Data Science & ML Agent Skills

DiffDock Molecular Docking

Predicts 3D binding poses for protein-ligand complexes using state-of-the-art diffusion-based deep learning.

Transformer Architecture Guide

Explains and implements core Transformer architecture components for LLM development, fine-tuning, and model analysis.

Adaptyv Protein Engineering

Facilitates automated protein testing and validation through cloud-based laboratory services and sequence optimization tools.

DeepChem Molecular Machine Learning

Streamlines molecular machine learning workflows for drug discovery, property prediction, and materials science using graph neural networks.

LLM Evaluation & Optimization

Evaluates LLM outputs and optimizes prompts using Evidently.ai metrics and LLM-as-a-judge patterns.

Adaptyv Protein Lab

Automates protein testing and validation workflows through cloud-based laboratory services and sequence optimization tools.

Gemini AI Integration

Integrates Google's Gemini AI models into Claude Code for advanced reasoning and multi-model code analysis.

Datamol Cheminformatics

Simplifies molecular cheminformatics and drug discovery workflows using a Pythonic interface for RDKit.

Parameter-Efficient Fine-Tuning (PEFT)

Optimizes LLM fine-tuning using LoRA, QLoRA, and Unsloth to drastically reduce memory requirements and accelerate training cycles.

Ollama Python Library

Provides a clean, Pythonic interface for interacting with Ollama to handle text generation, chat completions, and model management.

DeepChem Molecular ML

Applies advanced machine learning techniques to chemistry, biology, and materials science using the DeepChem library.

COBRApy Metabolic Modeling

Performs constraint-based reconstruction and analysis of metabolic models for systems biology and metabolic engineering.

Direct Preference Optimization (DPO)

Aligns AI models with human preferences using Direct Preference Optimization to improve reasoning and response quality without explicit reward models.

PyLabRobot

Automates laboratory workflows and controls liquid handling robots, plate readers, and other lab equipment using a hardware-agnostic Python SDK.

gget Bioinformatics Toolkit

Provides rapid, unified access to over 20 genomic and proteomic databases for sequence analysis and protein structure prediction.

Quantization & Model Optimization

Optimizes large language models for efficient inference and training using various precision types and memory estimation techniques.

Datamol Cheminformatics

Simplifies molecular cheminformatics workflows by providing a Pythonic wrapper around RDKit with sensible defaults and parallel processing.

NCBI Gene Database Integration

Queries the NCBI Gene database to retrieve comprehensive genetic information, sequences, and functional annotations via E-utilities and Datasets APIs.

Chroma Vector Database

Integrates ChromaDB capabilities for building AI applications with persistent memory and semantic search.

HMDB Metabolomics Database

Provides comprehensive access to the Human Metabolome Database (HMDB) for metabolite identification, chemical analysis, and clinical research.

LLM Supervised Fine-Tuning (SFT)

Streamlines the supervised fine-tuning of Large Language Models using Unsloth for optimized performance and reasoning model development.

LangChain Framework Support

Simplifies building LLM-powered applications by providing standardized abstractions for prompt engineering, model orchestration, and structured output parsing.

Data Visualization

Generates insightful, professional-grade charts and interactive dashboards using industry-standard libraries and design principles.

European Nucleotide Archive (ENA) Access

Accesses and retrieves genomic data, nucleotide sequences, and metadata from the European Nucleotide Archive (ENA) via REST APIs and FTP.

Cirq Quantum Computing

Builds, simulates, and optimizes quantum circuits for execution on leading quantum hardware and simulators.

ESM: Protein Modeling Toolkit

Provides a comprehensive toolkit for protein language models to design, predict, and analyze protein sequences and structures.

BioServices Bioinformatics Toolkit

Provides programmatic access to over 40 bioinformatics web services and databases for integrated biological data analysis.

Ollama Local LLM Manager

Manages local Ollama inference servers using Podman Quadlet to provide GPU-accelerated LLM capabilities.

Plotly Data Visualization

Generates interactive, publication-quality scientific and statistical visualizations for Python data analysis.

EdgarTools SEC Analysis

Accesses and analyzes real-time SEC filings and financial statements with token-efficient data retrieval.