Research Tools, Software and Workflows

Here are a selection of tools, software and workflows developed or in development at Bigelow Laboratory.

Data Portals

ecocaster: Experimental crowd-sourced daily forecasts for jellyfish, deer ticks, moose, and other species.

Environmental DNA portal: Data portal to view and download eDNA data from samples gathered as part of the Maine-eDNA project.

Software and Workflows

Ocean ‘Omics

The GORG-classifier: A modification of the kaiju workflow that uses the GORG-Tropics database to annotate marine metagenomic reads. Created and featured for this paper.

sag-mg-recruit: A workflow for recruitment of metagenomic reads to single amplified genomes. Created for and used in this paper.

Computational Ecology

twinkle: A set of R language tools to ease ecological work with modern geospatial data using the sf and stars packages.

rasf: A set of R language tools to ease ecological work with rasterized geospatial data.

neracoos: Access NERACOOS ocean buoy data using the R programming language.

oharvester: Public examples for harvesting online oceanographic datasets from R and Python programming languages.

tetramers: A suite of simple R tools to manage the workflow for tetramer analysis of sequences using principal component analyses.

maree: An R language wrapper around a local install of the xtide application to generate tide tables.

rtofs: OPeNDAP access to Real Time Ocean Forecasting System products using R language.

thredds: THREDDS Crawler for R language using xml2 package.

fishboxes: R tools for working with NMFS One Degree, Quarter Degree and Ten Minute Squares (ODS, QDS, TMS)

daymet: Simplified access to OPeNDAP daymet data served by ORNL thredds server.

compressr: Simple wrapper functions for tar, untar, zip and unzip from the R utils package.

fvcom: Convenience tools in R for accessing FVCOM datasets.

blastxml: Extract data from Blast XML files in R.

stsaav: Standard Time Series Analysis and Visualization in R.

Satellite Ocean Color

oc-satellite: Search, download and process satellite ocean color data from the NASA OB.DAAC.