Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
Repository Index
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CasADi is a symbolic framework for numeric optimization implementing automatic differentiation in forward and reverse modes on sparse matrix-valued computational graphs. It supports self-contained C-code generation and interfaces state-of-the-art codes such as SUNDIALS, IPOPT etc. It can be used from C++, Python, Matlab/Octave, Julia or Javascript
- optimization
- nonlinear
- derivatives
- code-generation
An implementation of chunked, compressed, N-dimensional arrays for Python.
- zarr
- ndimensional-arrays
- compressed
- python
SIMD-accelerated distances, dot products, matrix ops, geospatial & geometric kernels for 16 numeric types — from 6-bit floats to 64-bit complex — across x86, Arm, RISC-V, and WASM, with bindings for Python, Rust, C, C++, Swift, JS, and Go 📐
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
- diffusion-models
- docking
- binding
- computational-biology
Primary repository for the Trilinos Project
- snl-science-libs
- sandia-national-laboratories
- hpsf
- scientific-computing
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Numerical linear algebra software package
- linear-algebra
- hpc
- gpu-computing
- cuda
Generative biopolymer design with rich conditioning.
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
Advanced date, time and interval library for Java with sun/moon-astronomy and calendars like Chinese, Coptic, Ethiopian, French Republican, Hebrew, Hijri, Historic Christian, Indian National, Japanese, Julian, Korean, Minguo, Persian, Thai, Vietnamese
- java
- time4j
- calendar
- interval
The fastest automatic differentiation library for C++, with Python bindings. Forward, adjoint and higher-order derivatives, checkpointing, Eigen support and JIT. Reproducible benchmarks against CppAD, Adept and autodiff.
- automatic-differentiation
- aad
- algorithmic-differentiation
- autodiff
A simple script for fracturing polygons. Also adds nice helper functions for polygons like calculateArea, triangulate, getRandomPointsInPolygon, getBoundingRect)
- gdscript
- polygon2d-fracture
- godot-engine
- godot
Universal cheminformatics toolkit, utilities and database search tools
- indigo
- bingo
- cheminformatics
- chemistry
GraphDTA: Predicting drug-target binding affinity with graph neural networks
Source code for "DeepDTA: deep drug-target binding affinity prediction"
- protein-ligand-interactions
- convolutional-neural-networks
Ark -- Archetype-based Entity Component System (ECS) for Go.
- ecs
- entity-component-system
- go
- golang
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
- bioinformatics
- exact-optimization
- metabolomics
- paired-data
A simple cross platform .NET API for Intel MKL
- mkl
- cross-platform
- matrix
- linear-algebra
A framework for high-performance domain decomposition methods.
- c-plus-plus
- linear-algebra
- python
- fortran
Numpy-like library in swift. (Multi-dimensional Array, ndarray, matrix and vector library)
- swift
- math
- ndimensional-arrays
- ndarray
:pushpin: State of the art point location and neighbour finding algorithms for region quadtrees, in Go
- quadtree
- go
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
MAT is library for working with multi-dimensional arrays which supports efficient interfacing to foreign and CUDA code. BLAS and CUBLAS bindings are available.