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Skills في هذا المستودع
جمع SkillsMP عدد ٤٢٠ من skills من eightmm/codex-science. افتح أي skill لمراجعة مصدره وتفاصيله.
eightmm/codex-scienceعرض ٤٠ من أصل ٤٢٠ skills مجمعة.
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap),…
لغة النص الأصلي: الإنجليزية
Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided…
لغة النص الأصلي: الإنجليزية
Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer NumPy or SciPy when floating-point approximations are sufficient.
لغة النص الأصلي: الإنجليزية
Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction…
لغة النص الأصلي: الإنجليزية
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management.…
لغة النص الأصلي: الإنجليزية
Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF,…
لغة النص الأصلي: الإنجليزية
Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
لغة النص الأصلي: الإنجليزية
Run reproducible AlphaFold2 monomer or multimer inference with pinned code, parameters, sequence databases, template cutoff, and seeds. Use when a local AlphaFold2 installation or approved container/database setup is available; use AlphaFold DB lookup instead…
لغة النص الأصلي: الإنجليزية
Run the official AlphaFold3 inference pipeline for approved theoretical modeling of proteins, nucleic acids, ligands, modifications, and covalent complexes. Use only when the user has legitimately obtained model parameters and accepts the source, weight,…
لغة النص الأصلي: الإنجليزية
Construct and validate asymptotic and perturbative approximations. Use for dominant balance, regular or singular perturbations, boundary layers, matched expansions, multiple scales, WKB, Laplace methods, and stationary phase.
لغة النص الأصلي: الإنجليزية
Run reproducible local protein-ligand docking with AutoDock Vina and Meeko. Use for pose generation, redocking, or small virtual screens when a receptor and a justified binding pocket are available; do not use a Vina score as experimental affinity.
لغة النص الأصلي: الإنجليزية
Run a pinned BindCraft campaign for de novo protein binders using AlphaFold2 optimization, ProteinMPNN, PyRosetta, and configurable filters. Use only when the target structure, hotspot strategy, candidate budget, dependency licenses, and experimental handoff…
لغة النص الأصلي: الإنجليزية
Run pinned Borzoi models to predict RNA-seq and regulatory tracks from long DNA sequence and compare reference versus alternate alleles. Use for regulatory variant hypotheses with explicit genome assembly, sequence-window, tissue, and track provenance.
لغة النص الأصلي: الإنجليزية
Run pinned Chai-1 inference for proteins, complexes, nucleic acids, ligands, covalent bonds, templates, or restraints. Use when multimolecular structure prediction needs Chai-1-specific inputs and confidence outputs.
لغة النص الأصلي: الإنجليزية
Analyze nonlinear dynamical systems, bifurcations, and deterministic chaos. Use for flows and maps, phase portraits, fixed points, limit cycles, Lyapunov exponents, Poincare sections, attractors, continuation, and distinguishing chaos from noise or numerical…
لغة النص الأصلي: الإنجليزية
Integrate molecular formula, NMR, MS, IR, Raman, UV-Vis, chromatography, and diffraction evidence into ranked chemical structures with explicit contradictions and confidence. Use for unknown identification, structure confirmation, isomer discrimination,…
لغة النص الأصلي: الإنجليزية
Quantify analytes from chromatographic data with validated integration, calibration, quality controls, and uncertainty. Use for HPLC, UHPLC, GC, LC-MS, GC-MS, UV or fluorescence detection, targeted assays, purity estimates, retention data, and batch…
لغة النص الأصلي: الإنجليزية
Formulate, solve, simulate, and verify classical mechanics problems using Newtonian, Lagrangian, Hamiltonian, conservation-law, oscillation, rotation, and central-force methods. Use for particles, rigid bodies, constrained systems, collisions, orbital motion,…
لغة النص الأصلي: الإنجليزية
Solve and verify complex-variable and Fourier-analysis problems. Use for analytic functions, contour integrals, residues, branch cuts, Fourier series and transforms, convolution, spectral methods, sampling, and dispersion relations.
لغة النص الأصلي: الإنجليزية
Verify computational physics software, quantify numerical uncertainty, and validate models against experiments. Use for convergence studies, manufactured solutions, conservation audits, code-to-code comparisons, calibration, uncertainty quantification, and…
لغة النص الأصلي: الإنجليزية
Analyze condensed-matter and solid-state models and computations. Use for crystal symmetry, reciprocal space, electronic bands, density of states, Fermi surfaces, phonons, transport, magnetism, superconductivity, defects, and phase behavior.
لغة النص الأصلي: الإنجليزية
Formulate, solve, and verify continuum models for solids and fluids. Use for deformation, stress, strain, conservation laws, constitutive equations, elasticity, viscosity, boundary conditions, weak forms, and finite-element or finite-volume analysis.
