing, --induced-subgraph. Notice this is the same as summary but also includes several options dependent upon the --node-sets option.
	a	all-pairs-shortest-paths	Print the lengths of the shortest paths between all pairs of nodes; the file will also contain the number of such paths.
	b	betweenness	Compute the betweenness centrality every node AND edge in the network. This is and alias for using --node-betweenness and --edge-betweeenness.
	-	node-betweenness	Compute the betweenness centrality of each node in the network.
	-	edge-betweenness	Compute the betweenness centrality of each edge in the network.
	c	components	Compute the connected components of the network.
	-	comps-after-removing	For each set of nodes given by the --node-sets option, remove those nodes from the network and compute connected components.
	d	degree-distribution	Compute the degree distribution of the network.
	i	induced-subgraph	Compute the subgraph induced by each node set given by the --node-sets option.
	k	kcore	Compute the largest k-core of the network.
	s	separator	Compute the collection of nodes that separate each set of nodes given by the --node-sets option from the rest of the network.
	-	mcode	Run MCODE on the network.
	-	mcode-node-weight-fraction	A parameter f that controls how new nodes are added to a cluster: a new node's weight must be at least as large as (1 - f) times the weight of the seed node.
	W	node-weights	Name of file containing node weights. Each line has contains two columns: node identifier, node weight. Any node in the network that is not mentioned in this file gets a weight of 0.
	S	node-sets	Name of file containing node sets. Each line represents a node set and has at least two tab-delimited items; the first item is the identifier for the node set and the following items are the nodes in that set.