The RNA-Rocket RNA-Seq pipeline is temporarily unavailable while we negotiate with our cluster. Align your Illumina fastQ reads against supported genomes, view supported genomes, and estimate gene expression values using an RNA-Seq Pipeline running on Galaxy.
Host Response Data View Host Response proteomics and transcriptomics data collected and curated from multiple sources.
Pathogen Interaction Gateway Generate a network graph of Protein-Protein Interactions, including Host-Pathogen Interactions, from your custom selection of hosts/vectors, bacteria, viruses, and eukaryotic pathogens.
News & Announcements from the BRCs
PATRIC July 2014 Release Features New Circular Genome Viewer, Group Explorer, Integration of Protein-Protein Interaction Data, and New Genomic and Transcriptomic Data
11 Jul 2014-PATRIC
Over 6,000 new genomes, including over 1,500 Mycobacterium tuberculosis genomes from TB-ARC.
2 Jun 2014-IRDNext IRD Release
2 Jun 2014-ViPRMay 2014 ViPR Newsletter
1 May 2014-VectorBaseRelease VB-2014-04
7 Apr 2014-EuPathDB2014 Annual EuPathDB Workshop - June 15-18, 2014
12 Dec 2013-Pathogen PortalHost Response Data Updated
About the Pathogen PortalPathogen Portal's Infectious Disease Triangle perspective supports an integrative understanding of human disease through the study of multiple levels of interactions between a susceptible Host, an infectious Pathogen, and a conducive (to disease) Environment. Originating from plant pathology, this ecological approach is increasingly relevant to health sciences. Because some diseases include invertebrate Vectors as part of their ecology, the Disease Triangle broadly considers Environment to include Vectors.
The Pathogen Portal supports and links to five Bioinformatics Resource Centers (BRCs). Each BRC specializes in a different group of pathogens, focusing on, but not limited to, pathogens causing (Re-)Emerging Infectious Diseases, and those in the NIAID Category A-C Priority Pathogen lists for biodefense research. The scope of the BRCs also includes Invertebrate Vectors of Human Disease.
In addition to supporting, and serving as an entryway to, the BRCs, the Pathogen Portal's scientific focus is integrating host-response data that span the pathogens and vectors supported by the BRCs, thereby moving towards an integrative view of Host-Pathogen-Environment interactions, also known as the Disease Triangle. Originating from plant pathology, the concept of the Disease Triangle provides an ecological view of disease which is increasingly relevant to the Health Sciences. According to this view, disease arises when three criteria are met: an infectious Pathogen; a susceptible Host, and a conducive (to disease) Environment. Because some diseases include invertebrate Vectors as part of their ecology, the Disease Triangle broadly considers Vectors to be a component of the Environment.
The Pathogen Portal is developed and maintained by the CyberInfrastructure Division at the Virginia Bioinformatics Institute at Virginia Tech. New data and analysis tools are added regularly.
New data and analysis tools are added regularly to Pathogen Portal.