Data & Analytics

Use for reverse engineering stripped Go and Rust binaries including runtime recognition, pclntab/moduel data recovery, panic strings, and idiomatic decompilation recovery.

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

Use at the start of computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training mode...

Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples...

Expert-thinking profile for Geographic Information Scientist (GIS) (geospatial data engineering / CRS & topology / spatial statistics & geostatistics / network & hydrologic analysis / web GIS (OGC, STAC)): Reasons from location, topology, scale, and positional uncertainty through PostGIS/GDAL pipelines, explicit EPSG/datum choices, kriging with cross-validated variograms, and ISO 19115/FGDC metadata while treating MAUP and ecological fallacy, Web Mercator area statistics, floating-point slive...

Expert-thinking profile for Geochemist (lab / field sampling / isotope & aqueous geochemistry / thermodynamic modeling): Reasons from Gibbs equilibria, mass and isotope balance, and fluid–rock interaction through stable (δ) and radiogenic (ε, isochron) systems, ICP-MS/LA-ICP-MS/TIMS/MC-ICP-MS/IRMS, PHREEQC/Perple_X phase modeling, and EarthChem/GeoReM workflows while treating alteration, matrix effects, Pb loss, mixing arrays, and...

Use when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

Expert-thinking profile for Galactic Astronomer (Galactic archaeology / survey astrometry / stellar populations / chemodynamics / orbit modeling): Reasons from distance ladders, dust extinction, and survey selection functions through Gaia DR3 cross-matches, isochrone and Bayesian SFH fitting (PARSEC/MIST, Starfish), and orbit integration in named potentials (McMillan17, MWPotential2015) via galpy, Agama, and Gala, while treating parallax-S/N and RUWE failures...

DDA/DIA mass-spectrometry proteomics workflows with FragPipe, MSFragger, IonQuant, DIA-NN, Pyteomics, pyopenms, matchms, polars, and query. Use when searching raw proteomics data, controlling peptide/protein FDR, parsing mzML/mzIdentML/mzTab/MGF, or prototyping downstream proteomics analysis in Python.

Expert-thinking profile for Food Microbiologist (QC lab / food safety / spoilage ecology / HACCP / method validation (ISO 16140, BAM)): Reasons from food as a hurdle- governed matrix of water activity, pH, and redox through BAM/ISO reference methods, c/n/m/M sampling plans, PMA-v-qPCR, and ComBase kinetics while treating VBNC and injured cells, post-process contamination, matrix inhibition, and unconfirmed PCR hits as first-class failure modes.

Expert-thinking profile for Fluid Mechanics Engineer (plant hydraulics / piping & pump systems / CFD verification): Reasons from Navier–Stokes reductions through Darcy–Weisbach/Crane TP-410 pipe networks, pump system curves, NPSH/affinity laws, HI turbomachinery selection, and ASME V&V 20 CFD validation when simulation supports design.

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. Use when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

Bulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.

DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

Expert-thinking profile for Deep Learning Scientist (computational / architecture & large-scale training): Reasons from CNN/Transformer inductive bias, Li et al. loss landscapes, grokking/mode connectivity, and Kaplan/Chinchilla scaling (~20 tokens/param); designs ResNet/ViT/DiT/MoE/FlashAttention stacks with FLOPs-matched ablations; trains AdamW+cosine/WSD via Megatron-FSDP/DeepSpeed; evaluates FID/MMLU- Pro/MMLU-CF with...

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

Expert-thinking profile for Data Scientist (computational / analytics, ML & experimentation): Reasons from CRISP-DM business estimands, leakage-safe sklearn Pipelines and nested CV, SQL/warehouse semantic metrics, A/B power and SRM/AA guardrails, causal DAG covariate discipline, and Model Cards/Datasheets while treating train-test leakage, Simpson's paradox, peeking, and PSI>0.25 drift as first-class failure...

Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.

Expert-thinking profile for Crystallographer (crystal growth / X-ray & neutron diffraction / phasing & refinement / structure validation / deposition (PDB, CSD/CCDC)): Reasons from reciprocal-space diffraction data, Bragg's law, and space- group symmetry through XDS/DIALS scaling, Phaser/SHELX phasing, Coot/Olex2 building, and MolProbity/checkCIF validation while treating merohedral twinning, wrong space groups, model-bias density unsupported by omit/polder maps, and R_free...

Expert-thinking profile for Crop Scientist (field trials / agronomy / crop physiology / G×E×M / MET stability analysis): Reasons from genotype-by-environment-by-management interaction, yield-component partitioning, and phenology-gated critical periods through MET stability analysis (AMMI, Finlay-Wilkinson, GGE biplots), mixed models (ASReml-R, lme4), N-response curves (quadratic-plateau, MRTN), and crop models (APSIM, DSSAT) while...

Expert-thinking profile for Critical Care Researcher (clinical / research): Reasons from acute physiology trajectories, modular organ dysfunction, and cluster-aware trial design through APACHE/SAPS/SOFA scoring, Berlin/Sepsis-3/KDIGO definitions, MIMIC-IV phenotyping, and target-trial emulation with clone-censor-weighting while treating immortal-time bias, cluster contamination, competing...

Expert-thinking profile for Computational Scientist (computational / dry / simulation, UQ, and reproducible workflows): Reasons from Roache code/solution verification and ASME V&V 10/20/40 credibility through MMS/GCI, UQ ensembles, and Snakemake/Nextflow/CWL pipelines with conda-lock/Apptainer provenance while treating environment drift, workflow cache staleness, and validation-vs-calibration conflation as first-class failure modes.