Current biological research generates vast amounts of data; however, extracting value from this information requires advanced computing tools. BCBB develops custom bioinformatics software applications and analytical pipelines to meet this need and supports biomedical discovery by making these tools publicly available.
Areas of Expertise
Software Development
BCBB provides scientific software development in bioinformatics and computational biology, including the design of custom applications, analytical pipelines, novel algorithms for data analysis and data integration, high throughput processing, research workflow automation, and more.
Database Development
We develop scientific databases to support research analysis and data integration. Our working knowledge of biological databases, including those offered from the National Center for Biotechnology Information (NCBI), Universal Protein Resource (UniProt), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO), can help extend the scope of your dataset.
Custom Scripting
BCBB develops custom scripts and tools for data extraction, processing, pipeline development, and workflow automation. Existing scripts can be transformed into robust, publicly available, web applications that are easily maintained. These tools support tasks such as extracting and processing data from spreadsheets, querying and retrieving data, and reformatting datasets.
Products
Through these services, BCBB has developed a range of software applications that advance biomedical discovery for NIAID researchers, collaborators, and the public.
Nephele
Nephele is a microbiome analysis engine that integrates microbiome data and analysis tools within a cloud computing environment. Researchers across life and clinical science disciplines are exploring the impact of microbes and microbial community dynamics but may lack the resources or expertise to analyze complex, multidimensional metagenomic datasets. We developed Nephele with a user-friendly web interface with powerful pipelines that streamline data uploads and provide analysis and visualization of these datasets.
NIH 3D
NIH 3D is an open, community-driven portal for bioscientific and medical 3D models. Existing online resources for 3D printing often lack scientifically validated models and the expertise required to generate them. We designed NIH 3D to fill this gap by providing novel, web-based tools to empower users to create, share, and validate bioscientific and medical 3D models.
Papillomavirus Episteme (PaVE)
Papillomavirus Episteme (PaVE) is a web application to search, analyze, and explore highly organized and curated papillomavirus genomes. We developed this relational database to provide researchers with an integrated resource to analyze papillomavirus genome sequences.
Pathogens in Augmented Reality (PathogenAR)
Research has demonstrated the potential of augmented reality (AR) to dramatically change biomedical research, education, and clinical practice. That’s why we developed Pathogens in Augmented Reality (PathogenAR), an AR app that allows users to explore interactive stories about pathogens and pathogenic diseases. PathogenAR uses image-tracking-based interactivity to share structural and functional features of biomolecules and viruses.
Simple Insight Toolkit (SimpleITK)
The Simple Insight Toolkit (SimpleITK) platform allows researchers to load, process, and analyze images using the programming language they are most familiar with, including C++, Python, R, and more. This provides researchers with more accurate and precise image analysis without requiring complex workflow development.
Tuberculosis Portals (TB Portals)
Tuberculosis Portals (TB Portals) is an open, web-based platform to view and analyze clinical, bacterial genomic, and medical imaging data from TB patient cases. TB, particularly drug-resistant TB, remains a global health challenge, but data sources have historically been siloed and lacked patient case information. We developed TB Portals to harmonize data from international collaborators and make them openly available to support research and discovery.
Technologies
- Python
- Javascript/Typescript
- Postgres
Publications
Clinical exome sequencing of 1000 families with complex immune phenotypes: Toward comprehensive genomic evaluations. J Allergy Clin Immunol. 2022 Oct;150(4):947-954. doi: 10.1016/j.jaci.2022.06.009. Epub 2022 Jun 24.
Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat Cell Biol. 2021 Nov;23(11):1117-1128. doi: 10.1038/s41556-021-00788-6. Epub 2021 Nov 8. https://doi.org/10.1101/2021.09.24.21263853
Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics. 2018 Apr 15;34(8):1411-1413. doi: 10.1093/bioinformatics/btx617.
The Papillomavirus Episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res. 2017 Jan 4;45(D1):D499-D506. doi: 10.1093/nar/gkw879. Epub 2016 Oct 5.
Our Team
Read about our development team, their individual backgrounds, and projects they work on.