@researai/deepscientist 1.5.16 → 1.6.0

package/src/skills/science/references/package-index.min.json

@@ -0,0 +1,3616 @@
+{
+  "schema_version": 1,
+  "source": {
+    "name": "FermiLink skilled-scipkg catalog",
+    "repository": "https://github.com/TaoELi/FermiLink",
+    "upstream_commit": "93f089a333a43089fb1a08a73c37d05fd6683214",
+    "channel_id": "skilled-scipkg",
+    "generated_at": "2026-05-10T04:59:05.973483+00:00",
+    "notes": [
+      "DeepScientist uses this as package routing metadata and knowledge URLs.",
+      "Package source trees are not vendored by this generated catalog.",
+      "Package cards do not prove solver runtime availability."
+    ]
+  },
+  "package_count": 169,
+  "packages": [
+    {
+      "package_id": "abinit",
+      "title": "ABINIT Electronic-Structure Suite",
+      "description": "ABINIT is a first-principles atomic-scale simulation package for computing electronic, structural, vibrational, and dielectric properties of materials using DFT and related methods.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science"
+      ],
+      "tags": [
+        "abinit",
+        "dft",
+        "electronic-structure",
+        "materials-science",
+        "dfpt",
+        "first-principles"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/abinit",
+      "source_archive_url": "https://github.com/skilled-scipkg/abinit/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/abinit/abinit",
+      "homepage_url": "https://www.abinit.org",
+      "card": "references/packages/abinit.md"
+    },
+    {
+      "package_id": "acts",
+      "title": "ACTS Common Tracking Software",
+      "description": "ACTS is a modern C++ toolkit for experiment independent charged particle track reconstruction, detector geometry, and fast tracking simulation in high energy physics workflows.",
+      "domains": [
+        "high_energy_physics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "high-energy-physics",
+        "particle-tracking",
+        "track-reconstruction",
+        "detector-geometry",
+        "simulation",
+        "cpp"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/acts",
+      "source_archive_url": "https://github.com/skilled-scipkg/acts/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/acts-project/acts",
+      "homepage_url": "https://acts-project.github.io",
+      "card": "references/packages/acts.md"
+    },
+    {
+      "package_id": "aiida-core",
+      "title": "AiiDA Core Workflow Engine",
+      "description": "AiiDA-core is a scientific workflow and provenance platform that automates remote HPC calculations, tracks reproducible process graphs, and integrates simulation-code plugins.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "workflow",
+        "provenance",
+        "hpc",
+        "computational-science",
+        "reproducibility",
+        "scientific-automation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/aiida-core",
+      "source_archive_url": "https://github.com/skilled-scipkg/aiida-core/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/aiidateam/aiida-core",
+      "homepage_url": "https://aiida-core.readthedocs.io",
+      "card": "references/packages/aiida-core.md"
+    },
+    {
+      "package_id": "alamode",
+      "title": "ALAMODE Lattice Thermal Transport",
+      "description": "ALAMODE computes harmonic and anharmonic force constants from first-principles data to analyze phonons, lattice anharmonicity, and lattice thermal conductivity in crystalline and low-dimensional solids.",
+      "domains": [
+        "materials_science"
+      ],
+      "tags": [
+        "materials-science",
+        "phonons",
+        "thermal-transport",
+        "anharmonicity",
+        "lattice-dynamics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/ALAMODE",
+      "source_archive_url": "https://github.com/skilled-scipkg/ALAMODE/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/ttadano/ALAMODE",
+      "homepage_url": "http://sourceforge.net/projects/alamode",
+      "card": "references/packages/alamode.md"
+    },
+    {
+      "package_id": "amuse",
+      "title": "AMUSE Astrophysical Simulation Environment",
+      "description": "AMUSE is a Python-driven framework that couples specialized community solvers to build multi-physics astrophysical simulations across gravitational dynamics, hydrodynamics, stellar evolution, and other computational astronomy research workflows.",
+      "domains": [
+        "astronomy_astrophysics",
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "amuse",
+        "astrophysics",
+        "computational_astronomy",
+        "nbody",
+        "hydrodynamics",
+        "stellar_evolution"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/amuse",
+      "source_archive_url": "https://github.com/skilled-scipkg/amuse/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/amusecode/amuse",
+      "homepage_url": "http://www.amusecode.org",
+      "card": "references/packages/amuse.md"
+    },
+    {
+      "package_id": "anndata",
+      "title": "AnnData Annotated Data Matrices",
+      "description": "anndata provides an efficient annotated matrix container for single-cell and spatial omics, supporting metadata-rich observations, variables, sparse storage, and on-disk workflows.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "anndata",
+        "single-cell",
+        "omics",
+        "bioinformatics",
+        "h5ad"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/anndata",
+      "source_archive_url": "https://github.com/skilled-scipkg/anndata/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scverse/anndata",
+      "homepage_url": "http://anndata.readthedocs.io",
+      "card": "references/packages/anndata.md"
+    },
+    {
+      "package_id": "arbor",
+      "title": "Arbor Neural Simulation Library",
+      "description": "Arbor is a high-performance library for simulating morphologically detailed multi-compartment neuron and network models with performance portability across CPU and GPU architectures.",
+      "domains": [
+        "computational_neuroscience",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "computational-neuroscience",
+        "neuron-simulation",
+        "electrophysiology",
+        "multi-compartment",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/arbor",
+      "source_archive_url": "https://github.com/skilled-scipkg/arbor/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/arbor-sim/arbor",
+      "homepage_url": "https://arbor-sim.org",
+      "card": "references/packages/arbor.md"
+    },
+    {
+      "package_id": "arc",
+      "title": "ARC Alkali Rydberg Calculator",
+      "description": "Python toolkit for computing properties of highly excited Rydberg states and interactions in alkali and divalent atoms, including level structure, transition strengths, and electric-field Stark calculations.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "atomic-physics",
+        "rydberg-atoms",
+        "alkali-atoms",
+        "divalent-atoms",
+        "quantum-optics",
+        "stark-shifts"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/ARC-Alkali-Rydberg-Calculator",
+      "source_archive_url": "https://github.com/skilled-scipkg/ARC-Alkali-Rydberg-Calculator/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/nikolasibalic/ARC-Alkali-Rydberg-Calculator",
+      "homepage_url": "https://atomcalc.org",
+      "card": "references/packages/arc.md"
+    },
+    {
+      "package_id": "astropy",
+      "title": "Astropy Astronomy Core Library",
+      "description": "Astropy is the core Python library for astronomy, covering units, coordinates, time handling, FITS files, WCS, tables, and cosmology workflows.",
+      "domains": [
+        "astronomy_astrophysics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "astronomy",
+        "astrophysics",
+        "fits",
+        "coordinates",
+        "cosmology",
+        "units"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/astropy",
+      "source_archive_url": "https://github.com/skilled-scipkg/astropy/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/astropy/astropy",
+      "homepage_url": "https://www.astropy.org",
+      "card": "references/packages/astropy.md"
+    },
+    {
+      "package_id": "astroquery",
+      "title": "Astroquery Astronomical Data Access",
+      "description": "Astroquery provides a unified Python interface for querying online astronomical catalogs, mission archives, and object databases through service-specific modules and standardized query methods.",
+      "domains": [
+        "astronomy_astrophysics"
+      ],
+      "tags": [
+        "astronomy",
+        "astroinformatics",
+        "catalog-query",
+        "archive-access",
+        "observational-data",
+        "astropy-affiliated"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/astroquery",
+      "source_archive_url": "https://github.com/skilled-scipkg/astroquery/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/astropy/astroquery",
+      "homepage_url": "http://astroquery.readthedocs.org/en/latest/",
+      "card": "references/packages/astroquery.md"
+    },
+    {
+      "package_id": "atomate2",
+      "title": "Atomate2 Materials Workflow Library",
+      "description": "Atomate2 provides composable high-throughput computational materials science workflows for running and managing VASP and related calculations of electronic, vibrational, and defect properties at scale.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "materials-science",
+        "workflow-automation",
+        "high-throughput",
+        "dft",
+        "vasp",
+        "computational-materials"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/atomate2",
+      "source_archive_url": "https://github.com/skilled-scipkg/atomate2/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/materialsproject/atomate2",
+      "homepage_url": "https://materialsproject.github.io/atomate2/",
+      "card": "references/packages/atomate2.md"
+    },
+    {
