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	Software developed by the Louca lab   Audio processing Python scripts for working with bioacoustic audio files (WAV or FLAC), such as extracting clips, converting annotation tables, plotting spectrograms and computing acoustic parameter differences. × × Cariaco metabolic modeling MATLAB code for inverse linear transport modeling (ILTM), estimation of eddy diffusivity based on the spatiotemporal distribution of a conserved tracer, and spatial metabolic flux (SMF) analysis of microbial systems near steady state, exemplified for the Cariaco Basin sub-euphotic water column. Reference: Louca, S., Scranton, M. I., Taylor, G. T., Astor, Y. M., Crowe, S. A., Doebeli, M. (2019). Circumventing kinetics in biogeochemical modeling. PNAS 116:11329-11338 × × × × castor An R package for efficient phylogenetics on large trees. Reference: Louca, S., Doebeli, M. (2018). Efficient comparative phylogenetics on large trees. Bioinformatics 34:1053-1055 × × × × × FAPROTAX Database and software for mapping prokaryotic taxa to metabolic functional groups. Reference: Louca, S., Parfrey, L. W., Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272-1277 × × Fast-reaction-transport modeling MATLAB code demonstrating fast-reaction-transport biogeochemical models in 1-dimensional water and sediment columns. Reference: Louca, S., Taylor, G. T, Astor, Y. M., Buck, K., Muller-Karger, F. E. (2022). Transport-limited reactions in microbial systems. Environmental Microbiology 25:268-282 × × × MCM (Microbial Community Modeler) A computational framework for modeling microbial communities using dynamic flux balance analysis of genome-based cell models, in the context of a dynamical environment. Classical functional group models are also supported. Reference: Louca, S., Doebeli, M. (2015). Calibration and analysis of genome-based models for microbial ecology. eLife 4:e08208 × × × × × Metabolic control analysis of biogeochemical systems Python code for simulating and performing metabolic control analysis of biogeochemical reaction-advection-diffusion models, at steady state. Reference: Louca, S. (2025). Metabolic control analysis of biogeochemical systems. Communications Earth & Environment 6:161 × × peacots (Periodogram Peaks in Correlated Time Series) An R package for detecting cyclicity in time series using the Ornstein-Uhlenbeck state-space model (rather than simple white noise) as a null hypothesis. Reference: Louca, S., Doebeli, M. (2015). Detecting cyclicity in ecological time series. Ecology 96:1724-1732 × Saanich GCM (Gene Centric Model) Gene-centric biogeochemical model (MATLAB code) for the Saanich Inlet seasonally anoxic water column, under steady state conditions. Reference: Louca, S., Hawley, A. K., Katsev, S., Torres-Beltran, M., Bhatia, M. P., Kheirandish, S., Michiels, C. C., Capelle, D., Lavik, G., Doebeli, M., Crowe, S. A., Hallam, S. J (2016). Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. PNAS 113:E5925-E5933 × × × Response of SMTZs to perturbations in methane influx Python code for analyzing the response of marine sulfate-methane transition zones to perturbations in methane influx. Reference: Stilianos Louca (2026). Response of marine sulfate-methane transition zones to perturbations in methane fluxes. in review × × ×   Louca lab. Department of Biology, University of Oregon, Eugene, USA © 2026 Stilianos Louca all rights reserved