Research

Expert-thinking profile for Astrobiologist (planetary science / field analogs / mission astrobiology / origins): Reasons from habitability, redox disequilibrium, and Bayesian biosignature frameworks through Mars (Perseverance, Viking perchlorate lessons), Europa Clipper ocean worlds, agnostic signatures and the Ladder of Life Detection, while treating abiotic mimics, preservation, and LUCA phylogenomics as constraints—not...

Ask which skill or flow fits your situation. A router over the skills in this repo.

Detect Neanderthal and Denisovan introgression segments from modern human genomes

Expert-thinking profile for Antimicrobial Resistance Scientist (wet-lab / WGS resistome / surveillance & One Health AMR): Reasons from MIC distributions, ECOFFs, and phenotype–genotype concordance through EUCAST/CLSI AST, CARD/RGI and AMRFinderPlus resistomes, GLASS/WHONET/NARMS surveillance, carbapenemase/ESBL/MRSA mechanism panels, and heteroresistance PAP while treating breakpoint mixing, genotype-without-phenotype overclaim...

Expert-thinking profile for Antenna Engineer (RF simulation / antenna design / measurement & OTA): Reasons from gain–directivity–efficiency, Chu–Harrington bandwidth limits, and array factor through HFSS/CST/FEKO synthesis, IEEE 149-2021 NF/FF/CATR metrology, CTIA TRP/TIS/ECC OTA, and Friis link budgets while treating ground-plane truncation, active impedance in arrays, range ripple, and S₁₁≠pattern conflation as...

Expert-thinking profile for Animal Scientist (feeding/management trials / ruminant & monogastric nutrition / ration formulation (CNCPS, NRC) / welfare & carcass science / mixed-model...): Reasons from NRC nutrient requirements, ad libitum intake, energy/protein partitioning, and genotype x environment x management through ration software (CNCPS, NDS, NRC), pen-blocked trials with mixed models (lme4, PROC MIXED), and BCS, NIR, and rumen/BHBA diagnostics while treating intake collapse, milk fat...

Expert-thinking profile for Animal Nutritionist (applied / monogastric & ruminant / feed evaluation & formulation): Reasons from NASEM/AAFCO requirements, SID amino acids and ideal protein, CNCPS MP/NE balance, and NANP feed libraries through NIR-wet chemistry validation, ileal vs fecal digestibility, pen-structured mixed models, and ARRIVE reporting while treating intake confounds, NIR calibration drift, acidosis/sorting, and...

Expert-thinking profile for Anatomist (comparative morphology / museum collections / dissection & imaging): Reasons from homology, EPB, and von Baer principles through gross dissection, diceCT/μCT/MRI pipelines, UBERON–PATO EQ annotation, MorphoSource/oVert digitization, geometric morphometrics, and NAV/TA2 nomenclature while treating fixation shrinkage, segmentation artifacts, landmark homology error, and collection bias...

Expert-thinking profile for Analytical Chemist (wet-lab / separation science / spectroscopy / method validation): Reasons from the chemical measurement process through ICH Q2(R2) and USP <621> validation, CRM traceability, EURACHEM uncertainty budgets, and HPLC/GC/LC-MS/ICP-MS workflows while treating matrix effects, SST drift, peak tailing, and ion suppression as first-class failure modes.

Expert-thinking profile for Algorithms Researcher (algorithm design & analysis / proofs & cost models / approximation & online / empirical algorithmics (DIMACS, MIPLIB)): Expert profile for algorithms researcher — see AGENTS.md for field-specific methods and failure modes.

Expert-thinking profile for Algebraist (pure math / structure & morphisms / homological & representation theory / computational algebra (GAP, Sage, Singular) / formal proof (Lean...): Reasons from carriers, operations, and morphisms through isomorphism theorems, universal properties, exact-sequence and homological tools (Ext, Tor, snake lemma), and computational systems like GAP, Magma, SageMath, and Lean while treating silently smuggled hypotheses (commutativity, units, Noetherian, algebraic...

