Yaroslav Halchenko

No description.

Helper to setup and run various checks (like codespell or shellcheck) for a github project

Resume/CV. Rendered version is available from http://www.oneukrainian.com/resume/halchenko_vita.pdf

A bidirectional Git - Bazaar gateway

Debian development activity IRC bot

No description.

A Git extension for tracking the AI-generated code in your repos

A complete AI agency at your fingertips - From frontend wizards to Reddit community ninjas, from whimsy injectors to reality checkers. Each agent is a specialized expert with personality, processes, and proven deliverables.

Skill to give Claude Code (and any coding agent) the ability to generate beautiful and practical Excalidraw diagrams.

CiTO, the Citation Typing Ontology, is an ontology for the characterization of citations, both factually and rhetorically. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies.

Convert PDF to markdown + JSON quickly with high accuracy

Self-hosted outdoor activity tracker :bicyclist:

Face recognition with deep neural networks.

Behavioral Observation Research Interactive Software

Firmware and Hardware for the EweGo project

No description.

ClaimBound: open pre-registered public-source evidence cards for reproducible AI/ML/Data claim checks.

🔮 A bot to automatically update and merge GitHub PRs

A markup-based typesetting system that is powerful and easy to learn.

Repo for Better Code, Better Science book

Python repo for Better Code, Better Science

No description.

Best Practices for data packages. a gh-pages website, with sections for metadata concepts and aspects of data packaging

Keep scientific data under control by git and git-annex

The agent that grows with you

Open source framework for pulse sequences

Lore is a next-generation, open source version control system

One principle of BIDS is filename distinctness. Here the tool asks : what is the minimal information needed to distinguish files? this means, no ses- or run- if not needed, possibly limit acq- and dir- as well, etc

🏆Open Source Security Foundation (OpenSSF) Best Practices Badge (formerly Core Infrastructure Initiative (CII) Best Practices Badge)

PETPrep: A Robust Preprocessing Pipeline for PET Data

No description.

science-on-schema.org - providing guidance for publishing schema.org as JSON-LD for the sciences

The Meta-Species Oriented Biosystem Syntax in Python (MobsPy) was invented to facilitate the design of complex Chemical Reaction Networks

Open, self-hostable organization-of-record for AI agents — the accountable layer above any framework. Autonomy is earned, not assumed.

No description.

Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

No description.

Python implementation of the TRX file format

An implementation of several well-known dynamic Functional Connectivity assessment methods.

This is a collection of various Pulseq tutorials, which is supposed to grow in future

Podman: A tool for managing OCI containers and pods.

A tool that facilitates building OCI images.

👋 A set of useful tools for installing and running Postal.

📮 A fully featured open source mail delivery platform for incoming & outgoing e-mail

A non-official clone of git-annex established for DataLad purposes. No PRs will be merged, but could be used to test perspective git-annex patches. Official git-annex repository: https://git.kitenet.net/index.cgi/git-annex.git/

GUI and CLI tool for raw-to-BIDS conversion, curation, metadata editing, and validation for MRI, EEG, MEG, and physiological recordings.

Technology Compatibility Toolkit for the .ozx format (OME-Zarr RFC-9)

No description.

An open-source handbook of applied guidance and tools for sustainable software development and maintenance.

Rust tools for BIDS (Brain Imaging Data Structure) datasets

Rust validator for the Brain Imaging Data Structure

A BIDS tool for creating PDFs containing slices of nifti images

Data-Centric Pipelines and Data Versioning

Repository for documentation to support the IEEE 2791-2020 standard. Please see our home page for communications/publications:

Quantitative pediatric MRI re-analysis pipeline for research and education. Not for clinical use.

KGRAG - KnowledgeGraph RAG

Interactive Tables and Data Grids for JavaScript

Gnome Extension for getting windows list in wayland

Fast, secure, efficient backup program

Unbearably fast near-real-time pure-Python runtime-static type-checker.

UnitRefine is a machine-learning toolbox that simplifies spike sorting curation by reducing manual curation.

Agentic Development Environment (ADE) for teams using multiple coding agents

covenant.yml is a deterministic, machine-readable specification that defines the rules of engagement between human contributors and autonomous agents within a repository.

