agent based modelling
☆39Aug 28, 2024Updated 2 years ago
Alternatives and similar repositories for BacArena
Users that are interested in BacArena are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SMETANA: a tool to analyse interactions in microbial communities☆74May 6, 2025Updated last year
- Higher-Order Co-occurrence☆12Nov 9, 2021Updated 4 years ago
- Supplementary data for co-occurrence manuscript☆10Dec 19, 2019Updated 6 years ago
- Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks☆220Updated this week
- mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models☆15Aug 20, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Python package to study microbial communities using metabolic modeling.☆135Updated this week
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆20Oct 21, 2022Updated 3 years ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆15Jan 8, 2024Updated 2 years ago
- ReFramed: metabolic modeling package☆64Jun 26, 2026Updated 2 months ago
- CarveMe: genome-scale metabolic model reconstruction☆217Sep 12, 2025Updated 11 months ago
- CBMPy is a Python based platform for constraint based modelling and analysis.☆20May 26, 2026Updated 3 months ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆93Oct 9, 2025Updated 10 months ago
- Python interface for running COMETS simulations and analyzing the results☆16May 19, 2026Updated 3 months ago
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆273May 13, 2026Updated 3 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ☆51Jun 11, 2025Updated last year
- Plot microbiome time series in parallel☆27Nov 7, 2023Updated 2 years ago
- From annotated genomes to metabolic screening in large scale microbiotas☆77Jul 27, 2026Updated last month
- Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and …☆10Jun 19, 2019Updated 7 years ago
- ☆10Mar 5, 2019Updated 7 years ago
- ☆11Apr 17, 2025Updated last year
- 📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models☆10Aug 24, 2021Updated 5 years ago
- A javascript library for building, exploring, and sharing spatially structured models of biological systems☆16May 26, 2026Updated 3 months ago
- memote – the genome-scale metabolic model test suite☆151Aug 14, 2025Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A simulator for horizontal gene transfer (HGT) in microbial communities☆10Oct 5, 2020Updated 5 years ago
- Using MASST or fastMASST, adding metadata onto a tree ontology for microbes☆27Aug 14, 2026Updated 2 weeks ago
- Unsupervised learning based Microbial Interaction inference method using BAyesian esTimatiOn☆10Apr 22, 2021Updated 5 years ago
- Python package for creating, calibrating and simulating RBA models☆14Aug 19, 2026Updated last week
- An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as…☆70Aug 15, 2026Updated 2 weeks ago
- METAgenomic LONgitudinal Differential Abundance method☆16Dec 17, 2019Updated 6 years ago
- Automated synthetic microbial Community Design☆13Mar 26, 2021Updated 5 years ago
- Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species☆19Mar 17, 2021Updated 5 years ago
- ☆37Jan 21, 2026Updated 7 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32May 22, 2020Updated 6 years ago
- The code and distributable for designing minimal microbial communities with specified metabolic functions.☆11Aug 9, 2017Updated 9 years ago
- Calculate the normalizing factors for zeroinflated sequencing data such as microbiome sequencing data☆16Jan 31, 2025Updated last year
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing