stanfish06/skillquarium - Page 29

pandera-validation

DataFrame schema validation using pandera. Schema definitions, column checks, and decorator-based validation.

parallel-web

Search the web, extract URL content, enrich datasets, and run deep research using parallel-cli, prioritizing academic and scientific sources. Use for ANY web-related task: looking things up, fetching pages or academic PDFs, bulk data enrichment, and…

pathml

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For…

peer-review

Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.

pennylane

Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms…

pharmgx-reporter

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

phaser-2d-game

Implement 2D browser games with Phaser. Use when the user wants a Phaser, TypeScript, and Vite stack for scenes, gameplay systems, cameras, sprite animation, and DOM-overlay HUD patterns.

phylogenetics-builder

End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.

phylogenetics

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and…

plotly

Use when creating interactive Python visualizations with Plotly, including pan, zoom, hover charts, dashboard figures, interactive HTML output, or 3D plots. Trigger terms include plotly, interactive chart, interactive plot, dashboard chart, hover, and plotly…

plugin-eval

Help engineers evaluate a local skill or plugin, explain why it scored that way, show what to fix first, measure real token usage, benchmark starter scenarios, or decide what to run next. Use when the user says things like "evaluate this skill", "give me an…

pptx-posters

Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based…

pptx

Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.

pre-submission-reviewer

Runs a pre-submission review of a technical paper across five dimensions: macro logic, writing details, English grammar, LaTeX formatting, and figure quality. Uses a reviewer-style severity taxonomy (CRITICAL / MAJOR / MINOR) and flags banned AI-tone…

primekg

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

propose-security-hardening

Develop evidence-backed structural and architectural security hardening proposals from vulnerability disclosures, supplied findings, incident or assessment documents, source code, or a completed Codex Security scan. Use when a user asks for systemic…

proteomics

Mass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.

pubmed-summariser

Search PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language papers.

pufferlib-v2

PufferLib 2.x reinforcement learning workflows for the Dec 2024 API generation. Use when working with pufferlib>=2.0,<3.0, Puffer Ocean C environments, native PufferEnv/VecEnv-style vectorization, Gymnasium/PettingZoo compatibility wrappers, asynchronous…

pufferlib-v3

PufferLib 3.x reinforcement learning workflows for the Jun 2025 API generation. Use when working with pufferlib>=3.0,<4.0, the puffer CLI, pufferlib.pufferl training helpers, Ocean environments, PPO/PufferRL training, distributed torchrun runs, custom…

pybedtools

Python genomic interval arithmetic with BEDTools, complementing pysam, polars, and query for downstream tables. Use when intersecting, merging, subtracting, shuffling, finding closest features, computing coverage, or converting BED, GFF, GTF, VCF, BAM, and…

pyhealth

Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD…

pylabrobot

Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation.…

pymatgen

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

pymoo

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

pytdc

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

pytest

Testing Python code with pytest — fixtures, parametrization, markers, mocking, coverage, and configuration. Use when writing or running Python tests, setting up a test suite, debugging failing tests, adding fixtures or parametrized cases, measuring coverage,…

pytorch-lightning

Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP,…

query-stringdb

Query STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome. Triggers on "string", "protein interaction", "interaction network", "binding partners", "interactome", "PPI".

query-uniprot

Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".

qutip

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based…

ray

Distributed Python compute with Ray — @ray.remote tasks/actors for cluster-scale parallelism, Ray Data for large-batch preprocessing, Ray Train for distributed model training (DDP/FSDP/DeepSpeed), Ray Tune for scalable hyperparameter search, and Ray Serve for…

react-three-fiber-game

Build React-hosted 3D browser games with React Three Fiber. Use when the user wants pmndrs-based scene composition, shared React state, and 3D HUD integration inside a React app.

redesign-existing-projects

Upgrades existing websites and apps to premium quality. Audits current design, identifies generic AI patterns, and applies high-end design standards without breaking functionality. Works with any CSS framework or vanilla CSS.

report-template

Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.

research-grants

Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.

research-lookup

Look up current research information using parallel-cli search (primary, fast web search) or the Parallel Chat API (deep research). Automatically routes queries to the best backend. Use for finding papers, gathering research data, and verifying scientific…

scientific-critical-thinking

Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.

scientific-writing

Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure,…

scikit-image

A collection of algorithms for image processing in Python. Built on NumPy, SciPy, and Cython. It focuses on scientific image analysis including segmentation, geometric transformations, color space manipulation, analysis, and filtering.