ShEx interpreter for ShEx 2.0

Exca - Execution and caching tool for python

Python wheel sources for git-annex

Python JSON5 parser with round-trip preservation of comments

This is a mirror of https://codeberg.org/fsfe/reuse-tool

track file provenance in Python workflows using RDF and PROV

Bash and Python wrappers for SLURM that streamline HPC job submission, AWS S3 data transfers, and disk-based workflows; adaptable to any SLURM-based pipeline.

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Python suite for neuroscience research across all modalities.

FAIRsFAIR Research Data Object Assessment Service

YAML template engine

Imaging_PHD website

PRISM is an independent, BIDS-compatible framework and toolkit designed to enrich standard BIDS datasets with psychological and physiological metadata.

A JSON schema linter built for some specific purposes at Giant Swarm

No description.

A directory with the entire collection of dcm_qa repositories

The Realtime fMRI Cloud Framework is an open-source software package that makes it easier to build and deploy real-time fMRI experiments.

📚 Import Bibtex publications and Jupyter Notebook blog posts into your Markdown website or book. 将Bibtex转换为Markdown网站

A simple Python wrapper for Slurm with flexibility in mind.

Python 3.8+ toolbox for submitting jobs to Slurm

Security Scanner for Agent Skills

No description.

No description.

A conda-forge distribution.

Ephemeral Freestyle VMs + Playwright MCP for Assrt browser testing

A Claude Code plugin for detecting and eliminating code duplication using jscpd

Copy/paste detector for programming source code.

A generic framework for building AI-powered scientific data analysis agents.

Goose is a developer agent that operates from your command line to help you do the boring stuff.

Dark Data Discovery for Neuro Datasets

A general purpose scientific writer

A set of ready to use Agent Skills for research, science, engineering, analysis, finance and writing.

An agentic Machine Learning Engineer

OHBM BrainHack 2026

Unified neuroscience data schema integration platform

The fastest repo in history to surpass 50K stars ⭐, reaching the milestone in just 2 hours after publication. Better Harness Tools that make real things done. Now writing in Rust using oh-my-codex.

🐶 Automated code review tool integrated with any code analysis tools regardless of programming language

The open-source Git-native toolkit for CS education, built by educators and students!

Python 2.x/3.x bindings for libfuse 2.x

The Single Sign-On Multi-Factor portal for web apps, now OpenID Certified™

One-line install streaming server, terminal monitor, and browser dashboard for the PiEEG shields.

Claude Code as one-shot MCP server to have an agent in your agent.

Python 3 bindings for libfuse 3 with asynchronous API (Trio compatible)

Finally, a JSONPath implementation for Python that aims to be standard compliant. That's all. Enjoy!

Sourcebot is a self-hosted tool that helps developers and agents understand your codebase.

CLI tool for managing Nebari cloud infrastructure using OpenTofu, ArgoCD, and GitOps

No description.

Type-safe, distributed orchestration of agents, ML pipelines, and real-time inference — in pure Python with async/await.

Pythonic bindings for FFmpeg's libraries.

No description.

An autonomous semi-secret multi-agent research lab for acoustic physics, complex knowledge synthesis, and recursive reasoning

AI agents running research on single-GPU nanochat training automatically

GrimoireLab: platform for software development analytics and insights

Reproducing encoding models published by Lebel et al. 2023

Apache DevLake is an open-source dev data platform to ingest, analyze, and visualize the fragmented data from DevOps tools, extracting insights for engineering excellence, developer experience, and community growth.

Local support for Tuya devices in Home Assistant

Machine Learning Systems

RamaLama is an open-source developer tool that simplifies the local serving of AI models from any source and facilitates their use for inference in production, all through the familiar language of containers.

Virtual whiteboard for sketching hand-drawn like diagrams

Packer templates for building minimal Vagrant baseboxes for multiple platforms

Static low-bandwidth search at scale

Command line driven CI frontend and development task automation tool.

Keep track of you codex sessions per commit

Next generation frontend tooling. It's fast!

React Flow | Svelte Flow - Powerful open source libraries for building node-based UIs with React (https://reactflow.dev) or Svelte (https://svelteflow.dev). Ready out-of-the-box and infinitely customizable.

Ralph is an autonomous AI agent loop that runs repeatedly until all PRD items are complete.

sugar for s3

File-like object from url of remote file, optimized for use with h5py.

Lint your Python architecture.

No description.

Outcome driven agent development framework that evolves

PubPub: Open publishing

Process long and prosper

Provenance/Replay OBservation Engine: record what your processes are doing and replay it later

An orchestration platform for the development, production, and observation of data assets.