+      "package_id": "atomsmltr",
+      "title": "atomSmltr Laser Cooling and Trapping Simulator",
+      "description": "atomSmltr is a modular Python toolkit for simulating laser-cooled atoms in custom laser and magnetic field geometries with trajectory integration.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "atomic-physics",
+        "laser-cooling",
+        "cold-atoms",
+        "magneto-optical-trap",
+        "numerical-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/atomSmltr",
+      "source_archive_url": "https://github.com/skilled-scipkg/atomSmltr/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/adareau/atomSmltr",
+      "homepage_url": "https://atomsmltr.readthedocs.io/en/latest/",
+      "card": "references/packages/atomsmltr.md"
+    },
+    {
+      "package_id": "awkward",
+      "title": "Awkward Array",
+      "description": "Awkward Array enables NumPy-like, compiled operations on deeply nested, variable-length, and record-rich scientific data, making jagged JSON-like event structures fast and practical to analyze.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "awkward",
+        "ragged-arrays",
+        "jagged-data",
+        "columnar-analysis",
+        "scikit-hep"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/awkward",
+      "source_archive_url": "https://github.com/skilled-scipkg/awkward/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scikit-hep/awkward",
+      "homepage_url": "https://awkward-array.org",
+      "card": "references/packages/awkward.md"
+    },
+    {
+      "package_id": "batman",
+      "title": "BATMAN Exoplanet Transit Light-Curve Modeler",
+      "description": "BATMAN is a Python package for very fast computation of exoplanet transit light curves, supporting multiple limb-darkening laws for fitting and simulating planetary transit photometry.",
+      "domains": [
+        "astronomy_astrophysics"
+      ],
+      "tags": [
+        "astronomy",
+        "exoplanets",
+        "transit-light-curves",
+        "photometry",
+        "time-series"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/batman",
+      "source_archive_url": "https://github.com/skilled-scipkg/batman/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/lkreidberg/batman",
+      "homepage_url": "http://lkreidberg.github.io/batman",
+      "card": "references/packages/batman.md"
+    },
+    {
+      "package_id": "biopython",
+      "title": "Biopython",
+      "description": "Biopython provides Python tools for bioinformatics and computational molecular biology, covering biological sequence parsing, alignments, phylogenetics, and interfaces to common genomics and proteomics data sources.",
+      "domains": [
+        "bioinformatics"
+      ],
+      "tags": [
+        "bioinformatics",
+        "computational-biology",
+        "molecular-biology",
+        "sequence-analysis",
+        "genomics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/biopython",
+      "source_archive_url": "https://github.com/skilled-scipkg/biopython/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/biopython/biopython",
+      "homepage_url": "http://biopython.org/",
+      "card": "references/packages/biopython.md"
+    },
+    {
+      "package_id": "bloqade",
+      "title": "Bloqade Neutral Atom Quantum SDK",
+      "description": "Bloqade is QuEra's Python SDK and eDSL suite for programming, compiling, and simulating neutral-atom quantum computing workflows on Rydberg-atom hardware and related backends.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "quantum-computing",
+        "neutral-atoms",
+        "rydberg",
+        "quantum-sdk",
+        "edsl",
+        "quera"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/bloqade",
+      "source_archive_url": "https://github.com/skilled-scipkg/bloqade/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/QuEraComputing/bloqade",
+      "homepage_url": "https://bloqade.quera.com/latest/",
+      "card": "references/packages/bloqade.md"
+    },
+    {
+      "package_id": "brian2",
+      "title": "Brian2 Spiking Neural Network Simulator",
+      "description": "Brian2 is an open source Python simulator for building and running flexible spiking neural network models in computational neuroscience research and education.",
+      "domains": [
+        "computational_neuroscience"
+      ],
+      "tags": [
+        "computational-neuroscience",
+        "spiking-networks",
+        "neural-simulation",
+        "dynamical-systems"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/brian2",
+      "source_archive_url": "https://github.com/skilled-scipkg/brian2/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/brian-team/brian2",
+      "homepage_url": "http://briansimulator.org",
+      "card": "references/packages/brian2.md"
+    },
+    {
+      "package_id": "bullet3",
+      "title": "Bullet Physics SDK (bullet3)",
+      "description": "Bullet3 is a real time physics simulation library for rigid body dynamics and collision detection, with strong PyBullet workflows for robotics and reinforcement learning research.",
+      "domains": [
+        "workflow_provenance",
+        "robotics_physics"
+      ],
+      "tags": [
+        "physics",
+        "simulation",
+        "collision",
+        "rigidbody",
+        "robotics",
+        "pybullet"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/bullet3",
+      "source_archive_url": "https://github.com/skilled-scipkg/bullet3/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/bulletphysics/bullet3",
+      "homepage_url": "http://bulletphysics.org",
+      "card": "references/packages/bullet3.md"
+    },
+    {
+      "package_id": "calculix",
+      "title": "CalculiX Finite Element Program",
+      "description": "CalculiX is an open-source three-dimensional finite element package for structural and thermomechanical simulation, with ABAQUS-style input decks and engineering stress analysis workflows.",
+      "domains": [
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "finite-element",
+        "fea",
+        "structural-mechanics",
+        "thermomechanics",
+        "mechanical-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/CalculiX",
+      "source_archive_url": "https://github.com/skilled-scipkg/CalculiX/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/Dhondtguido/CalculiX",
+      "homepage_url": "https://github.com/Dhondtguido/CalculiX",
+      "card": "references/packages/calculix.md"
+    },
+    {
+      "package_id": "cantera",
+      "title": "Cantera Chemical Kinetics and Combustion",
+      "description": "Cantera is an open-source scientific toolkit for modeling chemical kinetics, thermodynamics, and transport, supporting equilibrium calculations, reactor-network simulations, and one-dimensional flame analyses across multiple programming interfaces.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "chemical-kinetics",
+        "combustion",
+        "thermodynamics",
+        "transport",
+        "reactor-modeling",
+        "flame-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/cantera",
+      "source_archive_url": "https://github.com/skilled-scipkg/cantera/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/Cantera/cantera",
+      "homepage_url": "https://cantera.org",
+      "card": "references/packages/cantera.md"
+    },
+    {
+      "package_id": "cavity-md-ipi",
+      "title": "CavMD: Cavity Molecular Dynamics",
+      "description": "CavMD simulates cavity-coupled molecular dynamics for vibrational strong and ultrastrong coupling, spanning classical and path-integral regimes with workflows for setup, job submission, post-processing, and plotting.",
+      "domains": [
+        "molecular_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "molecular-dynamics",
+        "cavity-qed",
+        "vibrational-coupling",
+        "chemical-physics",
+        "path-integral",
+        "qmmm"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/cavity-md-ipi",
+      "source_archive_url": "https://github.com/skilled-scipkg/cavity-md-ipi/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/TaoELi/cavity-md-ipi",
+      "homepage_url": "https://github.com/TaoELi/cavity-md-ipi",
+      "card": "references/packages/cavity-md-ipi.md"
+    },
+    {
+      "package_id": "ccdproc",
+      "title": "CCDProc CCD Image Reduction",
+      "description": "Astropy-affiliated toolkit for calibrating and reducing optical and infrared CCD observations with overscan, bias, dark, flat, bad-pixel masking, cosmic-ray cleaning, and uncertainty-aware processing.",
+      "domains": [
+        "astronomy_astrophysics"
+      ],
+      "tags": [
+        "astronomy",
+        "ccd",
+        "image-reduction",
+        "optical-ir",
+        "calibration"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/ccdproc",
+      "source_archive_url": "https://github.com/skilled-scipkg/ccdproc/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/astropy/ccdproc",
+      "homepage_url": "https://ccdproc.readthedocs.io",
+      "card": "references/packages/ccdproc.md"
+    },
+    {
+      "package_id": "celerite2",
+      "title": "celerite2 Gaussian Process Toolkit",
+      "description": "celerite2 provides numerically stable, fast one-dimensional Gaussian process regression in Python and C++, optimized for scalable time-series inference with structured kernels and astronomy-focused probabilistic modeling workflows.",
+      "domains": [
+        "astronomy_astrophysics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "gaussian-processes",
+        "time-series",
+        "astronomy",
+        "probabilistic-modeling",
+        "celerite"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/celerite2",
+      "source_archive_url": "https://github.com/skilled-scipkg/celerite2/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/exoplanet-dev/celerite2",
+      "homepage_url": "https://celerite2.readthedocs.io",
+      "card": "references/packages/celerite2.md"
+    },
+    {
