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aiorganoids

anc

Mirror of ANC code

awesome-vaes

A curated list of awesome work on VAEs, disentanglement, representation learning, and generative models.

biojazz

Evolve and Design Biochemical Reaction Networks

bionetgen

Rule-based modeling framework

biorxiv-word-template

MS Word template for styling a manuscript for a bioRxiv submission

d3flux

D3.js based visualizations of cobrapy metabolic models

deeplearning

Deep Learning (Python, C, C++, Java, Scala, Go)

emll

some code for linlog model simulation

facile

Facile repository saved for anc and biojazz

fbahv

FBAhv: FBA analysis of host-virus metabolic model (read related publication at: https://www.life-science-alliance.org/content/4/1/e202000869)

gitignore

A collection of useful .gitignore templates

helixcode

Emulating Helix editing in VS Code.

hybridcontagious

Hybrid Contagious

hypernetx

Python package for hypergraph analysis and visualization.

lapreprint

📝 A nicely formatted LaTeX preprint template

mechad

Python code for numerical simulations of self-assemly with optimization by automatic differentiation

mlreview_notebooks

Notebooks for "A high bias low-variance introduction to Machine Learning for physicists."

multi_assembly

nerdss

NonEquilibrium Reaction-Diffusion Self-assembly Simulator

neuromancer

Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.

nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks

oxidizer

🛠️ Simple & Extensible Dotfile Manager using Rust Toolchains ⛓️

pattrix

Automatic design of gene regulatory mechanisms for spatial pattern formation

persuasionseqanalysis

sequence analysis for persuasion projects

ppi_synechococus_elongatus

The computational model of Synechococcus elongatus

prochlorococcus_model

Materials for Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus paper

pyfba

A python implementation of flux balance analysis to model microbial metabolism

pykan

Kolmogorov Arnold Networks

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.