Pluggable sample-level metadata versioning for incremental multimodal pipelines.

Entire is a new developer platform that hooks into your git workflow to capture AI agent sessions on every push, unifying your code with its context and reasoning.

Archive Matrix room messages

💬 Fast, cross-platform CLI and GUI for batch transcription, translation, speaker annotation and subtitle generation using OpenAI’s Whisper on CPU, Nvidia GPU and Apple MLX.

Repository for TabICLv2: A state-of-the-art tabular foundation model

An AI-powered security review GitHub Action using Claude to analyze code changes for security vulnerabilities.

Kosmos: An AI Scientist for Autonomous Discovery - An implementation and adaptation to be driven by Claude Code or API - Based on the Kosmos AI Paper - https://arxiv.org/abs/2511.02824

NWB extension to store data from human wearables

Communicate with an LLM provider using a single interface

Pythonic task management & command execution.

Open Science Assistant - An extensible AI assistant platform for open science projects

Spec-driven development (SDD) for AI coding assistants.

This repository includes the official implementation of OpenScholar: Synthesizing Scientific Literature with Retrieval-augmented LMs.

Point at any URL/YouTube/Podcast or file. Get the gist. CLI and Chrome Extension.

"🐈 nanobot: The Ultra-Lightweight Clawdbot"

DeepAnalyze is the first agentic LLM for autonomous data science. 🎈你的AI数据分析师，自动分析大量数据，一键生成专业分析报告！

Mermaid diagrams in yours sphinx powered docs

Own your Telegram history. Automated, incremental backups with a local web viewer that feels just like the real app. Docker-ready and supports public chat sharing

Near Duplicate Video Detection (Perceptual Video Hashing) - Get a 64-bit comparable hash-value for any video.

a ✨special ✨ repository about myself

No description.

LLM-Assisted Development (LAD): Copilot + Claude Agent prompts & workflow for iterative Python feature implementation

Time command execution over multiple executions

Your own personal AI assistant. Any OS. Any Platform. The lobster way. 🦞

SpecStory's Open Source Documentation

GhostFS CC

The open source coding agent.

RAG based LLM chatbot to explore ABCD data dictionary

NBDCtools data package

Biomni: a general-purpose biomedical AI agent

A machine learning software for extracting information from scholarly documents

Switch between Claude accounts, Gemini, Copilot, OpenRouter (300+ models) via CLIProxyAPI OAuth proxy. Visual dashboard, remote proxy support, WebSearch fallback. Zero-config to production-ready.

No description.

MacOS inside a Docker container.

Windows inside a Docker container.

Tree for Unix/LInux

A registry of publicly available datasets on AWS

HED Language Server Protocol extension for VS Code

Generate Podman Quadlet files from a Podman command, compose file, or existing object

Interact with your documents using the power of GPT, 100% privately, no data leaks

A powerful Zotero AI and MCP plugin with ChatGPT, Gemini 3, Claude, Grok, DeepSeek, OpenRouter, Kimi, GLM, SiliconFlow, GPT-oss, Gemma 3, Qwen 3

GPT Meet Zotero.

Core repository for the EMBER ARCHIVE

Python script for batch downloading Google Takeout files with support for continuation, configurable delays, and progress tracking. Handles split archives up preserves Google's filename format. Built for WSL/Ubuntu environments.

🍃 JavaScript library for mobile-friendly interactive maps 🇺🇦

Video-based AI memory library. Store millions of text chunks in MP4 files with lightning-fast semantic search. No database needed.

Multi-Agent System for HED Annotation Generation

OpenSCAD - The Programmers Solid 3D CAD Modeller

WebRTC/RTSP/RTMP/LL-HLS bridge for Wyze cams in a docker container

HMTL & Javascript for the front end for the SNOMED CT Browser.

GitHub notifications on your menu bar. Available on macOS, Windows & Linux.

Jupyter notebooks for ipyniivue

In-browser Streamlit 🎈🚀

The swiss army knife of lossless video/audio editing

🦉 Data Versioning and ML Experiments

Central coordination and documentation for the Annotation Garden Initiative

Web-based annotation tool for static images in the Annotation Garden ecosystem

GUI for spikeinterface objects

SimpleFIN standard and website

Beancount: Double-Entry Accounting from Text Files.

A local-first personal finance app

No description.