+      "package_id": "cellrank",
+      "title": "CellRank Single-Cell Fate Mapping",
+      "description": "CellRank is a single-cell analysis framework that models cellular dynamics with Markov state methods to infer lineage fates, macrostates, and driver genes from multiview data.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "single-cell",
+        "fate-mapping",
+        "trajectory-inference",
+        "rna-velocity",
+        "markov-models",
+        "computational-biology"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/cellrank",
+      "source_archive_url": "https://github.com/skilled-scipkg/cellrank/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/theislab/cellrank",
+      "homepage_url": "https://cellrank.readthedocs.io/en/latest/",
+      "card": "references/packages/cellrank.md"
+    },
+    {
+      "package_id": "cesm",
+      "title": "CESM (Community Earth System Model)",
+      "description": "CESM is a coupled Earth system modeling framework for simulating climate dynamics across atmosphere, ocean, land, and sea ice components on HPC systems using CIME workflows.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "climate-modeling",
+        "earth-system",
+        "geoscience",
+        "hpc",
+        "coupled-model"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/CESM",
+      "source_archive_url": "https://github.com/skilled-scipkg/CESM/archive/refs/heads/cesm3.0-alphabranch.zip",
+      "upstream_repo_url": "https://github.com/ESCOMP/CESM",
+      "homepage_url": "http://www.cesm.ucar.edu/",
+      "card": "references/packages/cesm.md"
+    },
+    {
+      "package_id": "chemicals",
+      "title": "Chemicals Thermophysical Data Library",
+      "description": "Python library with on-demand databases and correlations for pure-component constants, thermophysical properties, safety information, and phase-equilibrium calculations used in chemical engineering workflows.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "chemical-engineering",
+        "thermodynamics",
+        "property-database",
+        "phase-equilibrium",
+        "thermophysical-properties",
+        "process-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/chemicals",
+      "source_archive_url": "https://github.com/skilled-scipkg/chemicals/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/CalebBell/chemicals",
+      "homepage_url": "https://github.com/CalebBell/chemicals",
+      "card": "references/packages/chemicals.md"
+    },
+    {
+      "package_id": "chempy",
+      "title": "ChemPy Chemical Modeling Toolkit",
+      "description": "ChemPy is a Python chemistry library focused on reaction kinetics, equilibrium systems, and physical chemistry relations, with practical property models for aqueous and acid solutions.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "chemistry",
+        "chemical-kinetics",
+        "equilibrium",
+        "physical-chemistry",
+        "analytical-chemistry",
+        "solution-chemistry"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/chempy",
+      "source_archive_url": "https://github.com/skilled-scipkg/chempy/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/bjodah/chempy",
+      "homepage_url": "https://github.com/bjodah/chempy",
+      "card": "references/packages/chempy.md"
+    },
+    {
+      "package_id": "cirq",
+      "title": "Cirq Quantum Circuit Framework",
+      "description": "Cirq is a Python framework for building, transforming, and simulating noisy intermediate-scale quantum circuits on simulators and hardware-aware quantum devices.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "cirq",
+        "quantum",
+        "nisq",
+        "quantum-circuits",
+        "simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/Cirq",
+      "source_archive_url": "https://github.com/skilled-scipkg/Cirq/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/quantumlib/Cirq",
+      "homepage_url": "https://quantumai.google/cirq",
+      "card": "references/packages/cirq.md"
+    },
+    {
+      "package_id": "coffea",
+      "title": "Coffea Collider HEP Analysis Framework",
+      "description": "Coffea provides columnar high-energy collider physics analysis tools with event processing, histogramming, corrections, and scalable execution from laptops to clusters in Python.",
+      "domains": [
+        "finite_element_engineering",
+        "high_energy_physics"
+      ],
+      "tags": [
+        "hep",
+        "collider",
+        "columnar",
+        "nanoaod",
+        "event-analysis",
+        "scikit-hep",
+        "distributed-execution"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/coffea",
+      "source_archive_url": "https://github.com/skilled-scipkg/coffea/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/scikit-hep/coffea",
+      "homepage_url": "https://coffea-hep.readthedocs.io",
+      "card": "references/packages/coffea.md"
+    },
+    {
+      "package_id": "cp2k",
+      "title": "CP2K Quantum Chemistry Suite",
+      "description": "CP2K is an atomistic simulation package for quantum chemistry and solid-state physics, supporting DFT and beyond for molecular, periodic, and materials systems with efficient parallel execution.",
+      "domains": [
+        "quantum_chemistry",
+        "molecular_dynamics"
+      ],
+      "tags": [
+        "cp2k",
+        "quantum-chemistry",
+        "electronic-structure",
+        "dft",
+        "molecular-dynamics",
+        "solid-state"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/cp2k",
+      "source_archive_url": "https://github.com/skilled-scipkg/cp2k/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/cp2k/cp2k",
+      "homepage_url": "https://www.cp2k.org",
+      "card": "references/packages/cp2k.md"
+    },
+    {
+      "package_id": "custodian",
+      "title": "Custodian JIT Simulation Job Manager",
+      "description": "Custodian is a Python framework for just-in-time management of long-running materials and chemistry calculations, providing automated error detection, correction, and restart workflows for high-throughput simulation campaigns.",
+      "domains": [
+        "quantum_chemistry",
+        "computational_chemistry",
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "materials-science",
+        "computational-chemistry",
+        "job-management",
+        "error-recovery",
+        "high-throughput",
+        "electronic-structure"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/custodian",
+      "source_archive_url": "https://github.com/skilled-scipkg/custodian/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/materialsproject/custodian",
+      "homepage_url": "https://github.com/materialsproject/custodian",
+      "card": "references/packages/custodian.md"
+    },
+    {
+      "package_id": "dart",
+      "title": "DART Robotics Dynamics Engine",
+      "description": "DART is a C++20 robotics and animation dynamics engine with stable articulated rigid-body simulation, collision and constraint handling, and Python bindings via dartpy.",
+      "domains": [
+        "robotics_physics"
+      ],
+      "tags": [
+        "robotics",
+        "physics-engine",
+        "dynamics",
+        "simulation",
+        "multibody",
+        "collision"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/dart",
+      "source_archive_url": "https://github.com/skilled-scipkg/dart/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/dartsim/dart",
+      "homepage_url": "https://dart.readthedocs.io",
+      "card": "references/packages/dart.md"
+    },
+    {
+      "package_id": "datamol",
+      "title": "Datamol Molecular Processing Toolkit",
+      "description": "Datamol is a lightweight RDKit-first toolkit for molecular standardization, structure conversion, fingerprints, conformer generation, visualization, and molecule file I/O with practical defaults for cheminformatics workflows.",
+      "domains": [
+        "computational_chemistry",
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "cheminformatics",
+        "molecular-processing",
+        "rdkit",
+        "small-molecules",
+        "molecular-io"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/datamol",
+      "source_archive_url": "https://github.com/skilled-scipkg/datamol/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/datamol-io/datamol",
+      "homepage_url": "https://docs.datamol.io",
+      "card": "references/packages/datamol.md"
+    },
+    {
+      "package_id": "dd4hep",
+      "title": "DD4hep Detector Description Toolkit",
+      "description": "DD4hep provides a unified detector description framework for high energy physics, spanning geometry, materials, visualization, readout, alignment, and calibration for simulation, reconstruction, and analysis.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "hep",
+        "detector",
+        "geometry",
+        "readout",
+        "simulation",
+        "reconstruction"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/DD4hep",
+      "source_archive_url": "https://github.com/skilled-scipkg/DD4hep/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/AIDASoft/DD4hep",
+      "homepage_url": "http://dd4hep.cern.ch",
+      "card": "references/packages/dd4hep.md"
+    },
+    {
+      "package_id": "dealii",
+      "title": "deal.II Finite Element Library",
+      "description": "deal.II is a C++ library for solving partial differential equations with adaptive finite elements, supporting scalable multiphysics simulations on serial and distributed-memory architectures.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "finite-elements",
+        "pde",
+        "adaptive-mesh",
+        "computational-mechanics",
+        "multiphysics",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/dealii",
+      "source_archive_url": "https://github.com/skilled-scipkg/dealii/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/dealii/dealii",
+      "homepage_url": "https://dealii.org",
+      "card": "references/packages/dealii.md"
+    },
+    {
