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Simulates microtubule assemblies with motor proteins using Monte Carlo dynamics, constrained collision handling, and massive parallelization.

Analysis framework for the Sloan Digital Sky Survey (SDSS-V) Milky Way Mapper.

Maps any astronomical image to sky coordinates (WCS) with no false positives, even without metadata, enabling real-time use across archives.

BridgeStan gives in-memory access to Stan models via multiple languages, exposing log densities, gradients, Hessians, transforms, and predictions.

CAMELS host more than 2 petabytes of data from 16,960 cosmological simulations.

Access theory friendly catalogs and theoretical mock catalogs for the Cosmic Assembly Near-infrared Deep Extragalactic Survey (CANDELS).

Enables fast 1D Gaussian Process regression with C++, Python, and Julia, using C++ for speed and Python for features.

MATLAB package for solving partial differential equations in two dimensional domains.

A collection of finite volume methods for linear and nonlinear hyperbolic systems of conservation laws.

A software project designed for ab initio electronic structure beyond density functional theory (DFT).

The CryoLike Python library is a fast and accurate algorithm for computing the likelihood of cryo-EM images given a cryo-EM map and atomic model.

cryoSBI is a Python module for simulation-based inference in cryo-electron microscopy.

A Python package for creating publication-quality probabilistic graphical models with an intuitive syntax, exportable in formats like PDF, PNG, EPS, and SVG.

A Python-based framework for solving and manipulating partial differential equations using sparse spectral methods.

Uses deep learning to predict chromatin effects of DNA variants, including TF binding, DNase sensitivity, and histone marks across cell types.

A Python implementation of an affine-invariant MCMC ensemble sampler for efficient Bayesian parameter estimation.

An open-source coordinate-agnostic particle-in-cell (PIC) code written in C++20 specifically targeted to study plasma physics in relativistic astrophysical systems.

Accelerating molecular dynamics via Ewald summation with prolates.

The EXP C++ library is an efficient N-body simulation toolkit that implements basis-function methods using hybrid CPU and GPU code alongside Python bindings.

FIt-SNE is a fast t-SNE implementation for dimensionality reduction, scaling to ~1M points in minutes for high-dimensional data visualization.

Generates shareable interactive visualizations from Python using cloud-stored data and ReactJS plugins via figurl.org.

Efficiently computes 1D–3D nonuniform FFTs with CPU and GPU support, plus interfaces for C, Python, MATLAB, Julia, and more.

Fast multipole methods in two dimensions.

Computes fast 3D N-body interactions (Laplace/Helmholtz) using the fast multipole method with SIMD acceleration and multithreading.

FMM-accelerated boundary integral equation solver.

Uses tissue-specific gold standards to build functional gene networks, prioritizing relevant data and enabling cross-tissue gene interaction comparisons.

An Astropy-affiliated Python package for Galactic Dynamics, offering fast, user-friendly tools for orbit integration, gravitational modeling, coordinate transformations, and nonlinear dynamics analysis.

A variant of Clawpack for geophysical flows.

A Python library for fast Gaussian Process regression using hierarchical low-rank approximations for scalable, efficient computation.

Builds tissue-specific gene networks, enables cross-tissue functional comparison, and reprioritizes GWAS signals to identify disease-associated genes.

Uses machine learning on large genomic datasets to discover new biological gene associations beyond existing literature knowledge.

Analyzes experimental results using cross-species gene networks to reveal functions and guide new experiments identifying gene–pathway roles.

Clustering algorithm for unknown unimodal clusters using projection-based tests, handling non-Gaussian data, with efficient C++/MATLAB implementation.

Supports the productive development of robust and efficient software based on tensor networks.

A functional-programming-forward implementation of many features from the exoplanet and starry packages built on top of JAX.

A network for sharing scientific data, results, and live feeds via content-addressed URIs for reproducible, cross-machine and browser-based workflows.

Imputes missing microarray data using k-nearest neighbors, shown to perform well compared to other missing-value estimation methods.

A package for computing stellar spectra from 1D model atmospheres and linelists assuming local thermodynamic equilibrium.

C++ macromolecular modeling libraries aiming to replace Rosetta, leveraging modern CPUs/GPUs and quantum hardware for NP-hard optimization tasks.

Modules for Experiments in Stellar Astrophysics (MESA), originally developed over a decade by Bill Paxton with broad astrophysics community involvement, is now maintained by a global team and …

The missing package manager for MATLAB.

A spike sorting and scientific data analysis platform built around MountainSort, enabling processing, sharing, and visualization of neural data.

A C++ infrastructure for building scalable, biologically grounded microscale multibody dynamics software.

Performs in silico nano-dissection to identify cell-lineage–specific genes using functional genomics data from tissue samples.

A statistical modeling framework for systems neuroscience specializing in GPU-accelerated optimizations.

A tool for spike sorting and visualization of neural electrophysiology recordings.

Fast, accurate Lomb–Scargle periodogram for time-series analysis using FINUFFT; faster than Astropy, with GPU support and integration.

Detects exoplanet transits using linear models and Gaussian processes while modeling correlated stellar noise with JAX-based tinygp.