Scientific Agent Skills

Run computational biology tools for protein structure prediction, design, docking, and molecular dynamics on managed cloud GPUs via REST API or MCP server.

Analyze recent screen activity via a local screenpipe daemon, detect repeated research workflows, and draft new skills or composition recipes for uncovered patterns.

Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.

Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.

Process satellite imagery, perform GIS analysis, and apply spatial machine learning across 70+ geospatial topics with code examples in 8 programming languages.

Extends pandas for geospatial vector data analysis, including reading/writing shapefiles, GeoJSON, GeoPackage, and PostGIS, performing spatial joins, geometric operations, coordinate transformations, and creating static or interactive maps.

Automates hypothesis generation and testing on tabular datasets using LLMs, combining data-driven discovery with literature integration for scientific research.

Parse PDFs, Office files, and images locally with layout-preserved text, bounding boxes, OCR, and page screenshots for RAG and multimodal agents.

Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.

Train quantum circuits like neural networks with automatic differentiation, device-independent programming, and integration with PyTorch or JAX.

Train reinforcement learning agents at millions of steps per second using optimized PPO, vectorized environments, and multi-agent support.

Store, query, and export genomic variant data (VCF/BCF) using TileDB's sparse array technology for scalable population genomics workflows.

Build and train graph neural networks for drug discovery, protein modeling, and molecular science using PyTorch-native tools.

Manipulate phylogenetic trees, detect evolutionary events, integrate NCBI taxonomy, and create publication-quality visualizations using the ETE toolkit.

Search the web and extract content from URLs using Exa, with support for academic and scientific sources.

Convert files and office documents to Markdown using Microsoft's MarkItDown tool. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.

Create publication-quality static, animated, and interactive plots with fine-grained control over every element using Matplotlib's pyplot and object-oriented APIs.

Search and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents, clinical trial registries, and UniProt/PDB/ChEMBL entries with the Paperclip CLI from GXL. Covers installing and authenticating the `paperclip` binary with a PAPERCLIP_API_KEY, the read-only virtual filesystem under /papers, /fda, /trials, /proteins and /clipboard, source-scoped semantic search, corpus-wide grep, metadata lookup and SQL, map/reduce reading across many papers, figure vision analysis, opt-in paper repositories with claim verification, and line-pinned citations. Use when asked to install paperclip, run paperclip search/grep/map/reduce/sql/repo, find or read biomedical literature, regulatory filings or clinical trials through paperclip, or produce citations with line numbers.

Validates inputs, generates samplesheets and launch scripts, and optionally executes nf-core/pacsomatic matched tumor-normal workflows from BAM files, supporting local runs and scheduler submission (LSF/Slurm/PBS/SGE).

Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Fetch feeds, read papers, leave feedback, and export data using the pz CLI.

Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.

Control liquid handling robots, plate readers, pumps, and other lab equipment through a unified Python interface across platforms.

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.

Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Use when you need spatial gene expression in log1p-CPM for 224x224 tiles at about 20x, want to query protein-coding genes by symbol instead of a fixed panel, or want to run prediction across a whole slide after tiling with histolab.

Provides deep generative models for single-cell omics analysis, including probabilistic batch correction, transfer learning, differential expression, and multi-modal integration.

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.

Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.

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.

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.

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

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.

Use when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus, the Compass eight-task benchmark, or the `waypoint` CLI from the `waypoint-bio` package. Covers embedding microbiome samples, fine-tuning on taxonomic abundance data, benchmarking a checkpoint on Compass, pretraining a GPT-2 model on taxonomic abundance profiles, and converting MetaPhlAn, Kraken2, QIIME 2, or MGnify abundance tables into waypoint format.

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.

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when analysing concentration-time data, deriving exposure metrics, fitting PK or PD models, or evaluating dosing regimens. Triggers include "pharmacokinetics", "pharmacodynamics", "PK/PD", "NCA", "non-compartmental", "AUC", "Cmax", "lambda z", "half-life", "clearance", "volume of distribution", "compartmental model", "population PK", "popPK", "NONMEM", "nlmixr2", "Pharmpy", "Monolix", "exposure-response", "Emax", "EC50", "indirect response", "effect compartment", "TMDD", "PBPK", "bioequivalence", "RSABE", "ABEL", "allometric scaling", "first-in-human", "MABEL", "drug-drug interaction", "DDI", "ICH M12", "concentration-QTc", "therapeutic drug monitoring", "MIPD", and "dosing regimen".

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.