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2017-henderson-revfishbio

Code and data for Henderson ME, Mills KE, Thomas AC, Pershing AJ, Nye JA (2017) Effects of spring onset and summer duration on fish species distribution and biomass along the Northeast United States continental shelf. Reviews in Fish Biology and Fisheries 27:411-424

2018-oceanography-paper

Data and code for Pershing et al. 2018 Oceanography paper "Evidence for Adaptation from the 2016 Marine Heatwave in the Northwest Atlantic"

ant-colony-optimization

Repository containing code for visualizing Ant Colony Optimization algorithms for clustering

assessing-global-fisheries

Materials for Ovando et al. (2021) "Improving estimates of the state of global fisheries depends on better data" Fish and Fisheries

auto-07p

AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.

auto07p

References, installation guide, and tutorial on "spatial pattern formation"

b.wang-et-al-pnas-2022

begputhinning

cellpylib

A library for working with Cellular Automata, for Python.

claridlands

OpenCL code for the Rietkerk model of spatial organisation of arid lands

clasts-pattern-mars

clcahnhilliard

OpenCL code that implements the classical Cahn-Hilliard model of phase separation in material science

clmdm

OpenCL code for the Mussel disturbance model of Fred Guichard (2003)

clmussels

OpenCL code for the musselbed self-organization model

clmussels-multscale

clmussels_phasesep

OpenCL code for small-scale, aggregative pattern formation in mussel beds, equivalent to phase separation

coastal-dune-model

Coastal Dune Model

continuous_plankton_recorder

Analyzing Zooplankton Trends in the Gulf of Maine Region

coral

Parallel spectral solver for partial differential equations in the plane layer geometry.

cosmos_analysis

Tools for analyzing CoSMoS image data

data_code_jappecol

The

deeplabcut

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans

deepposekit

a toolkit for pose estimation using deep learning

deeptrack2

DeepTrack-2.0

development

diatoms-motion-foraging

Supplementary movies for "Circular run-and-reversal motion optimizes foraging behavior in benthic diatoms" by Wensi Hu, Mingji Huang, H. P. Zhang, Feng Zhang, Wim Vyverman, Quan-Xing Liu for peer review.

dynamic-stability

Source scripts for Ushio et al. "Fluctuating interaction network and time-varying stability of a natural fish community"

earlywarnings-r

elastica

Software to simulate the dynamics of filaments that, at every cross-section, can undergo all six possible modes of deformation, allowing the filament to bend, twist, stretch and shear, while interacting with complex environments via muscular activity, surface contact, friction and hydrodynamics.

fairy-circles-patterns-on-saltmarshes

This code for "Fairy circles imply high resilience of self-organized salt marshes" by L.-X. Zhao, K. Zhang, K. Siteur, X.-Z. Li, Q.-X. Liu, J. van de Koppel. The codes were implemented on anaconda platform with pyopencl package and Jupyter.