N-D labeled arrays and datasets in Python
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47,133 repositories indexed
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Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
Multiphysics Object Oriented Simulation Environment: A robust, modern, extendable, finite element/finite volume framework that excels at creating complex multiphysics simulations.
- multiphysics
- simulation
- fem
- finite-elements
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
Lightweight, general, scalable C++ library for finite element methods
- finite-elements
- high-order
- high-performance-computing
- parallel-computing
Chai-1, SOTA model for biomolecular structure prediction
The repository host gives no description.
- foundation-model
- gpt
- single-cell
Primary repository for the Trilinos Project
- snl-science-libs
- sandia-national-laboratories
- hpsf
- scientific-computing
Python+Numpy+OpenGL: fast, scalable and beautiful scientific visualization
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
flybrainlabs authority nodes, complete simulation replay, archives, and service APIs.
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.
flybrainlabs native and WebAssembly simulation engines and browser mining.
:christmas_tree:Visualization and annotation of phylogenetic trees
- r
- visualization
- phylogenetic-trees
- annotations
QuadriFlow: A Scalable and Robust Method for Quadrangulation
- quadriflow
- quad
- remeshing
- quadrangulation
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Pathology Foundation Model - Nature Medicine
- foundation
- foundation-model
- histopathology
- mahmoodlab
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
Chebfun: numerical computing with functions.
Nonconvex embedded optimization: code generation for fast real-time optimization + ROS support
- embedded-optimization
- nonconvex
- model-predictive-control
- rust-library
Vision-Language Pathology Foundation Model - Nature Medicine
- bioimage-analysis
- bioimage-informatics
- conch
- foundation-model
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training