لغة النص الأصلي: الإنجليزية
Model dynamical systems, analyze stability, and design or verify feedback controllers. Use for state-space and transfer-function models, controllability, observability, PID, state feedback, estimation, optimal control, robustness, discretization, and…
لغة النص الأصلي: الإنجليزية
Run a pinned DiffDock release for diffusion-based protein-ligand pose prediction. Use for candidate pose generation from receptor coordinates and ligand structures, especially without a fixed pocket; do not interpret DiffDock confidence as affinity.
لغة النص الأصلي: الإنجليزية
Formulate, solve, simulate, and verify electrostatics, magnetostatics, circuits, induction, electromagnetic waves, and boundary-value problems using Maxwell's equations, potentials, constitutive relations, and conservation laws.
لغة النص الأصلي: الإنجليزية
Extract reproducible ESM-2 protein embeddings, residue representations, likelihoods, or zero-shot mutation scores. Use when a frozen protein language model is needed as a feature extractor or baseline.
لغة النص الأصلي: الإنجليزية
Run released Biohub ESMC protein language models for representations, masked likelihoods, sequence scoring, mutation analysis, or sparse-autoencoder features. Use as the current ESMC alternative to ESM-2 when model scale, revision, and inference boundaries…
لغة النص الأصلي: الإنجليزية
Run the legacy public ESMFold v1 single-sequence structure model reproducibly for proteins or simple multimers. Use for the 2022 ESM-2-based model; use the separate ESMFold2 skill for Biohub's 2026 diffusion/all-atom model.
لغة النص الأصلي: الإنجليزية
Run Biohub ESMFold2 locally from the released Hugging Face weights or through the approved Biohub Platform. Use for all-atom prediction of proteins, complexes, DNA, modifications, and ligands with optional MSA input and diffusion sampling; distinct from the…
لغة النص الأصلي: الإنجليزية
Run pinned Evo 2 DNA sequence scoring, embeddings, variant scoring, or controlled generation. Use for long-context genomic foundation-model analyses when compatible local GPU hardware and explicit genome/strand provenance are available.
لغة النص الأصلي: الإنجليزية
Formulate and verify geometry and topology arguments. Use for metric and topological spaces, continuity, compactness, connectedness, manifolds, curves and surfaces, homotopy, covering spaces, Euler characteristic, and geometric invariants.
لغة النص الأصلي: الإنجليزية
Run reproducible local GNINA docking or CNN rescoring on protein-ligand systems. Use when GPU-assisted pose generation, refinement, or CNN reranking is wanted; keep CNN pose score, predicted affinity, and experimental affinity as distinct quantities.
لغة النص الأصلي: الإنجليزية
Prepare and run staged, checkpointed molecular dynamics with a pinned GROMACS build. Use when GROMACS workflows, HPC execution, established .mdp protocols, or interoperability with GROMACS topology/trajectory formats is required.
لغة النص الأصلي: الإنجليزية
Build an evidence-traceable indication dossier for a disease, target, mechanism, drug, biomarker, or therapeutic hypothesis. Use for landscape assessment, target-indication rationale, clinical pipeline review, translational gaps, and evidence-backed go/no-go…
لغة النص الأصلي: الإنجليزية
Formulate and solve inverse problems with stable regularization and calibrated uncertainty. Use for parameter or field recovery, deconvolution, tomography, system identification, data assimilation, Bayesian inversion, and learned inverse models.
لغة النص الأصلي: الإنجليزية
Solve exact and numerical linear algebra problems with explicit field, dimensions, bases, rank structure, conditioning, and residual checks. Use for linear systems, vector spaces, linear maps, eigenproblems, least squares, SVD, quadratic forms, and matrix…
لغة النص الأصلي: الإنجليزية
Identify and quantify support for analytes from mass spectrometry with explicit acquisition context, calibration, false-discovery control, and isomer-aware evidence. Use for GC-MS, LC-MS, MS/MS, accurate mass, isotope patterns, adducts, fragments, library…
لغة النص الأصلي: الإنجليزية
Analyze OpenMM, GROMACS, and other molecular dynamics trajectories with MDAnalysis using topology-aware selections, periodic-boundary handling, prespecified observables, convergence checks, and uncertainty estimates.
لغة النص الأصلي: الإنجليزية
Drive a concrete scientific modeling problem from supplied inputs through model selection, falsifiable plan, one-time approval, environment setup, smoke test, full execution, downstream analysis, provenance, and review. Use when the user provides sequences,…
لغة النص الأصلي: الإنجليزية
Prepare receptors and small molecules for docking or simulation with explicit stereochemistry, protonation, tautomer, charge, conformer, cofactor, water, and pocket provenance. Use before AutoDock Vina, GNINA, DiffDock, OpenMM, GROMACS, or any protein-ligand…
لغة النص الأصلي: الإنجليزية