Skill rating

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embedding

Performs Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization experiments, cross-correlating

Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease context, and one- or two-hop paths. Use for PrimeKG r

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise mode

Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futures, chunking, schedulers, and distributed diagnostics. Use

Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion. Use for larger-than-RAM HDF5, Arrow, CSV, or Parquet

Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI

Writes scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas. Provides syntax references, document templates, accessibility guidance, and version-

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Supports DNAnexus data transfers, dxapp.json developmen

Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whene

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allomet

Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI. Supports recent recommendations, paper details, markdown-based summaries, r

Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON f

Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading, MIMIC-III/IV, eICU or OMOP prediction tasks, patient-l

Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference. Use

Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/acquisition checks, particle-stack consistency, gold-standard half sets, soft-mask va

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for vari

Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for quality review. Refines when the review requests improvement, with at most two gen

Conducts systematic, scoping, and narrative literature reviews using PubMed, arXiv, bioRxiv, Semantic Scholar, and other appropriate sources. Use for research synthesis, reproducible literature search

Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for explicit requests for DHDNA, cognitive-style reflection, a thinking-pattern profile,

Creates research posters in LaTeX using beamerposter, tikzposter, or baposter. Use for conference posters, academic presentations, multi-column scientific layouts, figure integration, typography, comp

Creates and reviews infographics with Nano Banana 2 via OpenRouter. Use for statistical summaries, timelines, comparisons, processes, and visual explanations with supplied data or optional Sonar resea

Creates and audits editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Used when the requested deliverable is a PowerPoint research/conference p

Converts heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, streams, Office/PDF/data format

Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts or composition recipes for review. Requires a rea

Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.

Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained encoder

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Ge

Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.

High-performance DataFrame library for Python ETL, analytics, and pandas migration. It supports expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-co

Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle scoring. Use whe

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard w

Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up,

Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation. Use when a task needs symbolic results,

Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model com

Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Supports aggregate or synthetic resea

Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifi

Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap

Prepares evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Supports authorized review of scientific manuscripts, protocols, preprints, or research proposals; rep

Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results. Applies to Adaptyv

Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded

Integrates with the official LabArchives ELN REST-like API and Inventory API v1. Supports regional endpoint selection, signed-request construction, user authorization and UID flows, local LA container

Performs zero-shot time-series forecasting with Google's TimesFM, including regular-grid CSV preparation, quantile forecasts, XReg covariates, and held-out evaluation. Uses the Apache-licensed TimesFM

Trains and evaluates single-agent reinforcement learning with Stable Baselines3 (PPO, SAC, DQN, TD3, DDPG, A2C), Gymnasium custom environments, vectorized rollouts, callbacks, and checkpoint normaliza

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds com

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection;

Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional checking, GUM uncertainty budgets, Type A

Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, C