Allison Smith

computational marine biology

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CODE


I write computer code for a range of research applications including mathamatical models, data analysis, and visualization of results. Code is increasingly important for scientific research and making code available is important for making research reproducible. Code for my research projects is available through my Github account. Once I complete code for a project, I make an official release of the code from Github available through Zenodo - the download links on this page are to code that is available through Zenodo.

NOAH LSM Mussel v2.0

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NOAH LSM Mussel v2.0 is a mathematical model that predicts mussel bed temperatures from atmospheric and oceanic data by mimicking the thermal properties of a mussel bed exposed to tidal inundation and wave run-up. The model is derived from the National Weather Service NOAH Land Surface Model. In v2.0, it is possible to change the within mussel bed contact which determines conductive heat transfer. Mussel survival is predicted using mussel bed temperatures from the model.

Intertidal mussel bed

NOAH Mussel Model

B

mussel

conductive heat

transfer

A

contact area

rock

z

y

x

ocean

land


Related Publications:

Mislan, K. A. S. and Wethey, D. S. (2015). A biophysical basis for patchy mortality during heat waves. Ecology, 96:902-907

Mislan, K. A. S., Helmuth, B., and Wethey, D. S. (2014). Geographical variation in climatic sensitivity of intertidal mussel zonation. Global Ecology and Biogeography, 23:744-756

Wethey, D. S., Brin, L. D., Helmuth, B., and Mislan, K. A. S. (2011). Predicting intertidal organism temperatures with modified land surface models. Ecological Modelling, 222:3568–3576


Microbial Remineralization Model v1.0

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The Microbial Remineralization Model v1.0 simulates the interactions between sinking particles and heterotrophic bacteria in the ocean water column in a 1-dimensional Eulerian framework. The model has 9 state variables including particulate organic carbon (POM), particle-attached bacteria (BP), free-living bacteria (BD), active exoenzyme in the particle (EP), inactive exoenzyme in the particle (XP), hydrolysate in the particle (HP), hydrolysate in the dissolved environment (HD), active exoenzyme in the dissolved environment (ED), and inactive exoenzyme in the dissolved environment (XD).

Mass Transfer

Mortality

ED

XP

Decay

POM

XD

EP

Action

Decay

HP

Uptake

HD

DOCs

BP

Uptake

Mortality

Growth

Growth

BD

Sinking

Related Publications:

Mislan, K. A. S., Stock, C. A., Dunne, J. P., and Sarmiento, J. L. (2014). Group behavior among model bacteria influences particulate carbon remineralization depths. Journal of Marine Research, 72:183-218