Passive Samplers

The Anderson research team invented the use of passive sampling wristbands as the first low-cost approach to measure external exposure to PAHs for people near a Superfund site. The low cost and ease of use lead to high rates of participant compliance and thereby increase substantially the value of the data. The methods will she has developed are helping site managers to assess the relative contributions of Superfund sites and other sources to people’s external exposures and to identify nearby locations where people experience the highest external exposures to PAHs and may therefore experience the greatest risk.

 

Disaster IRB

The Oregon State University Superfund Research Program developed a rapid, disaster IRB in 2017. The IRB has been used to respond to Hurricane Harvey and Hurricane Florence, and has been widely shared with collaborators. Our materials are listed here for reference.

 

Zebrafish Model

Research Translation Tools

Our research translation team has developed several resources and tools that are publically available. Click on the links below to access them.

 

Educational Materials

K-12 Educational Resources

  • Mercury, My Community and Me
  • K-12 Educational Resources

 

Bioinformatics Resource Manager

The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of microRNA (miRNA) target databases upon which to query target genes or to perform reverse target lookups using gene identifiers.  BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics’ data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly at https://cbb.pnnl.gov/brm/

 

Automatic Tool for Local Assembly Structures

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive pipeline that is massively parallel, scalable, and modular analysis pipeline for assembly, annotation, quantification and genome binning of Next-Generation Sequencing (NGS) metagenomics, metatranscriptomics, and a framework for reference metaproteomic database construction. ATLAS transforms raw NGS data into functional, taxonomic, taxonomy by function abundances at the microbial population level and provides genome-centric resolution using binning. ATLAS provides robust taxonomy of based on majority voting of protein-coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on github, and is implemented in snakemake for modular customizable work-flows. https://github.com/metagenome-atlas/atlas