All Skills

Perform nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows using the umap-learn library.

Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

Evaluate scientific manuscripts and grant proposals with structured, checklist-based peer review covering methodology, statistics, reproducibility, ethics, and reporting standards.

Fit statistical models (OLS, GLM, ARIMA, mixed models) with detailed diagnostics, residuals, and inference for econometrics and time series analysis.

Store and process large N-dimensional arrays with chunking, compression, and parallel I/O, integrating with NumPy, Dask, and Xarray for cloud-native scientific computing.

Generate publication-quality infographics using Nano Banana Pro AI with Gemini 3 Pro quality review and optional Perplexity Sonar research. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.

Search 10 academic literature APIs for papers, preprints, citations, and open-access full text with reproducible provenance.

Search the web, extract URL content, enrich datasets with web-sourced fields, and run deep research reports, prioritizing academic and scientific sources.

Create research posters using HTML/CSS that can be exported to PDF or PPTX, with AI-generated visual elements and responsive layouts.

Build and evaluate machine learning models using scikit-learn for classification, regression, clustering, dimensionality reduction, and preprocessing.

Load pre-trained models from Hugging Face Hub, run pipeline inference, generate text, and fine-tune models on NLP, vision, audio, and multimodal tasks using the Transformers library.

Query the U.S. Treasury Fiscal Data REST API for federal financial data including national debt, daily and monthly treasury statements, securities auctions, interest rates, exchange rates, savings bonds, and government revenue and spending statistics. No API key required.

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter with layout design, color schemes, multi-column formats, and figure integration.

Self-host an open-source research notebook with AI-powered note generation, multi-speaker podcast creation, and context-aware document chat, supporting 16+ AI providers.

Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.

Analyze any text to extract a cognitive fingerprint across 12 dimensions, revealing reasoning patterns, decision styles, and thinking signatures.

Generate and edit high-quality images using OpenRouter's AI models including FLUX.2 Pro and Gemini 3.1 Flash Image Preview.

Run structured What-If scenario analysis with 4-6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use for speculative questions about uncertain futures, strategic forks, contingency planning, or stress-testing decisions.

Query documented public database APIs with explicit endpoints, filters, pagination, and provenance for reproducible retrieval of scientific, regulatory, or financial facts.

Discovers and uses scientific datasets, models, blog posts, and interactive demos from a curated catalog for AI/ML work in domains like biology, chemistry, physics, and genomics.

Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC with agency-specific formatting, review criteria, budget preparation, and compliance guidance.

Look up current research and scientific information across three backends: fast web search, deep multi-source synthesis, and scholarly paper searches. Automatically routes each query to the best backend and saves every result for reproducible citation.

Perform survival analysis and time-to-event modeling in Python using scikit-survival, including Cox models, random survival forests, gradient boosting, survival SVMs, and evaluation metrics like concordance index and Brier score.

Build and train graph neural networks with PyTorch Geometric, covering node/link/graph classification, message passing layers, heterogeneous graphs, and custom datasets.

Generate concise (3-4 page) medical treatment plans in LaTeX/PDF format across all clinical specialties, with SMART goals, evidence-based interventions, and HIPAA compliance.

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues, academic conferences, research posters, and grant proposals.

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data, enabling efficient access to cell metadata, gene expression slices, summary counts, and embeddings without downloading whole datasets.

Generate comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports, clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries) with templates, regulatory compliance, and validation tools.

Submit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution, including protein expression, purification, quantification, RNA synthesis, and custom workflows via EstiMate.

Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.

GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, and other RAPIDS libraries for dramatic speedups on numerical, data, ML, graph, and simulation workloads.

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions.

Conduct systematic literature reviews by searching multiple academic databases, synthesizing findings, and generating professionally formatted documents with verified citations.

Access microscopy images and metadata via the OMERO Python API: retrieve datasets, analyze pixels, manage ROIs and annotations, and batch-process for high-content screening workflows.

Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), and distributed training (DDP, FSDP, DeepSpeed) for scalable neural network training.