+      "package_id": "deepchem",
+      "title": "DeepChem Molecular Machine Learning Toolkit",
+      "description": "DeepChem provides domain-focused machine learning tools for molecular property prediction, drug discovery, and scientific modeling across chemistry, materials science, quantum chemistry, and biology.",
+      "domains": [
+        "quantum_chemistry",
+        "computational_chemistry",
+        "materials_science",
+        "bioinformatics"
+      ],
+      "tags": [
+        "cheminformatics",
+        "drug-discovery",
+        "molecular-ml",
+        "quantum-chemistry",
+        "materials-science",
+        "computational-biology"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/deepchem",
+      "source_archive_url": "https://github.com/skilled-scipkg/deepchem/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/deepchem/deepchem",
+      "homepage_url": "https://deepchem.io/",
+      "card": "references/packages/deepchem.md"
+    },
+    {
+      "package_id": "delphes",
+      "title": "Delphes Fast Collider Simulation",
+      "description": "Delphes is a C++ framework for fast multipurpose collider detector-response simulation, producing reconstructed physics objects and ROOT trees from generated high-energy physics events.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "hep",
+        "collider",
+        "detector-simulation",
+        "fast-simulation",
+        "root"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/delphes",
+      "source_archive_url": "https://github.com/skilled-scipkg/delphes/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/delphes/delphes",
+      "homepage_url": "https://delphes.github.io",
+      "card": "references/packages/delphes.md"
+    },
+    {
+      "package_id": "devito",
+      "title": "Devito Stencil Compiler",
+      "description": "Devito is a symbolic Python DSL and compiler framework that generates optimized finite-difference and stencil operators for PDE simulations on CPUs, GPUs, and distributed-memory clusters.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "pde",
+        "finite-difference",
+        "stencil",
+        "symbolic-dsl",
+        "hpc",
+        "seismic"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/devito",
+      "source_archive_url": "https://github.com/skilled-scipkg/devito/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/devitocodes/devito",
+      "homepage_url": "http://www.devitoproject.org",
+      "card": "references/packages/devito.md"
+    },
+    {
+      "package_id": "dftb",
+      "title": "DFTB+ Atomistic Simulator",
+      "description": "DFTB+ performs fast quantum-mechanical atomistic simulations using density functional tight binding for efficient electronic-structure, molecular dynamics, and materials calculations with Slater-Koster parameter sets.",
+      "domains": [
+        "quantum_chemistry",
+        "molecular_dynamics"
+      ],
+      "tags": [
+        "quantum-chemistry",
+        "electronic-structure",
+        "atomistic-simulation",
+        "tight-binding",
+        "materials-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/dftbplus",
+      "source_archive_url": "https://github.com/skilled-scipkg/dftbplus/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/TEL-Research/dftbplus",
+      "homepage_url": "http://www.dftbplus.org",
+      "card": "references/packages/dftb.md"
+    },
+    {
+      "package_id": "dftd4",
+      "title": "DFT-D4 Dispersion Correction",
+      "description": "Fortran-based implementation of the D4 atomic-charge dependent London dispersion correction for DFT, providing energies, gradients, pairwise decomposition, periodic support, and C and Python interfaces.",
+      "domains": [
+        "quantum_chemistry"
+      ],
+      "tags": [
+        "quantum-chemistry",
+        "dft",
+        "dispersion",
+        "fortran",
+        "electronic-structure"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/dftd4",
+      "source_archive_url": "https://github.com/skilled-scipkg/dftd4/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/dftd4/dftd4",
+      "homepage_url": "https://dftd4.readthedocs.io",
+      "card": "references/packages/dftd4.md"
+    },
+    {
+      "package_id": "dftk-jl",
+      "title": "DFTK.jl Density-Functional Toolkit",
+      "description": "Julia package for plane-wave density-functional theory in solid-state simulations, emphasizing simple extensible algorithms for electronic-structure research with MPI parallelization and GPU support.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science"
+      ],
+      "tags": [
+        "density-functional-theory",
+        "electronic-structure",
+        "plane-wave",
+        "materials-science",
+        "julia"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/DFTK.jl",
+      "source_archive_url": "https://github.com/skilled-scipkg/DFTK.jl/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/JuliaMolSim/DFTK.jl",
+      "homepage_url": "https://docs.dftk.org",
+      "card": "references/packages/dftk-jl.md"
+    },
+    {
+      "package_id": "dolfinx",
+      "title": "DOLFINx",
+      "description": "DOLFINx is the next generation FEniCSx environment for parallel finite element solution of partial differential equations through interoperable C++ and Python interfaces.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "fenicsx",
+        "finite-element",
+        "pde",
+        "hpc",
+        "multiphysics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/dolfinx",
+      "source_archive_url": "https://github.com/skilled-scipkg/dolfinx/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/FEniCS/dolfinx",
+      "homepage_url": "https://fenicsproject.org",
+      "card": "references/packages/dolfinx.md"
+    },
+    {
+      "package_id": "drake",
+      "title": "Drake Robotics Toolkit",
+      "description": "Drake is an open-source robotics toolbox for model-based design, simulation, planning, control, and verification of complex robotic systems.",
+      "domains": [
+        "robotics_physics"
+      ],
+      "tags": [
+        "robotics",
+        "simulation",
+        "multibody",
+        "optimization",
+        "control",
+        "planning"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/drake",
+      "source_archive_url": "https://github.com/skilled-scipkg/drake/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/RobotLocomotion/drake",
+      "homepage_url": "https://drake.mit.edu",
+      "card": "references/packages/drake.md"
+    },
+    {
+      "package_id": "dumux",
+      "title": "DuMux Porous Media Simulator",
+      "description": "DuMux is an open source multiphysics simulation framework for finite volume modeling of flow and transport in porous media, supporting coupled domains, reactive processes, and geoscience applications.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "porousmedia",
+        "multiphysics",
+        "finitevolume",
+        "flowtransport",
+        "geoscience"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/dumux",
+      "source_archive_url": "https://github.com/skilled-scipkg/dumux/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/dumux/dumux",
+      "homepage_url": "https://dumux.org/",
+      "card": "references/packages/dumux.md"
+    },
+    {
+      "package_id": "elk",
+      "title": "Elk All-Electron DFT Code",
+      "description": "Elk is an all-electron full-potential linearized augmented-plane-wave code for first-principles electronic-structure calculations in solids using density functional theory and related methods.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science"
+      ],
+      "tags": [
+        "electronic-structure",
+        "density-functional-theory",
+        "all-electron",
+        "fp-lapw",
+        "materials-science",
+        "solid-state-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/elk",
+      "source_archive_url": "https://github.com/skilled-scipkg/elk/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/elk-code/elk",
+      "homepage_url": "https://elk.sourceforge.io/",
+      "card": "references/packages/elk.md"
+    },
+    {
+      "package_id": "elmerfem",
+      "title": "Elmer FEM",
+      "description": "ElmerFEM is an open-source multiphysics finite element simulation suite for solving coupled partial differential equations in engineering and physics, including fluid flow, heat transfer, electromagnetics, and structural mechanics.",
+      "domains": [
+        "electromagnetics",
+        "computational_fluid_dynamics",
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "finite-element",
+        "multiphysics",
+        "pde",
+        "computational-physics",
+        "cfd",
+        "structural-mechanics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/elmerfem",
+      "source_archive_url": "https://github.com/skilled-scipkg/elmerfem/archive/refs/heads/devel.zip",
+      "upstream_repo_url": "https://github.com/ElmerCSC/elmerfem",
+      "homepage_url": "http://www.elmerfem.org",
+      "card": "references/packages/elmerfem.md"
+    },
+    {
+      "package_id": "enzo-e",
+      "title": "Enzo-E Exascale Astrophysics Simulator",
+      "description": "Enzo-E is an exascale-oriented astrophysics and cosmology simulation code built on the Cello AMR framework for massively parallel hydrodynamics and structure-formation studies.",
+      "domains": [
+        "astronomy_astrophysics",
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "astrophysics",
+        "cosmology",
+        "amr",
+        "hpc",
+        "hydrodynamics",
+        "simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/enzo-e",
+      "source_archive_url": "https://github.com/skilled-scipkg/enzo-e/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/enzo-project/enzo-e",
+      "homepage_url": "https://github.com/enzo-project/enzo-e",
+      "card": "references/packages/enzo-e.md"
+    },
+    {
+      "package_id": "espresso",
+      "title": "ESPResSo Soft-Matter Molecular Dynamics",
