GPU CRF-CTC decoding for nanopore basecalling

Oxford Nanopore's Basecaller

C library for high-throughput sequencing data formats

Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

PyTorch tutorials.

The Triton Inference Server provides an optimized cloud and edge inferencing solution.

Reference CUDA implementation of training a small Bayesian neural network (BNN) using MCMC

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

Python mancala AI

A PyTorch Basecaller for Oxford Nanopore Reads

A simple C++11 Thread Pool implementation

De novo genome assembler for long uncorrected reads

Graph-based mapping of long sequences, noisy or HiFi.

NMF-mGPU web site:

A simulator-independent API for multi-compartmental modeling

Spell checker for the Maltese language

SDK for GPU accelerated genome assembly and analysis

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

Fast5 API provided by ONT Research

A simple example Python + CFFI package (including testing, development, and packaging)

This is a C++/OpenCL implementation of the PCISPH algorithm supplemented with a set of biomechanics related features applied to C. elegans locomotion

This package provides Python libNeuroML, for working with neuronal models specified in NeuroML

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

Package for fitting/optimization of NeuroML models

Online documentation for inspyred library

A Graphical User Interface with 3D Visualization features for NEURON simulation enviroment