Code

Software, in active development

The lab builds open tools for turning environmental DNA into insight — from field sampling to interactive dashboards. Releases are archived with DOIs on the data page's Zenodo community, and the preprints describing them are on the publications page.

Featured

All repositories

Every public repository on the personal account, grouped by the year it was last updated.

2026

• bacteria-the-game-scenariosScenario library for Bacteria!JavaScript
• winnipegcurrents-siteWinnipeg Currents Event SiteHTML
• danaSeqAnalysis Pipeline and Dashboard for Environmental MetagenomicsSvelte · ★ 1
• earthdnaEarthDNA: every SSU rRNA sequence and ASV on one navigable globe (fastsne spherical t-SNE)JavaScript
• microscape-appMicroscape -- Visualizing Microbial LandscapesTypeScript
• fastsneGPU t-SNE for 10M+ point TNF tables (nanopore reads, contigs)Cuda
• ecossdbEcosystem Services Database — maps metagenomic functional annotations to CICES 5.2 ecosystem servicesPython
• community-microbe-namingTemplate for community workshops naming newly discovered bacteria from local waters in local languages (SeqCode). Agent-oriented docs.JavaScript
• bacteria-the-gameBacteria! How long can you survive?JavaScript
• amundsen-gameJavaScript
• icecameraExploratory shipboard camera sea-ice classification and review toolsPython
• underwayScripts for real-time analysis of underway flow-through data aboard oceanographic research vesselsPython
• HABGDBHarmful Algal Bloom Genomic DatabaseHTML
• arctic-historyHistory of the Canadian Arctic Archipelago and Baffin Bay: a database, wiki and map layer for the CCGS Amundsen dashboardPython
• papa2Python-first amplicon denoising — byte-identical to R's DADA2Python · ★ 5
• microscapeVisualizing Microbial LandscapesPython · archived
• microscapeRmicroscapeR: Downstream analysis tools for amplicon sequencing (Bioconductor R package)R · archived
• microscape-nfMicroscape amplicon sequencing pipeline (Nextflow)Python
• winklewagAutomatically exported from code.google.com/p/winklewagPerl
• seaicespiralSea Ice Death Spiral animationPython · ★ 1
• mepipelinesMicrobial Ecology PipelinesPython
• arctic_wormsF*
• pi-benchPi memorization benchmark for LLMs Python
• LWFC2026Lake Winnipeg Field Course 2026HTML
• SARGDBSpecies at Risk Genomics DatabaseHTML
• AISGDBAquatic Invasive Species Genomic DatabaseHTML
• frostbitFrostbit: Adaptive testing platform with IRT-based computerized adaptive testing, AI question generation, and multi-model difficulty calibrationPython
• designrSwipe through Pinterest boards like Tinder, get an AI style read, save the keepersTypeScript
• omcThe Open Microbial Community — a git-native, AI-assisted platform for microbial ecologyHTML
• nclbNo Contig Left Behind — animist MAG bin refinement for metagenome-assembled genomesPython
• sleepalertPython

2025

• autofile_watchAutoFile uses a local LLM to automatically organize files into project folders after dropping into a designated Drop BoxPython
• autofileAutoFile uses a local LLM to automatically organize files into project foldersPython
• codex-testtesting Codex

2024

• CMO2024R · ★ 1
• RedRiverResearchData and scripts for RedRiverResearch.caShell
• ambwrAutomated Metagenomic Binning (With Receipts)Shell
• popsychPopular Psychology analysisR
• OSDOcean Sampling Day project filesR
• bbpipe-snakemakePython · ★ 1

2020

• Genomic-Signatures-of-OGT-2020-
• ag_thesisR
• pangenomeModels of the Microbial PangenomeR · ★ 9
• rml_thesisR

2019

• Research
• mettametagenome assembly, binning, and visualizationShell · ★ 1
• mlitesMachine Learning in the Environmental Sciences
• seattlecrowsAutomatically exported from code.google.com/p/seattlecrowsPHP
• sverdrupSverdrup's 1953 Critical Depth HypothesisR

2018

• diversity-scriptsR · ★ 1

2017

• BIOL342
• workShell
• hgtbaabscripts for Fuchsman et al. manuscript on Horizontal Gene Transfer Between Archaea And BacteriaR
• minionarealtime krona plots during a minION runShell · ★ 9
• longest-repeatsfinding the longest repeats in bacterial genomesR

2016

• repkAutomatically exported from code.google.com/p/repkPerl
• mds-mountain
• mail2clirun shell commands from an email attachment
• demultfirst crack at a demultiplexer for variable length dual indexed barcodes, wrapper for tagdustShell

2015

• microbial-phenotype-databaseAutomatically exported from code.google.com/p/microbial-phenotype-database
• daxterAutomatically exported from code.google.com/p/daxter
• pubsPublications and bibliographiesTeX

2013

• rec-genome-toolsPerl · ★ 10
• gcamelG+C Content AmeliorationR

2012

• ddmpDigital Database of Microbial Phenotypes. Like an online Bergey's Manual.PHP · ★ 14
• himaA Meta-database of Low Temperature Genomes and Metagenomes★ 3