sormi-assay-development

Summer Oyster Resilience & Mortality Index (SORMI) — A quantitative tool for improving field survival of Pacific oysters

Associated Google Drive Folder

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OVERVIEW

This repository is the canonical landing point for SORMI assay-development work with Pacific oysters (Magallana gigas). It contains the durable computational record: assay data, analysis code, protocols, generated outputs, dashboard source, and concise pointers to related planning materials in Google Drive.

Google Drive remains useful for collaborative planning documents, native Google Docs/Sheets, protocol PDFs, and literature collections. When Drive contains material that is not mirrored here, the difference should be visible from this README or from the relevant assay subdirectory README.

CANONICAL RECORD PLAN

1. Keep reproducible work in the repo: raw assay exports, layout/metadata files, scripts, notebooks, rendered summaries, and finalized protocol/reference files.
2. Keep collaborative drafting in Google Drive: planning docs, outreach docs, native Google Sheets, brainstorming notes, and literature folders that are not direct analysis inputs.
3. Mirror only stable Drive artifacts into the repo when they become part of the assay record.
4. Link Drive-only content from this README so users can tell what exists outside the repo without browsing Drive first.
5. Use each assay directory README to state whether Drive has additional protocol/planning/literature content.

REPOSITORY STRUCTURE

Path	What is included
Glycogen/	Development and analysis files for the Promega Glycogen-Glo assay. Includes R Markdown analyses, raw luminescence exports, Gen5 plate-reader experiment files, sample/tissue-weight CSVs, reference PDFs, and generated plots.
Resazurin/	Resazurin metabolic-rate assay experiments. Includes experiment-specific plate-reader exports (plate-<label>-T<hour>.txt), layout.csv metadata files, ImageJ measurements/images, R Markdown analyses, summary CSV outputs, figures, an example layout template, and the Huffmyer et al. preprint.
heat-survivorship/	Heat survivorship experiment data and analyses. Includes survivorship CSVs, family/image metadata, R Markdown analysis files, and Kaplan-Meier plot outputs.
NaK-ATPase/	Na/K ATPase assay protocol material, currently including the sampling protocol PDF.
Protein assay/	Landing directory for protein-assay protocol notes and future assay data. Current detailed protocol/manual materials are in Google Drive.
Total Antioxidant Capacity/	Landing directory for total antioxidant capacity assay development. Current kit documentation and question notes are in Google Drive.
Succinate/	Landing directory for succinate assay development. Current kit documentation is in Google Drive.
sampling-event-metadata/	Sampling-event metadata and images, including June 2026 USDA family sampling, ImageJ sizing measurements, sizing images, and sex-determination image folders.
scripts/resazurin/	Shared R scripts for parsing resazurin plate-reader exports and building dashboard-ready data and QC files.
.github/workflows/	GitHub Actions workflow for rebuilding the resazurin dashboard data, rendering the Quarto dashboard, and deploying GitHub Pages from main.

GOOGLE DRIVE DIFFERENCES

The linked Google Drive folder is broader and more planning-oriented than this repo.

Drive item	Repo status
Sampling Plan May 2026, SORMI Summary, and Engagement Outreach Tracking	Drive-only planning/admin documents. Summaries or finalized methods should be copied into repo READMEs when they become part of the durable record.
Assay List Google Sheet	Canonical editable assay list. The repo no longer keeps a separate Assay List.xlsx copy.
Glycogen Drive folder	Contains protocol/reference PDFs that are also represented in Glycogen/. The repo additionally contains raw data, code, and outputs.
Resazurin Drive folder	Contains the Huffmyer preprint, also represented in Resazurin/. The repo additionally contains raw data, code, images, and outputs.
Na/K ATPase Drive folder	Contains the sampling protocol PDF, also represented in NaK-ATPase/.
Protein assay, Total Antioxidant Capacity, and Succinate Drive folders	Drive currently holds protocol/manual/question documents. Matching repo landing directories now exist for future canonical data and analysis.
Reproductive investment / Sex determination Drive folder	Drive holds brainstorming and literature PDFs. Related measured sampling metadata lives under sampling-event-metadata/.
photos Drive folder	Drive-only small photo collection, separate from repo experiment image datasets.

KEY ROOT FILES

• resazurin-dashboard.qmd: Quarto source for the resazurin data dashboard.
• index.html: Static site landing page copied into the GitHub Pages build.
• CNAME: GitHub Pages custom-domain configuration for sormi.science; keep this file in the repo so the site remains connected to the custom domain.
• sormi-assay-development.Rproj: RStudio project file for the repository.

ORGANIZATION NOTES

• Assay folders generally use code/, data/, and outputs/ or output/ subdirectories.
• R Markdown files in assay code/ folders contain analysis workflows; rendered .md/.html files and plots are stored alongside or under matching output folders.
• Raw instrument exports and layout files are kept with each assay's data/ directory so analyses can be rerun from source data.
• Resazurin experiment folders are designed to be parsed automatically when they contain plate-reader files named like plate-<label>-T<hour>.txt and a matching layout.csv.
• Glycogen Gen5 experiment and raw luminescence files follow date/species/experiment naming conventions documented in the Glycogen subdirectory READMEs.