Theoretical Microbial Ecology Computational Tools

An intelligent, multi-agent framework for artificial biome simulation.

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:globe_with_meridians: Reproducible Research in Computational Ecology workshop

Open education resources for the landscape architecture studio on Computational Ecology

Website of the Computational Ecology and Global Change group (MAYBE_lab)

Code repository for a workshop on behavioural ecological models presented to participants of the BIOS2 - Sentinelle Nord - Computational Ecology Summer School held in Val-Morin, Québec, Canada.

General purpose tools for studying ecology in evolutionary computation

Projet de fin de formation "Reproducible Research in Computational Ecology"

A collection of guides for working in the Record Lab and Computational Ecology Lab

Repository for the Computational Methods course in the Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology

Open-source research on the ecological and biochemical mechanisms of regeneration. Models the interaction between Basidiomycete metabolites, mTOR/AMPK/SIRT1 signaling, and TP53/autophagy balance — bridging ecology, computation, and cellular longevity.

Male moths can locate remote females using pheromone filaments across large distances in a strongly turbulent vegetated areas. This repository provides a computational framework to understand the possible navigation methods and compare their performance. Useful for indoor localization, GPS-less navigation and ecology, among others.

An awesome list for computational ecology, conservation, and environmentalism

MSc Groupwork - Computational Methods in Ecology and Evolution - Silwood Park Imperial College London

Curated research literature collection — papers, references, and reading lists in Active Inference, ecology, and computational biology

Lecture material for the introductory Python course for R users for the 2023 Summer School in Computational Ecology

Creating a test package in R for the Computational Methods course in the Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology.

Publication Materials for "Extending Approximate Bayesian Computation with Supervised Machine Learning to Infer Demographic History from Genetic Polymorphisms Using DIYABC Random Forest" in *Molecular Ecology Resources* special issue

Imputation of missing interactions using SVD

A symbolic framework for interpreting and engineering emergent systems across domains: computation, ecology, cognition, meaning. © 2026 MUSHIKARATI. All rights reserved. This work is published to establish authorship. Redistribution, reproduction, or derivative use is prohibited without explicit permission.

Multi-LLM pipeline for validated extraction and structuring of species-level botanical and ecological knowledge.

Spatial interactions between neighboring plants are foundational to population and community ecology. Neighbor interactions include both positive (facilitation) and negative (competition) effects. The strength of interaction between neighboring plants decays with distance and is often modeled using non-linear functions that take into account a target plant and all its neighbors, resulting in large matrices that represent pairwise interactions. The structural complexity of neighbor interactions and the large size of neighborhood data structures results in long run times and convergence problems. In this talk, we demonstrate how Stan’s segment function can speed computation on sparse matrices of pairwise neighbors in plant-plant interaction models. In addition, we present solutions to common problems of fitting neighborhood models with hierarchical effects, including a comparison of centered vs. non-centered parameterizations. We conclude that the flexibility of the Stan programming language presents novel opportunities to fit classic spatial models in ecology.

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R package for ACESD computational ecology stuff

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Vignettes for computational ecology topics

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clean repo for ECOL 8910: statistical reasoning (fall 2024)