Results for “simulation”

Use when the user wants all 16 personality types (16-minds plugin) to vote on a proposal — yes/no/abstain — to see stakeholder distribution, detect hidden objections, or simulate organizational consensus. Triggers on Japanese phrases like 「全人格で投票」「16人格に賛否を聞いて」「ステークホルダーシミュ」「これ通せそう？」, English equivalents like "vote with all 16 minds" / "stakeholder simulation", or `--vote` flag on 16-minds commands. Different from /minds (which is for opinion divergence) — this is for binary judgment aggregation.

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Pass-the-Ticket (PtT) is a lateral movement technique that uses stolen Kerberos tickets (TGT or TGS) to authenticate to services without knowing the user's password. By extracting Kerberos tickets fro

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Simulates man-in-the-middle attacks using Ettercap, mitmproxy, and Bettercap in authorized environments to intercept, analyze, and modify network traffic for testing encryption enforcement, certificate validation, and detection capabilities.

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Build and configure a resilient command-and-control infrastructure using BishopFox's Sliver C2 framework with redirectors, HTTPS listeners, and multi-operator support for authorized red team engagements.

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High-performance numerical and quantum compute skill for scientific workloads; use when working on numeric algorithms, simulation, or acceleration.

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Simulate wave propagation — acoustic, electromagnetic, elastic, and quantum waves. FDTD, spectral methods, and absorbing boundary conditions for 1D/2D/3D wave equations with sources, scattering, and dispersion.

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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 modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

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Monte Carlo simulation for statistical mechanics — Ising model, Metropolis-Hastings, Wolff cluster algorithm, observables (magnetization, susceptibility, specific heat), finite-size scaling, and critical phenomena analysis.

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IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

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Nonlinear curve fitting for physics data with proper error propagation, chi-squared analysis, residual diagnostics, confidence intervals, and model comparison (AIC/BIC). Use for any parameter extraction from experimental or simulation data.

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Solve partial differential equations — finite differences, spectral methods, and physics-informed neural networks (PINNs via DeepXDE). Supports 1D/2D/3D, steady/transient, linear/nonlinear PDEs with Dirichlet, Neumann, and periodic boundary conditions.

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Solve ordinary differential equations (initial and boundary value problems). Supports stiff/non-stiff systems, event detection, Hamiltonian/symplectic integration, parameter sweeps, and phase space analysis. Use for any ODE system in physics, engineering, or applied math.

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Patterns for loading PDE simulation datasets (PDEBench, PhiFlow, JAX-CFD) from HDF5 files. Handles layout detection (single tensor vs separate variables), spatial/temporal downsampling, multi-variable systems, HuggingFace and DaRUS data sources, and efficient PyTorch DataLoader creation. Use when preparing PDE data for neural operator training.

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End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation. Supports RNA-only (pySCENIC) and multiome (SCENIC+) paths. Use when building gene regulatory networks from single-cell transcriptomic or multiome data.

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Stellar dApp / frontend development. Covers the JavaScript stellar-sdk (browser + Node.js), Freighter wallet, Stellar Wallets Kit (multi-wallet), Wallet Standard, smart accounts with passkeys, transaction building / signing / submission, smart contract invocation from the client, simulation, and error handling. Use when building a React/Next.js/Node.js app that talks to Stellar — classic operations or smart contracts.

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Plan purple-team / adversary-simulation exercises against systems you are contracted to test. High-level objectives and detection gaps only. No live attack procedures or payloads.

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.

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Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

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Track and report progress of a request to create and run an EcoSIM case for a site ("create an ecosim run for site US-UMB", "set up and run EcoSIM at <site>"). Records four stages — data preparation, namelist creation, model simulation, and output evaluation — in result/<SITE_ID>/progress.json and PROGRESS.md, derives step status from files and quality reports on disk, and records manual results such as the executable, test run, and evaluation verdicts. Use at the start of such a request, after each stage, and whenever the user asks where a site run stands.

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Inventory staged local EcoSIM data at project startup and validate input readiness for a selected site, simulation period, and preprocessing or analysis workflow. Use before data-dependent work or when relevant inputs change.

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

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