Expert-thinking profile for Agroecologist (field ecology / soil health / participatory on-farm trials / landscape GIS / agroecology transitions (FAO 10 Elements)): Reasons from socio-ecological farm systems, functional diversity, soil-biology-mediated fertility, and yield-service trade-offs through mother-baby and mixed-model trials, N/P/C mass balances, PLFA/amplicon and pollinator surveys, and NDVI/FRAGSTATS landscape analysis, while treating edge-effect and plot-size...

Expert-thinking profile for Aeronomy Scientist (remote sensing / MLT-thermosphere- ionosphere / ISR + resonance lidar / tides & coupling / empirical models (IRI, NRLMSIS)): Reasons from MLT lidar and ISR profiles through IRI/NRLMSIS benchmarks, treating ion-line spectra, metal-layer winds, and storm-time TEC as distinct observables.

Expert-thinking profile for Aeronautical Engineer (fixed-wing aircraft design / certification / flight test): Reasons from airfoil polars, drag buckets, and static margin through AVL/DATCOM stability derivatives, wind-tunnel blockage and wall corrections, FAR 25 §25.101–25.207 compliance matrices, and AC 25-7 flight-test evidence—not generic aerospace or pure CFD aerodynamics.

Expert-thinking profile for Aerodynamicist (wind tunnel / CFD / flight vehicle external aerodynamics): Reasons from circulation, Cp distributions, and boundary-layer physics through Re/Mach similitude, NACA airfoil polars, stall classification, wind- tunnel blockage/wall corrections, and SA/SST/LES external-aero CFD—not generic mechanical engineering.

Expert-thinking profile for Acoustics Physicist (wave acoustics / ultrasonics & underwater / transducer & array / impedance tube & anechoic / standards (ISO 10534, IEC 61672)): Reasons from impedance Z=p/u, Helmholtz number kL regime, and the sonar equation SL-TL-NL+DI+PG through impedance tubes (ISO 10534), anechoic and reverberation rooms, laser vibrometry, and k-Wave/COMSOL simulation while treating edge diffraction inflating absorption above one, near-field versus far-field confusion...

Estimate event depth by optimizing a scalar scaling factor on the in-event segment that minimizes polynomial baseline residual across the full signal

Exclude bias terms and LayerNorm weights from weight decay to prevent regularization from distorting normalization layers

Enforce mandatory pre-action verification checkpoints to prevent pattern-matching from overriding explicit reasoning. Use this skill when about to execute implementation actions (Bash, Write, Edit) to verify hypothesis-action alignment. Blocks execution when hypothesis unverified or action targets different system than hypothesis identified. Critical for preventing cognitive dissonance where correct diagnosis leads to wrong implementation.

Use when the user explicitly asks Rewrite Room to route documentation work, or when audit/sync/freshness, user-facing authoring, citation-driven writing, docs-to-skill conversion, and AI-instruction optimization overlap and exactly one workflow must be chosen.

Use when the primary outcome is creating publishable source-attributed content from URLs or supplied material, including research summaries, articles, briefs, and posts whose factual claims and quotations need reader-visible, verifiable citations.

Route summarization requests to the correct methodology and enforce fidelity rules. Activates on summarize, tl;dr, give me the highlights, what's important in this, break down this, what does this code do, explain this file, describe this image, read and summarize. Routes files, URLs, images, and multi-source content to type-specific strategies. Enforces anti-hallucination rules — read before summarizing, extract before abstracting, preserve counts, distinguish absence from nonexistence, prev...

Rules for orchestrators handling sub-agent results without lossy re-summarization. Activates when receiving agent output, relaying research results, passing data between agents, or combining agent findings. Prevents the failure mode where 'not found' becomes 'doesn't exist' and counts get dropped.

Use when facing unknowns, debugging without a clear cause, or making architecture decisions — enforces hypothesis-driven scientific reasoning through observation, hypothesis formulation, prediction, experiment design, and evidence-based conclusion. Use when previous attempts have failed or the problem space involves uncertainty.