+      "description": "ESPResSo is an extensible molecular dynamics engine for coarse-grained soft-matter systems, supporting advanced electrostatics, hydrodynamics coupling, and flexible Python-driven simulation workflows.",
+      "domains": [
+        "molecular_dynamics",
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "molecular-dynamics",
+        "soft-matter",
+        "coarse-grained",
+        "computational-physics",
+        "mesoscale-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/espresso",
+      "source_archive_url": "https://github.com/skilled-scipkg/espresso/archive/refs/heads/python.zip",
+      "upstream_repo_url": "https://github.com/espressomd/espresso",
+      "homepage_url": "https://espressomd.org",
+      "card": "references/packages/espresso.md"
+    },
+    {
+      "package_id": "exoplanet",
+      "title": "exoplanet Bayesian Exoplanet Inference Toolkit",
+      "description": "exoplanet provides fast, scalable probabilistic models for astronomical time-series, enabling Bayesian transit and radial-velocity inference for exoplanet systems using PyMC-based MCMC workflows.",
+      "domains": [
+        "astronomy_astrophysics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "astronomy",
+        "exoplanets",
+        "bayesian-inference",
+        "time-series",
+        "mcmc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/exoplanet",
+      "source_archive_url": "https://github.com/skilled-scipkg/exoplanet/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/exoplanet-dev/exoplanet",
+      "homepage_url": "https://docs.exoplanet.codes",
+      "card": "references/packages/exoplanet.md"
+    },
+    {
+      "package_id": "fairroot",
+      "title": "FairRoot Particle Physics Framework",
+      "description": "FairRoot is a C++ framework for detector simulation, event reconstruction, and physics analysis in nuclear and particle experiments, built on ROOT with Geant3 and Geant4 transport support.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "particle-physics",
+        "nuclear-physics",
+        "detector-simulation",
+        "event-reconstruction",
+        "root",
+        "geant"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/FairRoot",
+      "source_archive_url": "https://github.com/skilled-scipkg/FairRoot/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/FairRootGroup/FairRoot",
+      "homepage_url": "http://fairroot.gsi.de",
+      "card": "references/packages/fairroot.md"
+    },
+    {
+      "package_id": "fbpic",
+      "title": "FBPIC Spectral Quasi-3D PIC",
+      "description": "FBPIC is a Fourier-Bessel particle-in-cell simulator for relativistic plasma physics, optimized for laser and plasma wakefield acceleration studies on CPU and GPU.",
+      "domains": [
+        "plasma_particle_simulation"
+      ],
+      "tags": [
+        "plasma-physics",
+        "particle-in-cell",
+        "wakefield-acceleration",
+        "laser-plasma",
+        "spectral-simulation",
+        "gpu-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/fbpic",
+      "source_archive_url": "https://github.com/skilled-scipkg/fbpic/archive/refs/heads/dev.zip",
+      "upstream_repo_url": "https://github.com/fbpic/fbpic",
+      "homepage_url": "http://fbpic.github.io",
+      "card": "references/packages/fbpic.md"
+    },
+    {
+      "package_id": "fdtdbath-meep",
+      "title": "Modified Meep FDTD Electromagnetics Simulator for FDTD-Bath approach of condensed-phase polaritonics",
+      "description": "The modified Meep code with standard meep functions + fdtd-bath implementation for condensed-phase polaritonics",
+      "domains": [
+        "electromagnetics"
+      ],
+      "tags": [
+        "electromagnetics",
+        "fdtd",
+        "photonics",
+        "maxwell",
+        "computational-physics",
+        "wave-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/fdtdbath-meep",
+      "source_archive_url": "https://github.com/skilled-scipkg/fdtdbath-meep/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/TaoELi/fdtdbath-meep",
+      "homepage_url": "https://github.com/TaoELi/fdtdbath-meep",
+      "card": "references/packages/fdtdbath-meep.md"
+    },
+    {
+      "package_id": "geant4",
+      "title": "Geant4 Particle-Matter Simulation Toolkit",
+      "description": "Geant4 is a C++ toolkit for Monte Carlo simulation of particle interactions with matter across detector design, radiation transport, medical physics, and space science applications.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "particle-physics",
+        "monte-carlo",
+        "radiation-transport",
+        "detector-simulation",
+        "medical-physics",
+        "nuclear-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/geant4",
+      "source_archive_url": "https://github.com/skilled-scipkg/geant4/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/Geant4/geant4",
+      "homepage_url": "https://geant4.org",
+      "card": "references/packages/geant4.md"
+    },
+    {
+      "package_id": "geosx",
+      "title": "GEOSX Subsurface Multiphysics Framework",
+      "description": "GEOSX is an open-source high-performance simulation framework for coupled subsurface flow, transport, and geomechanics, targeting carbon sequestration, geothermal energy, and large-scale reservoir modeling.",
+      "domains": [
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "subsurface",
+        "geomechanics",
+        "multiphysics",
+        "reservoir",
+        "hpc",
+        "carbon-sequestration",
+        "geothermal"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/GEOSX",
+      "source_archive_url": "https://github.com/skilled-scipkg/GEOSX/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/EngSubsurfaceModeling/GEOSX",
+      "homepage_url": "https://github.com/EngSubsurfaceModeling/GEOSX",
+      "card": "references/packages/geosx.md"
+    },
+    {
+      "package_id": "gprmax",
+      "title": "gprMax Ground Penetrating Radar Simulator",
+      "description": "gprMax is an open-source 3D finite-difference time-domain simulator for electromagnetic wave propagation, primarily used for ground penetrating radar modelling and subsurface investigations.",
+      "domains": [
+        "electromagnetics"
+      ],
+      "tags": [
+        "electromagnetics",
+        "fdtd",
+        "gpr",
+        "geophysics",
+        "simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/gprMax",
+      "source_archive_url": "https://github.com/skilled-scipkg/gprMax/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/gprMax/gprMax",
+      "homepage_url": "https://www.gprmax.com",
+      "card": "references/packages/gprmax.md"
+    },
+    {
+      "package_id": "gromacs",
+      "title": "GROMACS Molecular Dynamics",
+      "description": "GROMACS is a high-performance molecular dynamics toolkit for simulating biomolecules, polymers, and liquids, with strong support for free-energy workflows and trajectory analysis.",
+      "domains": [
+        "computational_chemistry",
+        "molecular_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "gromacs",
+        "molecular-dynamics",
+        "computational-chemistry",
+        "biophysics",
+        "free-energy",
+        "trajectory-analysis"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/gromacs",
+      "source_archive_url": "https://github.com/skilled-scipkg/gromacs/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/gromacs/gromacs",
+      "homepage_url": "http://www.gromacs.org",
+      "card": "references/packages/gromacs.md"
+    },
+    {
+      "package_id": "gwaslab",
+      "title": "GWASLab Summary Statistics Toolkit",
+      "description": "GWASLab is a Python toolkit for loading, harmonizing, quality-controlling, converting, and visualizing genome-wide association study summary statistics across common GWAS formats and reference resources.",
+      "domains": [
+        "bioinformatics"
+      ],
+      "tags": [
+        "gwas",
+        "genomics",
+        "summary-statistics",
+        "statistical-genetics",
+        "visualization"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/gwaslab",
+      "source_archive_url": "https://github.com/skilled-scipkg/gwaslab/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/Cloufield/gwaslab",
+      "homepage_url": "https://github.com/Cloufield/gwaslab",
+      "card": "references/packages/gwaslab.md"
+    },
+    {
+      "package_id": "gz-sim",
+      "title": "Gazebo Sim (gz-sim)",
+      "description": "Open-source robotics simulator for high-fidelity physics, 3D rendering, and sensor modeling, enabling virtual robot testing through GUI, plugins, command-line tools, and distributed transport interfaces.",
+      "domains": [
+        "robotics_physics"
+      ],
+      "tags": [
+        "robotics",
+        "simulation",
+        "physics",
+        "sensors",
+        "gazebo",
+        "autonomy"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/gz-sim",
+      "source_archive_url": "https://github.com/skilled-scipkg/gz-sim/archive/refs/heads/gz-sim10.zip",
+      "upstream_repo_url": "https://github.com/gazebosim/gz-sim",
+      "homepage_url": "https://gazebosim.org",
+      "card": "references/packages/gz-sim.md"
+    },
+    {
+      "package_id": "hail",
+      "title": "Hail Genomics Analytics",
+      "description": "Hail is a cloud native Python framework for large scale genomic dataframes, enabling distributed variant analysis, GWAS pipelines, and cohort level quality control on massive sequencing datasets.",
+      "domains": [
+        "bioinformatics"
+      ],
+      "tags": [
+        "genomics",
+        "gwas",
+        "populationgenetics",
+        "variantqc",
+        "bioinformatics",
+        "distributedcomputing"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/hail",
+      "source_archive_url": "https://github.com/skilled-scipkg/hail/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/hail-is/hail",
+      "homepage_url": "https://hail.is",
