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ESM Protein Modeling Toolkit

K-Dense-AI/scientific-agent-skills

Combines ESM3 and ESM C protein language models to generate sequences, predict structures, condition functions, and extract embeddings via local or Forge API inference for protein design and engineering workflows.

Phylogenetic Tree Toolkit

K-Dense-AI/scientific-agent-skills

A toolkit for phylogenetic tree manipulation, event detection, NCBI taxonomy integration, and publication-quality visualization, streamlining phylogenomics workflows and gene family analysis.

GeoPandas Spatial Toolkit

K-Dense-AI/scientific-agent-skills

GeoPandas extends pandas for geospatial vector data, enabling reading/writing shapefiles, GeoJSON, GeoPackage and PostGIS, performing CRS management, spatial joins, overlays, buffering, area/distance calculations, and producing static or interactive choropleth maps.

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.

Genomic Interval Toolkit

K-Dense-AI/scientific-agent-skills

High-performance Rust toolkit with Python bindings for genomic interval analysis, covering overlap detection, coverage track generation, ML tokenization, reference sequence handling, fragment processing, and scoring workflows for sequencing datasets.

MarkItDown File Converter

K-Dense-AI/scientific-agent-skills

MarkItDown converts PDFs, DOCX, PPTX, XLSX, HTML, JSON, XML, archives, YouTube links, images via OCR, and audio via transcription into clean Markdown, providing token-efficient text ready for LLMs and documentation workflows.

Medchem Filtering Toolkit

K-Dense-AI/scientific-agent-skills

Medchem Filtering Toolkit is a Python library offering drug-likeness heuristics, structural alert and PAINS filters, group detection, catalogs, and complexity scoring to triage compound libraries and prioritize leads in drug discovery 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.

Molecular Featurization Hub

K-Dense-AI/scientific-agent-skills

Molfeat is a Python toolkit that converts SMILES/RDKit molecules into embeddings via 100+ calculators, transformers, and pretrained models for QSAR, screening, similarity search, and deep learning pipelines.

Network Graph Toolkit

K-Dense-AI/scientific-agent-skills

Comprehensive Python toolkit for building, analyzing, and visualizing complex networks; supports algorithms, I/O, generation, and community detection across social, biological, transportation, and citation data.

NeuroKit2 Biosignal Processing

K-Dense-AI/scientific-agent-skills

NeuroKit2 is a Python biosignal processing toolkit for ECG, EEG, EDA, RSP, EMG, and EOG data that automates cleaning, feature extraction, and HRV/complexity analysis for psychophysiology, clinical, and HCI 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.

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