This repository is a curated collection of 177+ domain-specific scientific 'skills' for AI agents, following the Agent Skills standard. Each skill is a self-contained module providing a CLI tool, documentation, and tests for a specific scientific or technical task—ranging from single-cell RNA-seq analysis (scanpy) and molecular docking (diffdock) to clinical report validation and ISO standards readiness. The architecture is a monorepo of independent skills, each with its own scripts/, references/, assets/, and tests/. Skills are designed to be safe, bounded, and reproducible: they validate inputs before execution, enforce resource limits, avoid network access unless explicitly required, and produce structured JSON reports. The repository also includes a shared test infrastructure (skill_contract) and a meta-skill (autoskill) that can automatically propose new skills from screen activity. While primarily an application library for AI agents, it has strong data/research characteristics due to its heavy use of scientific data formats and validation of research artifacts.
BoltzGen is a deep learning pipeline for computational protein and peptide binder design. It provides a command-line interface (boltzgen) that orchestrates a multi-step workflow: diffusion-based backbone generation, inverse folding (sequence design given structure), folding with Boltz-2, affinity prediction, analysis, and filtering/ranking of designs. The system supports diverse protocols including protein, peptide, nanobody, antibody, and small-molecule targeting, with extensive conditioning options like binding sites, disulfide bonds, cyclization, and per-residue constraints. The codebase is structured as a Python package with modular components for data parsing (YAML design specs, mmCIF/PDB), featurization, tokenization, cropping, and model layers (pairformer, attention, diffusion, inverse folding). It includes training pipelines with Hydra configuration, PyTorch Lightning, and validation splits. While primarily an application, it also contains research-grade example datasets and a Jupyter notebook for filtering, reflecting its origin in a bioRxiv publication. The architecture is well-organized but shows some technical drift (hardcoded paths, print statements, broad exception handling) and dependency on specific CUDA versions.
This repository is a curated, comprehensive list of academic papers on the application of deep learning to protein design. It is not a software application or a data pipeline; rather, it is a living bibliography organized by research area (e.g., inverse folding, diffusion-based design, language models, antibody design). The README.md file contains hundreds of paper entries with links to publications, code repositories, and supplementary materials, updated frequently (last update shown as 2026.08.02). There is no executable code, no datasets, and no computational workflows. The value lies in its role as a reference index for researchers and practitioners tracking the rapidly evolving field of AI-driven protein design.
This repository is a curated markdown list of links to free online video courses in computer science and related fields. It contains no source code, no data pipelines, no applications, and no tests. The entire substantive content resides in README.md, which organizes hundreds of video links under topical headings such as algorithms, machine learning, operating systems, and computer vision. CONTRIBUTING.md and NOTES.md provide brief guidelines explaining the philosophy of the list (concise, link-centric, no course descriptions) and contribution rules. The repository functions as a community-maintained directory or bookmark collection rather than as a software project or data research repository. While it has high star and fork counts, the code base is nonexistent; the only files of significance are three markdown documents. The last commit was in June 2026, but the list nature means that link rot is likely over time, and there is no automated validation of links.