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SkillsMP has collected 420 skills from eightmm/codex-science. Open a skill to review its source and details.
eightmm/codex-scienceShowing 40 of 420 collected skills.
Process, assign, and verify molecular NMR evidence. Use for 1D or 2D solution NMR, FID processing, chemical shifts, multiplicities, couplings, integrations, COSY, HSQC, HMBC, NOE or ROE evidence, mixture assessment, and molecular structure or stereochemical…
Formulate and verify nuclear and particle physics calculations. Use for reactions, decays, relativistic kinematics, conservation laws, cross sections, lifetimes, quantum numbers, detector yields, backgrounds, and statistical significance.
Classify, solve, approximate, and verify ordinary and partial differential equations with explicit domains, initial or boundary data, well-posedness, residuals, and convergence checks. Use for IVPs, BVPs, dynamical systems, eigenvalue problems, Fourier…
Parameterize drug-like small molecules for molecular simulation with pinned OpenFF Toolkit/force fields and explicit charge, stereochemistry, and coverage checks. Use before OpenMM or GROMACS when ligands or nonstandard organic molecules need parameters.
Run pinned OpenFold3 preview inference for proteins, nucleic acids, noncanonical residues, and small-molecule complexes. Use when an open AlphaFold3-style workflow is wanted and preview-status limitations are acceptable.
Build, equilibrate, run, checkpoint, and analyze reproducible molecular dynamics with OpenMM. Use for proteins, nucleic acids, solvated complexes, or parameterized protein-ligand systems when local CPU/GPU simulation is requested.
Model and verify optical and wave phenomena. Use for ray optics, wave propagation, polarization, interference, diffraction, coherence, resonators, dispersion, scattering, imaging, and electromagnetic boundary problems.
Formulate, solve, and verify finite-dimensional optimization and calculus-of-variations problems. Use for convex programs, constrained extrema, KKT systems, duality, optimal control, Euler-Lagrange equations, and numerical optimization.
Profile noncovalent protein-ligand interactions with a pinned PLIP release and compare interaction fingerprints across experimental structures, docking poses, or trajectory representatives. Use after structure preparation or pose generation.
Formulate, solve, simulate, and verify probability and stochastic-process problems. Use for conditional probability, random variables, limit theorems, Markov chains, Poisson processes, martingales, stochastic simulation, and uncertainty in random systems.
Design or score protein sequences for fixed backbones with ProteinMPNN, LigandMPNN, or SolubleMPNN. Use for backbone-conditioned design, ligand-context design, soluble-protein design, residue constraints, or side-chain packing.
Run pinned Protenix structure prediction for protein, nucleic-acid, ligand, antibody-antigen, template, MSA, or constrained complexes. Use Protenix-v2 or another explicitly selected released model with a recorded training-data cutoff and inference budget.
Formulate, solve, simulate, and verify nonrelativistic quantum mechanics problems using states, operators, boundary conditions, symmetries, stationary and time-dependent evolution, approximation methods, measurement, and open-system dynamics.
Formulate and verify special- and general-relativity problems. Use for Lorentz transformations, four-vectors, relativistic kinematics, metrics, geodesics, curvature, gravitational fields, horizons, and stress-energy dynamics.
Run pinned RFdiffusion for unconditional generation, motif scaffolding, binder backbones, symmetric assemblies, partial diffusion, or macrocyclic peptide design. Use when structural conditioning and a downstream sequence/refolding validation funnel are…
Run RoseTTAFold All-Atom for proteins, nucleic acids, small molecules, metals, covalent modifications, and higher-order assemblies. Use when its Hydra input model and confidence metrics fit the problem and licensed dependencies are available.
Run pinned scGPT checkpoints for single-cell embeddings, cell-type annotation, reference mapping, perturbation modeling, or fine-tuning. Use when a pretrained single-cell transformer is requested and donor/batch/feature provenance can be preserved.
Build and evaluate reproducible scvi-tools workflows for single-cell RNA, protein, chromatin, spatial, or multimodal data using scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, or related models.
Run Apple's released SimpleFold flow-matching protein structure models with PyTorch or MLX. Use for single-protein folding, conformer ensembles, or Apple-silicon inference when model-size and model-license constraints are acceptable.
Analyze experimental spectra with traceable preprocessing, calibration, peak or band inference, uncertainty, and alternative-model checks. Use for UV-Vis, fluorescence, IR, Raman, absorbance, emission, reflectance, and related one-dimensional spectral…
Compute and verify tensor-calculus and differential-geometry results. Use for coordinate transformations, metrics, differential forms, covariant derivatives, connections, geodesics, curvature, Lie derivatives, and coordinate-independent geometric identities.
Solve and verify equilibrium thermodynamics and statistical mechanics problems using explicit systems, sign conventions, equations of state, thermodynamic potentials, ensembles, partition functions, fluctuations, and phase-equilibrium conditions.
Analyze and verify X-ray diffraction and scattering data. Use for powder XRD, phase identification, indexing, lattice parameters, Rietveld refinement, crystallite size or strain, texture, amorphous content, SAXS, WAXS, pair distributions, and comparison with…
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…
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,…
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.
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.
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…
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.
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.
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…
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,…
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…
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,…
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.
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…
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.
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.
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…
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.