johnbarton / ACELinks
Fast and flexible code for solving the inverse Ising/Potts inference problem
☆27Updated 2 years ago
Alternatives and similar repositories for ACE
Users that are interested in ACE are comparing it to the libraries listed below
Sorting:
- Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)☆14Updated 3 years ago
- Python-interface C++ library for Bayesian phylogenetics via optimization☆39Updated last year
- A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.☆36Updated 2 years ago
- Simulate microbial community batch culture experiments.☆43Updated last year
- Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I☆101Updated 3 years ago
- topological data analysis of population-scale microbiomes☆31Updated 2 years ago
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆27Updated 2 years ago
- Encoding Dynamic Flux Balance Analysis in SBML☆12Updated 5 years ago
- Benchmarking and metadata tracking for Python. Extensible, with distributed/cluster support.☆20Updated 3 weeks ago
- An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuris…☆24Updated this week
- A COBRApy extension for genome-scale models of metabolism and expression (ME-models)☆35Updated 6 years ago
- bioinformatics visualization tools with pyviz/bokeh☆20Updated 2 years ago
- ☆14Updated last year
- HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs☆36Updated last year
- LaTeX template to create a compiled PDF (text+figures) e.g. for bioRxiv.org☆21Updated 9 years ago
- Pyro models of SARS-CoV-2 variants☆77Updated last year
- A graphical interface for sklearn classification to introduce machine learning to biologists☆13Updated 8 months ago
- ☆12Updated 3 years ago
- Interpretable genotype-phenotype landscape modeling☆36Updated 2 years ago
- BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)☆29Updated 8 months ago
- Causal and probabilistic reasoning with continuous time dynamical systems☆19Updated 3 months ago
- framed: a metabolic modeling package for python☆26Updated 6 years ago
- Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.☆23Updated last month
- A template repository for how I structure my scientific research☆102Updated last year
- PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks☆29Updated this week
- A high-fidelity E. coli RNA-seq compendium☆33Updated 4 years ago
- Analyzing RNA-Seq with approximate likelihood☆26Updated 4 years ago
- ☆26Updated 3 years ago
- Scripts for building computational models of gene regulation with tensorflow☆27Updated 2 years ago
- Fast Inference of Networks from Directed Regulations☆22Updated 2 years ago