Lists (29)
Advancing Julia
Repos that advance Julia as a compelling scientific programming language.AI-Assisted Engineering
Programming will never be the same.Bioinformatics
"Bioinformatics is terrible. Everybody knows bioinformatics is terrible...it’s not a good situation that we’re in."Biology in the Frontend
Interactive simulations, visualizations, and demos served in the browser.Command-line Utilities
Future-facing command-line tools written in innovative languages or that raise the bar in some other way.Data Visualization
Know your data by seeing it.Design as Code
Functional Programming
Writing composable, refactorable, and robust code with an FP paradigmGenomic epidemiology🦠🧬
Get started in Bioinformatics
Looking for inspiration to get started with making sense of noisy biological data? These repos punch above their weight.GIS
Spatial statistics, cartography, and other spatially explicit methodsGleam is cool
Glimpses of Jai
Early looks at the Jai programming language, which remains in closed betaGo in Bioinformatics
Tools built in Go that can be interfaced with in the command line, or in Go source code.i use neovim, btw
we don't talk about vscode in this householdLearning Me a Haskell
Finally giving in and learning Haskell—I may never be the sameMetagenomics is hard :(
but fun?Python as a Glue Language
Python is beautiful...but slow. These tools help bring out its best side: as an elegant glue language connecting faster pieces of software.R in Science
"The best thing about R is it was designed by statisticians. The worst thing about R is it was designed by statisticians."Reading
Open-source books and docs distributed on GitHubRust in Bioinformatics (and Beyond!)
Tools built in Rust that can be interfaced with in the command line, or in Rust source code.Scientific Reproducibility
Tools that make doing reproducible science—a very difficult task!—easier.Simulation & Testing
Software for Biodiversity
Software developed to help understand and solve the biodiversity crisis and advance our understanding of ecology and evolution in general.Standards for Excellent Programs
TUIs
I love TUIs and I don't care who knows itTurns out your app is a database
Repos that are explicitly--or accidentally--database projects.TypeScript Eats the World
We all give into TypeScript eventually...Workflow Orchestration
Tools for deploying many steps of dataflow across a variety of infrastructuresStars
aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.
A library for efficient similarity search and clustering of dense vectors.
Parsing gigabytes of JSON per second : used by Facebook/Meta Velox, the Node.js runtime, ClickHouse, WatermelonDB, Apache Doris, Milvus, StarRocks
A focused launcher for your desktop — native, fast, extensible
lightweight, standalone C++ inference engine for Google's Gemma models.
Functional programming language for signal processing and sound synthesis
Compiler for multiple programming models (SYCL, C++ standard parallelism, HIP/CUDA) for CPUs and GPUs from all vendors: The independent, community-driven compiler for C++-based heterogeneous progra…
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
Python and C++ code for reading and writing genomics data.
Versatile open-source tool for microbiome analysis
Ultra-fast and memory-efficient (meta-)genome assembler
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Lower-latency OpenMP-style minimalistic scoped thread-pool designed for 'Fork-Join' parallelism in Rust and C++, avoiding memory allocations, mutexes, CAS-primitives, and false-sharing on the hot p…
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
De novo genome assembler for long uncorrected reads
Ultra-fast preprocessing and quality control for long-read sequencing data