ITM Probe - Information Flow in Interaction Networks

ITM Probe is a web application for modelling information flow in interaction networks based on discrete time random walks.


Each random walk simulates a possible information path. A walker starts at a node in the network and at each discrete time step moves randomly to a node that is adjacent to its originating node. The probability of moving to a particular destination node is proportional to the weight of the link from the originating node to it. Unlike the classical random walks, our framework allows the walker a certain probability to dissipate, that is, to leave the network at each step. Each walk terminates either by dissipation or by reaching a boundary node.


We distinguish two types of boundary nodes: sources and sinks. Each source serves as origin of random walks and hence emits information, while each sink absorbs information. ITM Probe framework contains three general modes: absorbing, emitting, and channel.


Please refer to ITM Probe documentation or the references below for more information.



Web application: ITM Probe: Models

Standalone script (Python package qmbpmn-tools): FTP

Cytoscape plugin: FTP

Documentation: HTML, PDF

Publications:
1. Stojmirović A, Yu YK (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics, 25: 25.
PMID: 19561335

2. Stojmirovic A, Yu YK (2010) Information flow in interaction networks II: channels, path lengths and potentials. ArXiv, v2: q-bioMN.
arXiv: 0901.0287

3. Stojmirović A, Yu YK (2007) Information flow in interaction networks. J Comput Biol, 14: 14.
PMID: 17985991