+      "card": "references/packages/hail.md"
+    },
+    {
+      "package_id": "hiphive",
+      "title": "hiphive Force-Constant Modeling",
+      "description": "hiphive builds sparse high-order interatomic force constant models from first-principles data to enable phonon calculations, lattice dynamics analysis, and anharmonic thermal transport workflows in crystalline materials.",
+      "domains": [
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "materials-science",
+        "lattice-dynamics",
+        "phonons",
+        "force-constants",
+        "atomistic-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/hiphive",
+      "source_archive_url": "https://github.com/skilled-scipkg/hiphive/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/hiphive/hiphive",
+      "homepage_url": "https://github.com/hiphive/hiphive",
+      "card": "references/packages/hiphive.md"
+    },
+    {
+      "package_id": "hoomd-blue",
+      "title": "HOOMD-blue Particle Simulation",
+      "description": "HOOMD-blue is a Python package for GPU and CPU molecular dynamics and hard-particle Monte Carlo simulations of soft-matter and general particle systems.",
+      "domains": [
+        "molecular_dynamics",
+        "high_energy_physics"
+      ],
+      "tags": [
+        "molecular-dynamics",
+        "monte-carlo",
+        "soft-matter",
+        "particle-simulation",
+        "gpu-computing",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/hoomd-blue",
+      "source_archive_url": "https://github.com/skilled-scipkg/hoomd-blue/archive/refs/heads/trunk.zip",
+      "upstream_repo_url": "https://github.com/glotzerlab/hoomd-blue",
+      "homepage_url": "http://glotzerlab.engin.umich.edu/hoomd-blue",
+      "card": "references/packages/hoomd-blue.md"
+    },
+    {
+      "package_id": "itensor",
+      "title": "ITensor Tensor Network Library",
+      "description": "ITensor is a C++ library for efficient tensor network calculations, featuring automatic index-aware contractions for matrix product states and quantum many-body algorithms.",
+      "domains": [
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "tensor-networks",
+        "quantum-many-body",
+        "dmrg",
+        "mps",
+        "cpp"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/ITensor",
+      "source_archive_url": "https://github.com/skilled-scipkg/ITensor/archive/refs/heads/v3.zip",
+      "upstream_repo_url": "https://github.com/ITensor/ITensor",
+      "homepage_url": "http://itensor.org",
+      "card": "references/packages/itensor.md"
+    },
+    {
+      "package_id": "itensors-jl",
+      "title": "ITensors.jl Tensor Network Library",
+      "description": "ITensors.jl is a Julia package for efficient index-aware tensor operations and tensor network primitives used in quantum many-body and numerical physics workflows.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "julia",
+        "tensor-networks",
+        "computational-physics",
+        "quantum-many-body",
+        "tensor-algebra"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/ITensors.jl",
+      "source_archive_url": "https://github.com/skilled-scipkg/ITensors.jl/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/ITensor/ITensors.jl",
+      "homepage_url": "https://itensor.org",
+      "card": "references/packages/itensors-jl.md"
+    },
+    {
+      "package_id": "jdftx",
+      "title": "JDFTx",
+      "description": "JDFTx is a high-performance electronic-structure code implementing joint density functional theory for quantum simulations of solids, surfaces, and electrochemical interfaces with continuum solvation and advanced DFT capabilities.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science"
+      ],
+      "tags": [
+        "electronic-structure",
+        "density-functional-theory",
+        "joint-dft",
+        "electrochemistry",
+        "materials-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/jdftx",
+      "source_archive_url": "https://github.com/skilled-scipkg/jdftx/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/shankar1729/jdftx",
+      "homepage_url": "http://jdftx.org",
+      "card": "references/packages/jdftx.md"
+    },
+    {
+      "package_id": "jobflow",
+      "title": "Jobflow Computational Workflow Library",
+      "description": "Jobflow is a Python library for defining, composing, and executing dynamic computational workflows as connected jobs and flows, with remote execution options and persistent scientific output storage.",
+      "domains": [
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "workflow",
+        "computational-workflows",
+        "materials-science",
+        "high-throughput",
+        "job-orchestration",
+        "scientific-automation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/jobflow",
+      "source_archive_url": "https://github.com/skilled-scipkg/jobflow/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/materialsproject/jobflow",
+      "homepage_url": "https://materialsproject.github.io/jobflow",
+      "card": "references/packages/jobflow.md"
+    },
+    {
+      "package_id": "kadanoffbaym-jl",
+      "title": "KadanoffBaym.jl",
+      "description": "Julia package for adaptive numerical integration of nonequilibrium Kadanoff-Baym equations and real-time Green function dynamics in many-body quantum systems.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "julia",
+        "nonequilibrium",
+        "many-body",
+        "quantum-dynamics",
+        "green-functions",
+        "kadanoff-baym"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/KadanoffBaym.jl",
+      "source_archive_url": "https://github.com/skilled-scipkg/KadanoffBaym.jl/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/NonequilibriumDynamics/KadanoffBaym.jl",
+      "homepage_url": "https://github.com/NonequilibriumDynamics/KadanoffBaym.jl",
+      "card": "references/packages/kadanoffbaym-jl.md"
+    },
+    {
+      "package_id": "kite",
+      "title": "KITE Quantum Transport Suite",
+      "description": "KITE is a Python/C++ package for large-scale real-space tight-binding simulations of electronic structure and bulk quantum transport in disordered materials, including DC/AC conductivity, DoS, and wave-packet dynamics.",
+      "domains": [
+        "quantum_chemistry",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "quantum-transport",
+        "tight-binding",
+        "electronic-structure",
+        "condensed-matter",
+        "hpc",
+        "disorder"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/kite",
+      "source_archive_url": "https://github.com/skilled-scipkg/kite/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/quantum-kite/kite",
+      "homepage_url": "https://quantum-kite.com",
+      "card": "references/packages/kite.md"
+    },
+    {
+      "package_id": "kratos",
+      "title": "Kratos Multiphysics",
+      "description": "Kratos Multiphysics is a modular, parallel framework for coupled finite-element simulations across fluid dynamics, structural mechanics, contact, DEM, and fluid-structure interaction domains.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "multiphysics",
+        "finite-element",
+        "cfd",
+        "structural-mechanics",
+        "fsi",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/Kratos",
+      "source_archive_url": "https://github.com/skilled-scipkg/Kratos/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/KratosMultiphysics/Kratos",
+      "homepage_url": "https://kratosmultiphysics.github.io/Kratos/",
+      "card": "references/packages/kratos.md"
+    },
+    {
+      "package_id": "kwant",
+      "title": "Kwant Quantum Transport Toolkit",
+      "description": "Kwant is an open-source Python package for numerical calculations on tight-binding models with a strong focus on quantum transport in mesoscopic systems.",
+      "domains": [
+        "quantum_chemistry",
+        "plasma_particle_simulation"
+      ],
+      "tags": [
+        "quantum-transport",
+        "tight-binding",
+        "mesoscopic-physics",
+        "condensed-matter",
+        "nanodevices",
+        "quantum-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/kwant",
+      "source_archive_url": "https://github.com/skilled-scipkg/kwant/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/kwant-project/kwant",
+      "homepage_url": "https://kwant-project.org/",
+      "card": "references/packages/kwant.md"
+    },
+    {
+      "package_id": "lammps",
+      "title": "LAMMPS Molecular Dynamics",
+      "description": "LAMMPS is a high-performance molecular dynamics package for atomistic and coarse-grained simulations of materials, soft matter, and related many-particle systems.",
+      "domains": [
+        "molecular_dynamics",
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "molecular-dynamics",
+        "atomistic-simulation",
+        "materials-science",
+        "hpc",
+        "classical-md"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/lammps",
+      "source_archive_url": "https://github.com/skilled-scipkg/lammps/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/lammps/lammps",
+      "homepage_url": "https://www.lammps.org",
+      "card": "references/packages/lammps.md"
+    },
+    {
+      "package_id": "lightkurve",
+      "title": "Lightkurve Kepler and TESS Light-Curve Analysis",
+      "description": "Lightkurve offers user-friendly tools to retrieve, clean, visualize, and analyze Kepler and TESS astronomical flux time series, including light curves and target pixel files for exoplanet and stellar variability studies.",
+      "domains": [
+        "astronomy_astrophysics"
+      ],
+      "tags": [
+        "astronomy",
+        "photometry",
+        "time-series",
+        "exoplanets",
+        "kepler",
+        "tess"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/lightkurve",
+      "source_archive_url": "https://github.com/skilled-scipkg/lightkurve/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/lightkurve/lightkurve",
