Everything behind this project is public and reproducible. The models, the processed data, and the methods are on GitHub. If you study coral, symbionts, reef optics, or coastal oceanography, we would love your eyes on it, and there are specific measurements that would sharpen the science.
For the full, review-ready write-up, the Methods & Data page documents every dataset, the analysis pipeline, statistics, results (with figures), limitations, and data/code availability, written for scientific review and potential peer-reviewed publication. The Open Questions page is the live research agenda and data-request list.
| Path | Contents |
|---|---|
| /models | Every model as a runnable Python script: herbivory bistability, thermal/DHW, satellite ocean-color, turbidity shading, carbonate chemistry, sediment-plume + upwelling (Lagrangian), black-sand redox (PHREEQC), and the first-flush / dry-season-storm catalog + hypoxia setup-index. |
| /data | Processed outputs: per-site metrics (CSV/JSON) and figures for each model. |
| /site | This website (static HTML/CSS). |
| README | Methods, data sources, and how to reproduce each result. |
Code released under MIT; processed data and text under CC-BY 4.0. Large raw model fields (GLORYS subsets, particle trajectories) are available on request.
| Source | Used for | Access |
|---|---|---|
| NOAA Coral Reef Watch 5 km | SST & Degree Heating Weeks, 1985, present | NOAA / PacIOOS ERDDAP |
| NASA MODIS-Aqua ocean color | Turbidity (Kd490) & chlorophyll, 2003-2022 | NOAA CoastWatch ERDDAP |
| Copernicus GLORYS12 reanalysis | Currents, subsurface temperature, upwelling | Copernicus Marine Service |
| Airport METAR / ASOS | June-2023 storm ground-truth (La Ceiba, Roatán, San Pedro Sula) | Iowa Environmental Mesonet |
| Black-sand XRF (6 scans, 2 sites) | Sediment geochemistry driving the redox model | Field XRF (Tela Coral), 2026 |
| Field benthic surveys | Coral cover, Diadema density | Coral Reef Alliance / Operation Wallacea |
numpy scipy pandas matplotlib PyCO2SYS runs the self-contained models
(herbivory, thermal, ocean-color, turbidity, carbonate) directly. The Lagrangian sediment/upwelling model adds
copernicusmarine + parcels + xarray. Each script prints its results and
writes a CSV/figure. See the README for exact commands and parameters.
The models make specific, falsifiable predictions. These measurements would confirm or kill them:
| Open question | Measurement that would settle it |
|---|---|
| Acute-hypoxia trigger? | In-situ dissolved-oxygen + CTD loggers on the reef, ideally before the next dry-season-break storm, to catch a stratification + oxygen crash in the act. |
| Is the black sand's manganese bioavailable? | A benchtop leach assay of the iron-free lagoon sand (oxic vs anoxic), measuring dissolved Mn/Fe release plus its trace-metal profile. The single most useful next measurement for the treatment idea. |
| Heat-tolerant symbiont? | Symbiodiniaceae typing (ITS2) of Banco Capiro corals, shallow vs deep. The one mechanism we cannot model. |
| Turbidity shading? | In-situ PAR/temperature loggers by depth, and bleaching-vs-depth scoring during a heat event. |
| Carbonate subsidy? | Total alkalinity, DIC and nutrients at the Ulúa mouth and over the reef; the alkalinity:DIC ratio. |
| Grazing budget | Quantitative Diadema and herbivore-fish transects to calibrate the bistability model. |
| Sub-bay circulation | Higher-resolution or in-situ current/residence measurements the 1/12° model can't resolve. |
| Bleaching history | Any historical bleaching observations at Banco Capiro, by year and depth, to ground-truth the DHW record. |
Editable templates (not sent automatically). Add your own name, links and the recipient's specifics.
Subject: Banco Capiro reef, open models and a field trip Hi [Name], We are studying why Banco Capiro in Tela Bay holds 60 to 70% live coral in warm, turbid, nutrient-loaded water that is degrading the reefs nearby. We rebuilt the site from first principles and put the models and data online, and a team is going to measure the key clues on site. Your work on [topic] lines up closely with what we are finding. If you are open to it, we would value your read on the approach, and there may be a natural collaboration around [symbiont genetics / reef optics / carbonate chemistry]. Everything is here: https://steps-re.github.io/rebel-reef and the code is at https://github.com/steps-re/rebel-reef Thanks, [Your name], Tela Coral
Subject: Symbiont typing for Banco Capiro corals Hi [Name], Quick, concrete ask. Our modeling can explain most of Banco Capiro's heat survival through shading, feeding and grazing, but not the shallow elkhorn, where we suspect a heat-tolerant symbiont. That is the one piece we cannot resolve without genetics. On the upcoming trip we can collect tissue samples under the right permits. Would your lab be open to ITS2 typing of paired shallow and deep samples? We would share all data openly and credit the work. Sampling window is [dates]. Details and methods: https://steps-re.github.io/rebel-reef/researchers.html Thanks, [Your name], Tela Coral
Reach out via Tela Coral or open an issue on the GitHub repository.