Name: Jamie Collins
Type: User
Company: Environmental Defense Fund
Bio: Marine biogeochemical scientist at the Environmental Defense Fund. Interests: Oceanography, biogeochemistry, carbon dioxide removal, natural climate solutions.
Twitter: jamesrco
Location: Bend, OR
Blog: https://www.edf.org/people/jamie-collins
Jamie Collins's Projects
Suite of scripts for evaluating, calculating, and plotting rates of marine bacterial production using liquid scintillation counter data from the 3H-leucine microcentrifuge method
A port of the Airspace theme by ThemeFisher to Jekyll.
Investigations into weird stuff that goes on during bottle incubations
Dependencies for code in other repos, and some generally useful scripts.
Analysis of various data from the 2015-2016 diel cycle experiments at Station ALOHA
Code for manipulation and analysis of data from PHORCYS and AutoBOD
Drawio GitHub Integration
Setup for untargeted metabolomics
Interactively calculate rates of bacterial exoenzyme hydrolysis using fluoresence data from incubations with fluorogenic substrates
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
Various scripts for data input/output and data massaging, mostly useful for earth scientists (and maybe biologists)
A more reasonable estimate of CO2 emissions from benthic trawling
A multilingual glossary package.
A Tool for automated Optimization of XCMS Parameters - See vignette/IPO.Rmd for help
LATEX code & dependencies for production of my dissertation
Scripts for data processing, visualization, and statistical analysis of lipidomics data
Data and code for Collins et al., "The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters"
Git repository for the R package "LOBSTAHS" (Lipid and Oxylipin Biomarker Screening Through Adduct Hierarchy Sequences)
xcms-compatible tools for handling & manipulation of fragmentation spectra
Code and data files for 2015 GBC paper on North Atlantic particle flux; also used in Laber et al. 2018 Nat. Micro. paper
Workup of 16S/18S data from three cruises in the NW Pacific
Repository for all the code associated with the paper "Reconciling biodiversity protection, food production, and climate change mitigation in the global ocean" from Sala et al, 2020
Read in, parse, analyze marine optical and photochemical data
Analysis of spill & release data from Oregon and Washington
Pair-End AssembeR
Evaluating the potential for seaweed aquaculture to sequester carbon and mitigate climate change
Samsung SmartThings SmartApps and Device Handlers