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Glycoengineering Toolkit

glycoengineering

K-Dense-AI/scientific-agent-skills

Analyzes protein sequences to locate canonical N-glycosylation sequons, predict O-glycosylation hotspots, and mutate or design glycosylation sites for therapeutic proteins, vaccines, and biosimilar comparisons using curated glycoengineering resources.

Automated Hypothesis Discovery

K-Dense-AI/scientific-agent-skills

Hypogenic automates LLM-driven hypothesis generation and testing over tabular datasets, blending literature insights with empirical analysis to accelerate discovery in domains like deception detection or AI content evaluation.

Scientific Hypothesis Formulation

hypothesis-generation

K-Dense-AI/scientific-agent-skills

Guides structured hypothesis generation by combining literature searches, evidence synthesis, competing explanations, and experimental design, with mandatory AI-generated scientific schematics for complete reports.

Codebase Gap Analysis and Validation

kiro-validate-gap

This skill analyzes the implementation gap by comparing approved feature requirements against the existing codebase, architecture, and context. It helps identify missing capabilities, potential integration challenges, and necessary technical research areas. The output provides multiple viable implementation options and a comprehensive analysis report, guiding the transition from requirements definition to technical design.

LabArchives API Workflow

labarchive-integration

K-Dense-AI/scientific-agent-skills

Integrates with the LabArchives ELN API to programmatically manage notebooks, entries, attachments, backups, reports, and third-party tools (Protocols.io, Jupyter, REDCap) for research workflow automation.

LaminDB Biological Data Platform

K-Dense-AI/scientific-agent-skills

LaminDB is a Python-driven open-source framework for managing biological datasets, ensuring traceable, reproducible, FAIR data through lineage tracking, schema validation, ontology annotation, workflow integration, and lakehouse-style querying.

Matplotlib Visualization Guide

K-Dense-AI/scientific-agent-skills

Guides using matplotlib to craft static, animated, and interactive plots through both pyplot and object-oriented APIs, detailing styling, subplots, and export options for publication-ready scientific workflows.

Molecular Dynamics Toolkit

molecular-dynamics

K-Dense-AI/scientific-agent-skills

Run OpenMM-powered molecular dynamics simulations and MDAnalysis trajectory workflows to build protein or small-molecule systems, minimize energy, equilibrate conditions, and characterize RMSD/RMSF, contacts, and free-energy surfaces for structural biology or drug studies.

Neuropixels Analysis Toolkit

neuropixels-analysis

K-Dense-AI/scientific-agent-skills

End-to-end Neuropixels recording analysis covering SpikeGLX/OpenEphys/NWB loading, preprocessing, motion correction, Kilosort4 sorting, quality metrics, Allen/IBL curation, and AI-assisted visualization for extracellular electrophysiology.

OMERO Microscopy Integration

omero-integration

K-Dense-AI/scientific-agent-skills

Manage microscopy data with the OMERO Python API: access projects/datasets/images, retrieve and analyze pixel data, handle ROIs and annotations, store results in tables, and automate batch workflows for high-content screening.

Open Notebook Research Hub

K-Dense-AI/scientific-agent-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.

Opentrons Protocol Integration

opentrons-integration

K-Dense-AI/scientific-agent-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.

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