jrcasey

John Casey's repositories

PanGEM

Pangenome-scale metabolic network reconstruction, analysis, and strain-model extraction

Language:MATLABMIT7 10

mse_AMT

Microbial Simulation Environment - A toolbox for the simulation of genome-scale metabolic network reconstructions in the marine environment. A case study with the AMT-13 cruise transect is included.

Language:MATLAB3 10

NutrientUptake

Accompanying code to Casey and Follows, 2020. A flexible and easy-to-use model of microbial acclimation to nutrient availability.

Language:MATLABMIT3 10

mse_AMT_deprecated

MSE adapted for AMT cruise

Language:MATLAB1 10

bayesian_cbiomes

notebooks and files for the Bayesian CBIOMES workshop

Language:Jupyter Notebook000

Bioremdiation

Collection for Bioremediation LDRD-LW proposal

MIT000

evolutionABM

Agent Based Modeling of mutation with community dFBA

MIT010

jrcasey.github.io

My website

Language:JavaScriptMIT000

mse

Microbial Simulation Environment - A toolbox for the simulation of genome-scale metabolic network reconstructions in the marine environment. A case study with the AMT-13 cruise transect is included

Language:MATLABMIT010

mse_EqPac

MSE toolbox applied to a 1992 EqPac transect of the equatorial Pacific along the 140W line.

Language:MATLABMIT000

OldSite

Homepage

Language:RubyCC0-1.0000

PheArrMe

Phenotype array guided GEM gap-filling

Language:PythonMIT000