+      "homepage_url": "https://lightkurve.github.io/lightkurve/",
+      "card": "references/packages/lightkurve.md"
+    },
+    {
+      "package_id": "limix",
+      "title": "LIMIX Genomic Linear Mixed Models",
+      "description": "LIMIX provides efficient linear mixed model methods for genomic association, interaction, and variance decomposition analyses, supporting workflows such as single-variant tests, set tests, and eQTL-style statistical genetics studies.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "genomics",
+        "statistical-genetics",
+        "linear-mixed-models",
+        "gwas",
+        "eqtl",
+        "association-testing"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/limix",
+      "source_archive_url": "https://github.com/skilled-scipkg/limix/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/limix/limix",
+      "homepage_url": "https://github.com/limix/limix",
+      "card": "references/packages/limix.md"
+    },
+    {
+      "package_id": "maxwelllink",
+      "title": "MaxwellLink Light-Matter Co-Simulation",
+      "description": "MaxwellLink is a modular Python framework for self-consistent electromagnetic molecular co-simulation, coupling EM solvers with quantum, force-field, and first-principles molecular dynamics drivers.",
+      "domains": [
+        "molecular_dynamics",
+        "electromagnetics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "light-matter",
+        "electrodynamics",
+        "multiphysics",
+        "molecular-dynamics",
+        "quantum-dynamics",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/MaxwellLink",
+      "source_archive_url": "https://github.com/skilled-scipkg/MaxwellLink/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/TaoELi/MaxwellLink",
+      "homepage_url": "https://taoeli.github.io/MaxwellLink/",
+      "card": "references/packages/maxwelllink.md"
+    },
+    {
+      "package_id": "mcdc",
+      "title": "MC/DC Neutron Transport",
+      "description": "MC/DC is a scalable Monte Carlo neutron transport package for fully transient reactor and radiation simulations, enabling rapid methods development with performant, machine-portable Python implementations.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "neutron-transport",
+        "monte-carlo",
+        "reactor-physics",
+        "radiation-transport",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/MCDC",
+      "source_archive_url": "https://github.com/skilled-scipkg/MCDC/archive/refs/heads/dev.zip",
+      "upstream_repo_url": "https://github.com/CEMeNT-PSAAP/MCDC",
+      "homepage_url": "https://mcdc.readthedocs.io/en/latest/",
+      "card": "references/packages/mcdc.md"
+    },
+    {
+      "package_id": "meep",
+      "title": "Meep Electromagnetic FDTD Simulator",
+      "description": "Meep is an open-source finite-difference time-domain simulator for modeling electromagnetic wave propagation, resonances, and scattering in photonic structures across 1D, 2D, 3D, and cylindrical geometries.",
+      "domains": [
+        "electromagnetics"
+      ],
+      "tags": [
+        "electromagnetics",
+        "fdtd",
+        "photonics",
+        "nanophotonics",
+        "maxwell",
+        "wave-optics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/meep",
+      "source_archive_url": "https://github.com/skilled-scipkg/meep/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/NanoComp/meep",
+      "homepage_url": "https://github.com/NanoComp/meep",
+      "card": "references/packages/meep.md"
+    },
+    {
+      "package_id": "mfem",
+      "title": "MFEM Finite Element Library",
+      "description": "MFEM is a modular, scalable C++ finite element library for high-order PDE discretization, adaptive meshing, and MPI/GPU-enabled scientific simulation from laptops to supercomputers.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "finite-element",
+        "pde",
+        "scientific-computing",
+        "hpc",
+        "cpp",
+        "amr"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/mfem",
+      "source_archive_url": "https://github.com/skilled-scipkg/mfem/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/mfem/mfem",
+      "homepage_url": "http://mfem.org",
+      "card": "references/packages/mfem.md"
+    },
+    {
+      "package_id": "mitgcm",
+      "title": "MIT General Circulation Model (MITgcm)",
+      "description": "MITgcm is a flexible geophysical fluid dynamics package for simulating ocean and atmospheric circulation, with coupled ocean sea ice and climate process capabilities.",
+      "domains": [
+        "computational_fluid_dynamics"
+      ],
+      "tags": [
+        "mitgcm",
+        "ocean-model",
+        "climate-model",
+        "atmospheric-circulation",
+        "geophysical-fluids",
+        "sea-ice"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/MITgcm",
+      "source_archive_url": "https://github.com/skilled-scipkg/MITgcm/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/MITgcm/MITgcm",
+      "homepage_url": "http://mitgcm.org/",
+      "card": "references/packages/mitgcm.md"
+    },
+    {
+      "package_id": "modflow6",
+      "title": "MODFLOW 6 Groundwater Model",
+      "description": "MODFLOW 6 is the USGS modular hydrologic simulator for groundwater flow and transport, supporting integrated surface-water interactions, time-varying stresses, and extensible packages for basin-scale hydrogeologic modeling.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "groundwater",
+        "hydrology",
+        "hydrogeology",
+        "usgs",
+        "modflow",
+        "aquifer-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/modflow6",
+      "source_archive_url": "https://github.com/skilled-scipkg/modflow6/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/MODFLOW-ORG/modflow6",
+      "homepage_url": "https://modflow6.readthedocs.io/",
+      "card": "references/packages/modflow6.md"
+    },
+    {
+      "package_id": "molecool",
+      "title": "MoleCool Molecular Laser Cooling Simulator",
+      "description": "MoleCool simulates laser-driven molecular dynamics and spectra, combining optical Bloch and rate-equation solvers, cooling-force mapping, and Monte Carlo trajectories for AMO cooling and trapping experiment design.",
+      "domains": [
+        "molecular_dynamics",
+        "high_energy_physics"
+      ],
+      "tags": [
+        "amo-physics",
+        "laser-cooling",
+        "molecular-spectroscopy",
+        "optical-bloch",
+        "rate-equations",
+        "monte-carlo"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/MoleCool",
+      "source_archive_url": "https://github.com/skilled-scipkg/MoleCool/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/LangenGroup/MoleCool",
+      "homepage_url": "https://arxiv.org/abs/2510.16203",
+      "card": "references/packages/molecool.md"
+    },
+    {
+      "package_id": "mom6",
+      "title": "MOM6 Modular Ocean Model",
+      "description": "Modular Ocean Model (MOM6) is a finite-volume ocean general circulation model for ocean-only and coupled climate simulations, supporting tracer transport, stratified dynamics, and realistic large-scale ocean process studies.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "ocean-modeling",
+        "climate-modeling",
+        "ocean-circulation",
+        "geophysical-fluid-dynamics",
+        "earth-system"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/MOM6",
+      "source_archive_url": "https://github.com/skilled-scipkg/MOM6/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/mom-ocean/MOM6",
+      "homepage_url": "https://github.com/mom-ocean/MOM6",
+      "card": "references/packages/mom6.md"
+    },
+    {
+      "package_id": "moose",
+      "title": "MOOSE Multiphysics Framework",
+      "description": "MOOSE is an object-oriented finite-element framework for fully coupled implicit multiphysics simulations with adaptive meshing, scalable parallel solvers, and engineering-focused APIs.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "finite_element_engineering",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "multiphysics",
+        "finite-element",
+        "pde",
+        "simulation",
+        "hpc",
+        "engineering"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/moose",
+      "source_archive_url": "https://github.com/skilled-scipkg/moose/archive/refs/heads/next.zip",
+      "upstream_repo_url": "https://github.com/idaholab/moose",
+      "homepage_url": "https://mooseframework.inl.gov",
+      "card": "references/packages/moose.md"
+    },
+    {
+      "package_id": "mpas-model",
+      "title": "MPAS Model for Prediction Across Scales",
+      "description": "MPAS-Model is an unstructured-mesh earth system modeling framework for atmosphere, ocean, sea ice, and land ice simulations used in climate, regional climate, and weather research.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "mpas",
+        "climate-modeling",
+        "earth-system",
+        "atmosphere",
+        "ocean",
+        "sea-ice",
+        "weather-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/MPAS-Model",
+      "source_archive_url": "https://github.com/skilled-scipkg/MPAS-Model/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/MPAS-Dev/MPAS-Model",
+      "homepage_url": "https://github.com/MPAS-Dev/MPAS-Model",
+      "card": "references/packages/mpas-model.md"
+    },
+    {
+      "package_id": "mujoco",
+      "title": "MuJoCo Physics Simulator",
+      "description": "MuJoCo is a high-performance multi-joint rigid-body physics engine for contact-rich simulation in robotics, biomechanics, control, and differentiable dynamics research.",
+      "domains": [
+        "robotics_physics"
+      ],
+      "tags": [
+        "physics-simulation",
+        "robotics",
+        "rigid-body-dynamics",
+        "contact-dynamics",
+        "biomechanics",
+        "optimal-control"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/mujoco",
