HSLS Update

PathwayAssist Interaction Explorer Software

 HSLS is pleased to announce the availability of PathwayAssist - a software tool for visualization and exploration of biological pathways, gene regulation networks, and protein-protein interactions.

Researchers in the signal transduction field, and those wanting to analyze gene expression data from microarray and SAGE experiments will find this software useful.

How Pathway Assist Works

PathwayAssist contains an automated natural language processing-based information extraction system called MedScan, and a database of protein interactions and cellular pathways known as ResNet (Research Network). MedScan is a text mining tool that can extract biological interactions by reading digital text documents (e.g. biomedical journal articles and abstracts). It efficiently scans sentences, searching for co-occurrences of biological terms to locate connecting verbs - such as binds, inhibits, modulates or phosphorylates - between the co-occurring terms. ResNet is a repository of over 500,000 biological interactions for more than 50,000 proteins (human, mouse, rat, yeast, drosophila, and C. eligans) extracted from the current literature.

By combining MedScan’s powerful search algorithm with the ResNet repository of biological interactions, PathwayAssist can:

•  identify biological interactions among genes of interest from the published literature, and provide links to the supporting sentences in the matching journal article citations (for articles available online through PubMed);
•  connect two molecules with the shortest possible path;
•  import a list of genes and arrange them  into a pathway;
•  import affymatrix gene expression results and display as a heat map, as well as a pathway map;
•  find common upstream and downstream regulators of a gene;
•  display array results according to subcellular localization.

PathwayAssist is a PC compatible software package that requires the Windows 2000 or XP operating system, and a recommended system configuration of 2.0 GH CPU, 512 RAM and 2 GB of disk space.

HSLS currently provides five concurrent user licenses for Pathway Assist.  For download information, please contact Ansuman Chattopadhyay (412-648-1297, ansuman@pitt.edu) or  Yi-Bu Chen  (412-383-6887, ybchen@cbmi.pitt.edu)

--Ansuman Chattopadhyay