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ModelSEEDpy Public
Forked from ModelSEED/ModelSEEDpyPython package for building and analyzing models using ModelSEED
Python MIT License UpdatedMay 21, 2025 -
simulation_envs Public
Simulation environments for applying deep learning models to microbiomes
Python MIT License UpdatedMay 20, 2025 -
xinProject Public
Repository for files and code for internship project
Jupyter Notebook UpdatedMay 7, 2025 -
AiSchool Public
Repository for code and documents of the School of Artificial Intelligence Applied to Microbiomes
UpdatedApr 10, 2025 -
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hungerGamesModel Public
Dynamic model of a synthetic gut community
Python MIT License UpdatedNov 28, 2024 -
sharedColabBooks Public
Shared Google Colab notebooks used for teaching
Jupyter Notebook MIT License UpdatedNov 26, 2024 -
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FastNNGapfiller Public
Gapfill GSMMs with costs. Compatible with the ModelSEED db and aplicable to GapSeq draft reconstructions.
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microbialTimeSeries Public
Practicals of the School on the Analysis of Microbial Time Series Data
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ChemSamp Public
Gillespie-like algorithm for microbial reaction networks
Python Apache License 2.0 UpdatedNov 21, 2022 -
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miaSim Public
Forked from microbiome/miaSimmicrobiome data simulation package
R UpdatedSep 20, 2021 -
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microsimR Public
Forked from gheysenemma/microsimRA Simulator Package with a collection of basic community models that outputs count data of microbial communities
R Artistic License 2.0 UpdatedMay 20, 2021 -
SyntheticMicrobiome Public
Modeling the dynamics of a synthetic human gut microbial community
Python UpdatedDec 14, 2020 -
state_of_the_art_gapfilling Public
Given an incomplete bacterial gene reaction network... complete it!
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reaction_set_evolution Public
Nature or nurture: disentagling the drivers of metabolic network evolution in bacteria
Python UpdatedFeb 3, 2020 -
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