Resources for Researchers
The Bioinformatics and Computational Biosciences Branch (BCBB) offers a suite of scientific services and resources for the NIAID research community and its collaborators. BCBB provides expertise and computational solutions to researchers at all levels of experience.
The NIAID-funded Bioinformatics Resource Centers provide data-driven, production-level, sustainable computational platforms to enable sharing and access to data, portable computational tools, and standards that support interoperability for the infectious diseases research community.
FLUTE is a Functional Genomics Center funded by NIAID, with the goal of discovering the roles of genes from Mtb with previously unknown functions. In addition FLUTE aims to establish an efficient pathway for identifying gene function that could serve as a paradigm for other bacterial species.
GUNK center is part of the NIAID Functional Genomics Program. This center was created to investigate the role of previously uncharacterized genes of A. baumannii in its ability to cause human disease. Three projects have been established to:
The GCID use and develop or improve innovative applications of genomic technologies, such as RNA sequencing and metagenomics, and provide rapid and cost-efficient production of high-quality genome sequences of microorganisms, invertebrate vectors of infectious diseases, and hosts and host microbiomes. Multiple strains and isolates of specific microbial species, populations and communities have been and continue to be sequenced.
Heterogeneity in Human Immune Cells is a website providing interactive figures (iFigs) for a recent study of protein expression heterogeneity in human immune cells conducted by Dr.
The Immcantation framework is developed as a start-to-finish analytical ecosystem for large-scale characterization of B cell receptor (BCR) and T cell receptor (TCR) repertoires from high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) datasets.
A common data model for sharing observational HIV data has been developed by the International epidemiology Databases to Evaluate AIDS (IeDEA). The IeDEA DES is used by the seven operational regions of IeDEA to exchange data with each other for collaborative research studies.
Nephele is a microbiome analysis engine which brings together microbiome data and analysis tools in a cloud computing environment. It offers robust, multi-step microbiome analysis pipelines, with no setup time or cost.
NIAID’s microbiome sequencing facility studies the structure and function of the microbiome associated with various hosts and body sites. This facility has one dedicated team and is equipped with an Ilumina MiSeq, which can sequence whole genomes or specific amplicons.
The NIH 3D Print Exchange provides models in formats that are readily compatible with 3D printers, and offers a unique set of tools to create and share 3D-printable models related to biomedical science.
The PapillomaVirus Episteme (PaVE) provides highly organized and curated papillomavirus genomics information and tools to the scientific community for research on the Papillomaviridae family of viruses. The PaVE consists of a database and web applications that support the storage, annotation, analysis, and exchange of information. To the extent possible, the PaVE adopts an open source software approach and emphasizes integration and reuse of existing tools.
PathogenAR is an Augmented Reality application from the National Institute for Allergy and Infectious Diseases (NIAID). Explore interactive stories about pathogens and pathogenic disease using touch gestures or a Merge Cube Device.
This Gene Set Enrichment-type test designed for analysis of microarray and RNASeq data is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. QuSAGE extends previous methods with a complete probability density function (PDF).
SimpleITK is a simplified programming interface to the algorithms and data structures of the Insight Toolkit (ITK). It supports interfaces for multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby and TCL.
SPICE is a data-mining software application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically. SPICE enables users to discover potential correlations in their experimental data within complex data sets.
The Systems Biology Consortium for Infectious Diseases is a community of systems biologists who integrate experimental biology, computational tools and modeling across temporal and spatial scales to improve our understanding of infectious disease
TBRNAT presents all known M. tuberculosis transcriptional factors that regulate the expression of a gene of interest as an interactive regulatory network along with additional data in tabular form.