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