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jimothy-dev/README.md

James Simpson

Computer Science graduate (University of Washington Tacoma) working on ocean and environmental data: CTD profiles, satellite imagery, and computer vision for biodiversity monitoring. US Army veteran. Looking for entry-level data science or research software roles in ocean and environmental science.

Featured projects

Project What it is
CTD_Grapher_Web React / TypeScript / Plotly.js app that draws multi-station depth profiles and transect sections from Sea-Bird .cnv CTD casts, entirely in the browser: nothing to install, files never leave your computer. Use it.
CTD_Grapher_v2 Colab notebook that parses any Sea-Bird .cnv cast from its own header and draws interactive multi-station depth profiles (Plotly HTML + PNG). Live example.
drone-intertidal-species-id SAM 3 + BioCLIP 2 pipeline that finds and identifies intertidal organisms in consumer-drone photos, with geometry / confidence / agreement gates. Built at OceanHackWeek 2026, Bamfield Marine Sciences Centre.
HerringIdentificationProject Herring Spawn Labeler: FastAPI web app that pulls Sentinel-2 and Landsat scenes from Google Earth Engine around DFO spawn records, labels them, exports GeoTIFF training chips, and adds SAM 3 point-prompt segmentation with a spectral spawn score. Started at OceanHackWeek 2026.
centennial-park-point-cloud Three.js viewer for a georeferenced textured mesh of a boat launch and moorage from a DJI Mini SE survey, compressed 102 MB to 11 MB for the web. View.
BioinformaticsStudy R / DESeq2 analysis of MorPhiC RNA-seq (GEO GSE288289) testing whether knockout method changes the differentially expressed genes for four transcription factors; volcano and UpSet plots.
CTD_Grapher First version of the CTD grapher (Excel + Google Drive workflow) written for a UW Tacoma estuarine field course. Superseded by v2.

Skills

Languages — Python, R, Java, SQL, JavaScript

ML & CV — PyTorch, Hugging Face Transformers, Segment Anything (SAM 3 / SAM 2.1), BioCLIP / CLIP-style zero-shot classification, DESeq2 and Bioconductor, NumPy, pandas, SciPy

Ocean data — Sea-Bird CTD .cnv processing, photogrammetry

Tools — Git and GitHub (Pages, CLI), Google Colab, Jupyter and JupyterHub, FastAPI, Plotly, Matplotlib, ggplot2, Linux and Windows

Contact

Pinned Loading

  1. CTD_Grapher_Web CTD_Grapher_Web Public

    Depth profiles and transect sections from Sea-Bird .cnv CTD casts, in the browser

    TypeScript

  2. CTD_Grapher_v2 CTD_Grapher_v2 Public

    Interactive multi-station CTD depth profiles from any Sea-Bird .cnv file, in one Colab notebook. Plotly HTML + PNG output; columns read from the file header, no instrument config.

    Jupyter Notebook

  3. drone-intertidal-species-id drone-intertidal-species-id Public

    Intertidal species identification from consumer-drone photos. SAM 3 open-vocabulary segmentation finds organisms, BioCLIP 2 names them, three gates reject false positives. Colab notebook tuned on r…

    Jupyter Notebook

  4. HerringIdentificationProject HerringIdentificationProject Public

    Herring Spawn Labeler: local FastAPI app that pulls Sentinel-2 and Landsat scenes from Google Earth Engine around DFO Pacific herring spawn records, labels them, exports GeoTIFF training chips, and…

    Python

  5. centennial-park-point-cloud centennial-park-point-cloud Public

    Interactive Three.js viewer for a georeferenced textured mesh of the Centennial Park boat launch and moorage, from a DJI Mini SE survey (UTM 10N, meshopt-compressed glTF).

    JavaScript

  6. BioinformaticsStudy BioinformaticsStudy Public

    R/DESeq2 analysis of MorPhiC bulk RNA-seq (GEO GSE288289): does knockout method (KO, critical-exon, PTC) change the DEGs for MXD1, RUNX1, NCOA3 and BHLHE40? Volcano and UpSet plots.

    Jupyter Notebook