Theano was a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It is being continued as PyTensor: www.github.com/pymc-devs/pytensor
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🔩 Like builtins, but boltons. 250+ constructs, recipes, and snippets which extend (and rely on nothing but) the Python standard library. Nothing like Michael Bolton.
- python
- utilities
- cache
- data-structures
Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
g2o: A General Framework for Graph Optimization
- g2o
- slam
- c-plus-plus
- graph-optimization
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
LAPACK development repository
- linear-algebra
- lapack
- blas
- lapacke
Linear algebra, eigenvalues, FFT, Bessel, elliptic, orthogonal polys, geometry, NURBS, numerical quadrature, 3D transfinite interpolation, random numbers, Mersenne twister, probability distributions, optimisation, differential equations.
- scientific-computing
- linear-algebra
- differential-equations
- sparse-systems
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
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
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
Digital Signal Processing for Go
A header-only C++ library for large scale eigenvalue problems
- eigenvalues
- arpack
- linear-algebra
- spectra
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
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
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
The Chemistry Development Kit
- code4lib
- chemistry
- java
- cheminformatics
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
The open source air traffic simulator
- python
- traffic
- aircraft
- simulation
R package for detecting doublets in single-cell RNA sequencing data
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
Sequential regulatory activity predictions with deep convolutional neural networks.