whoigit / shelltox

Shellfish Toxicity Modeling in the Gulf of Maine

Shellfish Toxicity Modeling

Red tide is a type of harmful algae bloom that affects human and wild marine activities. This project seeks to correlate the Hazardous Algae Bloom (HAB) cell counts of Alexandrium Catenella (red tide) with toxin concentration (Saxitoxin hydrochloride) in Blue Mussels (Mytilus edulis). This project focuses on data collected off of the coast of Maine. The lead scientist for this project is Don Anderson.

From cell counts, a model of shellfish toxicity is projected over time. Uptake and Depuration constants (beta and gamma) are determined from correlating historical measured toxicities with modeled toxicity over a range of constants.

The tools presented herein are designed to present the collected data and calculated toxicity models, and to determine good uptake and depuration constants.

Installation

Create a conda environment with the following command. Run programs from this git under this shelltox environment.

conda create -n shelltox python=3.7 bokeh=1.0 pandas=0.23 requests

BetaGamma

betagamma is a CLI tool for calculating best uptake and depuration constants for a series of years and data-locations. It also calculates estimated best overall constants for a given input series.

Basic usage: python betagamma.py betagamma.ini --src ../data

Here, betagamma.ini is a configuration file containing year-location triplets with a strong corellation between HAB and measured shellfish toxicity.

Bokeh App

bokeh_app is a graphical modeling tool for viewing and interacting with data and models. restart_bokeh.sh is a script for restarting web-application service. If installed on a server other that shelltox.whoi.edu it would have to be edited to work properly again.