Foundation Models for Genomics & Transcriptomics
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Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
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
:1234: Bits, bytes and general-purpose calculator
- storage
- storage-unit-converter
- command-line
- standalone
Official release of the ProGen models
- language-model
- protein
- generative-model
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
FiPy is a Finite Volume PDE solver written in Python
- scientific-computing
- scientific-computing-with-python
- phase-field
- materials-science
bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.
- huggingface
- bert
- chemical-modelling
- chemical-smiles-data
open source software for bidimensional and tridimensional remeshing
- mesh
- mesh-adaptation
- anisotropic-mesh-adaptation
- isotropic-mesh-adaptation
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
Tools for computational pathology
- machine-learning
- digital-pathology
- computational-pathology
- biomedical-image-processing
Python-centric Cookiecutter for Molecular Computational Chemistry Packages
- cookiecutter
- python-packages
- molecular-sciences
- conda-environment
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Benchmarking analysis of data integration tools
PyKEP is a scientific library providing basic tools for research in interplanetary trajectory design.
- interplanetary
- mission-analysis
- astrodynamics
- aerospace
Iterative Linear Quadratic Regulator with auto-differentiatiable dynamics models
- trajectory-optimization
- differential-dynamic-programming
- theano
- dynamics-models
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
JavaScript helper functions for manipulating GeoJSON
Encapsulate measurements and their units in Ruby and Ruby on Rails.
The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)
- ai-for-science
- diffusion-models
- drug-design
- equivariant-networks
Solve automatic numerical differentiation problems in one or more variables.
Fundamentals 5 Code Library for FreePascal and Delphi