Repository Index

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

a lean linear math library, aimed at graphics programming. Supports vec3, vec4, mat4x4 and quaternions

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

WebGL accelerated JavaScript molecular graphics library

• molecular-graphics
• molecular-modeling
• computational-biology
• computational-chemistry

Geometry, simplified.

• swift
• geometry
• trigonometry
• coregraphics

This rocq library aims to formalize a substantial body of mathematics using the univalent point of view.

• coq
• mathematics
• unimath
• coq-library

A coupling library and ecosystem for partitioned multi-physics and multi-scale simulations, including surface and volume coupling.

• multi-physics
• fluid-structure-interaction
• high-performance-computing
• conjugate-heat-transfer

:spider_web: Gmsh for Python

• python
• pypi
• mesh-generation
• engineering

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

C library for high-throughput sequencing data formats

• htslib
• bioinformatics
• sam
• bam

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

:four_leaf_clover: Evolutionary optimization library for Go (genetic algorithm, partical swarm optimization, differential evolution)

• go
• optimization
• parallel
• machine-learning

Parallel solvers for sparse linear systems featuring multigrid methods.

• math-physics
• library
• hpc
• radiuss

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

Open-source cross-platform symbolic algebra library for C# and F#. Can be used for both production and research purposes.

• csharp
• algebra
• integration
• latex

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

• foundation-models
• genomics
• language-models

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter

:triangular_ruler: Numerical integration (quadrature, cubature) in Python

• quadrature
• integration
• mathematics
• engineering

Throw in the towel.

• dotnet
• towel
• csharp
• library

An open library for the analysis of molecular dynamics trajectories

• molecular-dynamics
• python
• mdtraj
• rmsd

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology

A flexible framework for solving PDEs with modern spectral methods.

• spectral-methods
• fluid-dynamics
• pde-solver

RBDL is a C++ library that contains some essential and efficient rigid body dynamics algorithms such as the Articulated Body Algorithm (ABA) for forward dynamics, Recursive Newton-Euler Algorithm (RNEA) for inverse dynamics, the Composite Rigid Body Algorithm (CRBA) for the efficient computation of the joint space inertia matrix and is also able to compute forward dynamics with external contact constraints and collision impulses. Furthermore it has some basic support for forward and inverse kinematics.

• articulated-body-algorithm
• inverse-dynamics
• forward-dynamics
• multi-body-dynamics