What Services Are Provided?
The Bioinformatics Resource Centers (BRCs) for Infectious Diseases program was initiated in 2004 with the main objective of collecting, archiving, updating, and integrating a variety of research data and providing such information through user friendly interfaces and computational analysis tools to be made freely available to the scientific community. The BRC program consists of four centers, each specializing in a different group of pathogens. Pathogens examined by the BRCs include, but are not limited to, those in the NIAID list of emerging and re-emerging infectious diseases, which includes NIAID Category A-C priority pathogens. The four BRCs specialize in the following groups of pathogens:
- All bacterial species
- All viral families including influenza virus
- All eukaryotic pathogen species including fungi
- Invertebrate vectors of human pathogens
Each center
- Stores, updates, integrates, and displays the following types of data and associated metadata: genome sequence and annotation, functional genomics, proteomics, metagenomics, other, “-omics,” epidemiology, surveillance, population genetics, genotype/phenotype association, antimicrobial resistance, antigenic expression, host-pathogen interactions, host response, basic and clinical
- Makes available analytical resources, bioinformatics tools, workspaces and services for data analysis
- Offers bioinformatics training at the BRC sites, scientific conferences, or at the requesting institution or laboratory
- Collaborates with and supports data generated by the scientific community including NIAID-funded programs including the Centers of Excellence for Influenza Research and Surveillance (CEIRS), International Centers of Excellence for Malaria Research (ICEMR), Functional Genomics Program, Genomic Centers for Infectious Diseases, and Systems Biology for Infectious Diseases Research.
- Responds rapidly to new and emerging pandemic threats
Where Are Services Provided?
The four Bioinformatics Resource Centers provide data, tools, and services related to the above-mentioned groups of pathogens, which can be accessed through publicly available sites including
Access
Data, bioinformatics tools, and services provided by the BRCs are freely and publicly available to the scientific community through user-friendly Web interfaces. The BRCs provide documents, online tutorials, and user support and training to facilitate the navigation of the website, submission of data and metadata, and utilization of the data analysis tools.
Bioinformatics training opportunities are available to the scientific community at no cost upon request to the BRCs.
Data Release
Information and Related Resources
- News and Announcements
- Publications
- Related NIAID-Supported Services
Responding to the Ebola Outbreak
The NIAID-funded ViPR Bioinformatics Resource Center launched a new Ebolavirus portal to provide quick access to bioinformatics tools and workbench for analysis of Ebolavirus data. New Ebolavirus sequences and additional associated metadata, including clinical phenotype data, will be retrieved, curated and released on a daily basis through ViPR. The ViPR Scientific Team conducted a genome sequence variation analysis using data available in ViPR from the 2014 outbreak to determine the sequence diversity and evolution of the Ebolavirus. For more information, please visit the Scientific Reportpdf.
Support for FungiDB
EuPathDB has received funding through the NIAID Bioinformatics Resource Centers program to expand informatics support for Ascomycota, Basidiomycota, Zygomycota, and Chytrid fungal species. FungiDB, which uses the same infrastructure and user interface as EuPathDB, contains sequence and annotation for over 70 species including many human pathogens from the Coccidiodes and Cryptococcus genera. The range of organisms available through FungiDB are informative to many NIAID-supported researchers based on their phylogenetic position and/or experimental utility as model organisms, with extensive genomic and phenotyping data providing insight into pathogenic species.
There is more information at FungiDB.
Responding to Zika Virus Spread
The NIAID-funded ViPR Bioinformatics Resource Center launched a new Zika virus portal to provide quick access to bioinformatics tools and workbench for analysis of Zika virus data. New Zika sequences and additional associated metadata is retrieved, curated, and released on a weekly basis through ViPR. Immune epitope, gene, protein, and protein structure for information Zika virus is available through the ViPR website. The ViPR Scientific Team has coordinated with the JCVI sequencing center and international collaborators to gather and curate 90 complete Zika virus genome sequence from 22 countries.
The NIAID-funded VectorBase Bioinformatics Resource Center launched a new Zika virus portal to provide quick access to bioinformatics tools and data resources for analysis of Aedes aegypti and Aedes albopictus – the arthropod vectors for Zika virus transmission. Genome assemblies, mitochondrial genomes, and predicted gene sets are available for both species of mosquito along with tools aimed at the study of arthropod vectors.
NIAID Bioinformatics Resources on the Front Line of Research Combatting Antimicrobial Resistance (AMR)
To gain new insights into the acquisition, transmission, and mechanisms of antimicrobial resistance (AMR) researchers require advanced data analysis services and visualization tools. PATRIC, the NIAID-funded Bioinformatics Resource Center for bacterial pathogens has focused on the emerging needs to couple analysis and visualization tools with the analysis of AMR-related and other system-level omics data in a user-friendly manner to facilitate rapid characterization of clinical genomes and metagenomes.
PATRIC has focused AMR curation efforts to provide users with the ability to rapidly recognize and project unknown ARM genome features to new genomes in an automated fashion, and to use comparative genomics approaches for the discovery of new resistance mechanisms. All new AMR-related functions entered in the databases will be annotated with those functions in newly analyzed genomes, and annotations to genomes similar to PATRIC references will automatically include AMR annotations from the reference genome. These tools will enable the quick recognition of AMR-related functions in genomes analyzed through PATRIC and the use of comparative genomics approaches for the discovery of new mechanisms of resistance.
Most recently PATRIC has developed a machine learning based computational tool to predict AMR-related genomic features and phenotypes in Acinetobacter, Mycobacterium, Staphylococcus and Streptococcus. This work was published in Nature Scientific Reports in June 2016. This technique is the first step in moving beyond culture-based AMR detection techniques and may enable swifter clinical response and accelerate the identification and discovery of antibiotic resistance mechanisms. PATRIC Antibiotic Resistance Search
Antiviral Resistance Data and Analysis in ViPR and IRDThe Bioinformatics Resource Centers for Viruses and Influenza, ViPR and IRD, are developing a comprehensive infrastructure for antiviral drug data management and analysis. Antiviral drug data, including descriptive drug information, 3D structures for drug/protein target complexes, specific drug interaction sites, and antiviral resistance mutations, have been curated, integrated, and made accessible on the ViPR and IRD websites. Utilizing their Phenotypic Variant Type computational pipeline, ViPR/IRD has developed a novel sequence-based prediction tool for antiviral drug resistance. This tool annotates user-provided sequences with curated antiviral drug data to enable users to predict whether a viral strain is potentially sensitive or resistant to an antiviral drug. This prediction tool is available for Hepatitis C Virus, Picornaviridae, and Herpeseviridae. External link to the tool can be found here.