Data Science & ML Agent Skills

Reactome Database Integration

Integrates Reactome's curated pathway database into Claude for advanced systems biology research and gene enrichment analysis.

ETE Toolkit for Phylogenetics

Manipulates, analyzes, and visualizes phylogenetic and hierarchical trees for biological research and genomic data.

Scientific Data Visualization

Generates publication-quality scientific figures and multi-panel layouts compliant with major journal standards.

AlphaFold Database Access

Facilitates the retrieval and analysis of over 200 million AI-predicted protein structures from the AlphaFold DB for biological research and drug discovery.

Statsmodels Statistical Analysis

Performs rigorous statistical modeling, econometric analysis, and hypothesis testing using Python's statsmodels library.

Statistical Analysis Toolset

Performs comprehensive hypothesis testing, regression analysis, and Bayesian statistics with automated assumption checking and APA-style reporting.

Scientific Context Initialization

Configures workspace environments to automatically prioritize established scientific research patterns, database access protocols, and package usage guidelines.

Modernize Scientific Stack

Migrates legacy Python 2 scientific computing code to Python 3 using modern libraries like pandas, numpy, and pathlib.

NCBI GEO Database Explorer

Accesses and retrieves gene expression and functional genomics data from the NCBI Gene Expression Omnibus (GEO) repository.

LLM Inference Batching Scheduler

Optimizes LLM inference request grouping and scheduling to minimize operational costs while satisfying latency and padding constraints.

PyMC Bayesian Modeling

Builds and validates complex Bayesian models using PyMC's probabilistic programming framework.

ARC-AGI Git Merge & Pattern Tasks

Facilitates solving complex pattern recognition tasks by combining git workflow management with mathematical grid transformation analysis and implementation.

Raman Spectroscopy Peak Fitting

Analyzes and fits peaks in Raman spectroscopy data using physically-constrained models like Lorentzian, Gaussian, and Voigt functions.

Data Resharding and Partitioning

Reorganizes large-scale datasets into hierarchical directory structures while enforcing strict file size and item count constraints.

Transformers

Integrates state-of-the-art machine learning models for NLP, computer vision, and audio tasks using the Hugging Face ecosystem.

Torch Pipeline Parallelism

Implements PyTorch pipeline parallelism to distribute large language model training across multiple GPUs using All-Forward-All-Backward (AFAB) scheduling.

Protein Assembly

Designs and optimizes multi-component fusion protein sequences for FRET biosensors and gene synthesis.

Protein Assembly

Designs optimized DNA gBlock sequences for fusion proteins by combining sequences from multiple databases with precise linker and codon constraints.

Modernize Scientific Stack

Upgrades legacy Python 2 scientific computing code and analysis pipelines to modern Python 3 standards using contemporary libraries like NumPy and pandas.

PyTorch Model Recovery

Reconstructs PyTorch model architectures from saved state dictionaries, enables selective layer fine-tuning, and facilitates TorchScript conversion for deployment.

SAM Cell Segmentation

Implements SAM-based biological image segmentation pipelines, converting binary masks to polygon coordinates for microscopy data processing.

DNA Insert Primer Design

Designs specialized primers for inserting DNA sequences into circular plasmids using Q5 site-directed mutagenesis and inverse PCR techniques.

MTEB Retrieval and Ranking

Optimizes semantic similarity retrieval tasks through expert guidance on document preprocessing, embedding model selection, and similarity ranking.

Data Commons Client

Accesses global statistical data from the Data Commons knowledge graph to analyze demographics, economics, health, and environmental trends.

RStan to PyStan Translation

Translates Bayesian inference workflows and Stan model implementations from RStan to PyStan with high precision and numerical stability.

HuggingFace Model Inference

Deploys pre-trained HuggingFace Transformer models as robust REST API inference services using Flask or FastAPI.

Distribution Search

Finds probability distributions that satisfy specific statistical constraints like KL divergence targets through mathematical analysis and optimized parameterization.

ReLU Model Extraction

Extracts internal weight matrices and biases from black-box ReLU neural networks using input-output query strategies and functional equivalence testing.

Biopython for Bioinformatics

Streamlines computational molecular biology tasks including sequence manipulation, NCBI database queries, and structural analysis.

Economist Analyst

Analyzes market events and policy changes using rigorous economic frameworks and diverse schools of thought.