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Open Notebook Research Hub

K-Dense-AI/claude-scientific-skills

Self-hosted open-source alternative to NotebookLM for organizing research, ingesting diverse sources, generating AI notes, running context-aware chats, performing vector search, producing multi-speaker podcasts, and automating workflows via a REST API.

OpenAlex Research Explorer

openalex-database

K-Dense-AI/claude-scientific-skills

Use the OpenAlex client to query 240M+ scholarly works for literature searches, citation tracking, open access discovery, and bibliometric studies across papers, authors, and institutions.

Open Targets Explorer API

opentargets-database

K-Dense-AI/claude-scientific-skills

Provides GraphQL queries to the Open Targets Platform for target-disease associations, tractability, safety, drugs, and multi-omics evidence to guide therapeutic target identification, safety assessment, and repurposing research workflows.

Opentrons Protocol Integration

opentrons-integration

K-Dense-AI/claude-scientific-skills

Provides the official Opentrons Protocol API v2 integration for OT-2 and Flex robots, enabling Python-based automation of liquid handling, module control, labware setup, pipetting flows, and protocol testing before execution.

Academic Paper Transformations

K-Dense-AI/claude-scientific-skills

Transforms LaTeX or PDF papers into interactive websites, narrated videos, and print-ready posters via the Paper2All pipeline, ideal for conference preparation, research promotion, and explorable academic showcases.

PathML Computational Pathology Toolkit

K-Dense-AI/claude-scientific-skills

PathML is a Python toolkit for computational pathology workflows, loading 160+ slide formats, preprocessing H&E images, constructing spatial graphs, training HoVer-Net/HACTNet models, and analyzing multiplex imaging for ML-ready pathology data.

PDB Structure Explorer

K-Dense-AI/claude-scientific-skills

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

Scientific Peer Review Checklist

K-Dense-AI/claude-scientific-skills

Structured manuscript and grant review guidance that walks reviewers through methodology, statistics, reporting compliance, and constructive feedback for rigorous scientific evaluation across disciplines.

Hardware-Agnostic Quantum ML

K-Dense-AI/claude-scientific-skills

Hardware-agnostic quantum ML framework enabling gradient-based training of quantum circuits, hybrid quantum-classical models, and seamless integration with PyTorch/JAX/TensorFlow alongside device portability across IBM/Google/Rigetti/IonQ.

Perplexity Web Search

perplexity-search

K-Dense-AI/claude-scientific-skills

AI-powered search using Perplexity models via LiteLLM and a single OpenRouter API key for real-time, web-grounded answers with citations, ideal for up-to-date research, literature surveys, fact checking, and domain-specific queries beyond model cutoffs.

Plotly Interactive Charts

K-Dense-AI/claude-scientific-skills

Plotly is a Python graphing library for interactive, publication-quality visuals that bring hover, zoom, animation, and dashboard-ready exports to exploratory analysis and presentations.

Polars Fast DataFrame

K-Dense-AI/claude-scientific-skills

Polars is a blazing fast in-memory DataFrame library based on Apache Arrow that replaces pandas for 1-100GB workloads, offering expression-based lazy execution, parallel operators, and rich I/O for ETL pipelines.

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