+      "source_archive_url": "https://github.com/skilled-scipkg/mujoco/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/google-deepmind/mujoco",
+      "homepage_url": "https://mujoco.org",
+      "card": "references/packages/mujoco.md"
+    },
+    {
+      "package_id": "mumax3",
+      "title": "MuMax3 Micromagnetic Simulator",
+      "description": "MuMax3 is a GPU-accelerated micromagnetic simulation package for modeling magnetization dynamics, spintronic effects, and nanomagnetic device behavior using Landau-Lifshitz-Gilbert equation solvers.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "micromagnetics",
+        "gpu",
+        "spintronics",
+        "nanomagnetism",
+        "magnetization"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/3",
+      "source_archive_url": "https://github.com/skilled-scipkg/3/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/mumax/3",
+      "homepage_url": "https://github.com/mumax/3",
+      "card": "references/packages/mumax3.md"
+    },
+    {
+      "package_id": "nekrs",
+      "title": "nekRS CFD Solver",
+      "description": "nekRS is a GPU-accelerated high-order spectral-element computational fluid dynamics solver for incompressible and low-Mach Navier-Stokes flows on massively parallel HPC systems.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "cfd",
+        "hpc",
+        "gpu",
+        "spectral-elements",
+        "navier-stokes",
+        "fluid-dynamics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/nekRS",
+      "source_archive_url": "https://github.com/skilled-scipkg/nekRS/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/Nek5000/nekRS",
+      "homepage_url": "https://nek5000.mcs.anl.gov/",
+      "card": "references/packages/nekrs.md"
+    },
+    {
+      "package_id": "nessi",
+      "title": "NESSi Non-Equilibrium Systems Simulation",
+      "description": "NESSi is an open-source package for simulating nonequilibrium many-body dynamics using contour-ordered Green's functions on the Kadanoff-Baym contour with equation-of-motion solvers and scalable reciprocal-space parallelization.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "many-body-physics",
+        "nonequilibrium",
+        "green-functions",
+        "quantum-dynamics",
+        "kadanoff-baym",
+        "condensed-matter"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/nessi",
+      "source_archive_url": "https://github.com/skilled-scipkg/nessi/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/nessi-cntr/nessi",
+      "homepage_url": "https://github.com/nessi-cntr/nessi",
+      "card": "references/packages/nessi.md"
+    },
+    {
+      "package_id": "nest-simulator",
+      "title": "NEST Spiking Neural Network Simulator",
+      "description": "NEST is a scalable simulator for large spiking neural networks, supporting diverse neuron and synapse models to study cortical dynamics, plasticity, and electrophysiology-inspired experiments.",
+      "domains": [
+        "computational_neuroscience"
+      ],
+      "tags": [
+        "computational-neuroscience",
+        "spiking-networks",
+        "neural-simulation",
+        "synaptic-plasticity",
+        "brain-network-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/nest-simulator",
+      "source_archive_url": "https://github.com/skilled-scipkg/nest-simulator/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/nest/nest-simulator",
+      "homepage_url": "http://www.nest-simulator.org",
+      "card": "references/packages/nest-simulator.md"
+    },
+    {
+      "package_id": "netket",
+      "title": "NetKet Quantum Many-Body ML",
+      "description": "NetKet is a Python library for variational and machine-learning methods in many-body quantum physics, supporting neural quantum states, Monte Carlo sampling, and optimization of lattice Hamiltonian ground states and dynamics.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "quantum-physics",
+        "many-body",
+        "variational-monte-carlo",
+        "neural-quantum-states",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/netket",
+      "source_archive_url": "https://github.com/skilled-scipkg/netket/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/netket/netket",
+      "homepage_url": "https://www.netket.org",
+      "card": "references/packages/netket.md"
+    },
+    {
+      "package_id": "neuron",
+      "title": "NEURON Neural Simulator",
+      "description": "NEURON is a scientific simulator for biophysical neuron and neural network models, supporting multicompartment electrophysiology, synaptic mechanisms, and MOD-defined ion-channel dynamics for computational neuroscience research.",
+      "domains": [
+        "computational_neuroscience"
+      ],
+      "tags": [
+        "computational-neuroscience",
+        "neuron-modeling",
+        "electrophysiology",
+        "biophysical-simulation",
+        "neural-networks"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/nrn",
+      "source_archive_url": "https://github.com/skilled-scipkg/nrn/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/neuronsimulator/nrn",
+      "homepage_url": "http://nrn.readthedocs.io",
+      "card": "references/packages/neuron.md"
+    },
+    {
+      "package_id": "nextflow",
+      "title": "Nextflow Scientific Workflow Engine",
+      "description": "Nextflow is a dataflow-driven DSL and runtime for building reproducible, portable scientific pipelines that scale from laptops to HPC schedulers and cloud batch systems.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "workflow",
+        "pipelines",
+        "bioinformatics",
+        "genomics",
+        "hpc",
+        "reproducibility"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/nextflow",
+      "source_archive_url": "https://github.com/skilled-scipkg/nextflow/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/nextflow-io/nextflow",
+      "homepage_url": "http://nextflow.io",
+      "card": "references/packages/nextflow.md"
+    },
+    {
+      "package_id": "nwchem",
+      "title": "NWChem Computational Chemistry",
+      "description": "NWChem is a high-performance computational chemistry package for scalable ab initio and molecular simulations, including quantum electronic structure, molecular dynamics, and spectroscopy on HPC systems.",
+      "domains": [
+        "quantum_chemistry",
+        "computational_chemistry",
+        "molecular_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "computational-chemistry",
+        "quantum-chemistry",
+        "electronic-structure",
+        "molecular-dynamics",
+        "hpc",
+        "ab-initio"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/nwchem",
+      "source_archive_url": "https://github.com/skilled-scipkg/nwchem/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/nwchemgit/nwchem",
+      "homepage_url": "http://nwchemgit.github.io",
+      "card": "references/packages/nwchem.md"
+    },
+    {
+      "package_id": "openbabel",
+      "title": "Open Babel",
+      "description": "Open Babel is an open-source chemical toolbox for converting, searching, and analyzing molecular and materials data across many cheminformatics file formats.",
+      "domains": [
+        "computational_chemistry",
+        "bioinformatics"
+      ],
+      "tags": [
+        "cheminformatics",
+        "chemistry",
+        "molecular-data",
+        "file-conversion",
+        "smiles",
+        "inchi"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/openbabel",
+      "source_archive_url": "https://github.com/skilled-scipkg/openbabel/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/openbabel/openbabel",
+      "homepage_url": "http://openbabel.org/",
+      "card": "references/packages/openbabel.md"
+    },
+    {
+      "package_id": "openems",
+      "title": "openEMS Electromagnetic Solver",
+      "description": "openEMS is an open-source EC-FDTD electromagnetic field solver for simulating antennas, RF and microwave structures, and wave propagation in three-dimensional computational electromagnetics workflows.",
+      "domains": [
+        "electromagnetics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "electromagnetics",
+        "fdtd",
+        "rf",
+        "microwave",
+        "antenna",
+        "simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/openEMS",
+      "source_archive_url": "https://github.com/skilled-scipkg/openEMS/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/thliebig/openEMS",
+      "homepage_url": "http://openEMS.de",
+      "card": "references/packages/openems.md"
+    },
+    {
+      "package_id": "openff-toolkit",
+      "title": "Open Force Field Toolkit",
+      "description": "Python toolkit for applying and developing SMIRNOFF molecular mechanics force fields with direct chemical perception, parameter assignment, and cheminformatics workflows for small molecules.",
+      "domains": [
+        "computational_chemistry",
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "computational-chemistry",
+        "molecular-mechanics",
+        "force-fields",
+        "cheminformatics",
+        "parameterization"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/openff-toolkit",
+      "source_archive_url": "https://github.com/skilled-scipkg/openff-toolkit/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/openforcefield/openff-toolkit",
+      "homepage_url": "http://openforcefield.org",
+      "card": "references/packages/openff-toolkit.md"
+    },
+    {
+      "package_id": "openfoam-dev",
+      "title": "OpenFOAM-dev CFD Platform",
+      "description": "OpenFOAM-dev is the OpenFOAM Foundation development codebase for finite-volume CFD and multiphysics simulation, supporting incompressible and compressible flow, turbulence, heat transfer, and extensible solver workflows.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "cfd",
+        "finite-volume",
+        "multiphysics",
+        "turbulence",
+        "meshing",
+        "openfoam"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/OpenFOAM-dev",
+      "source_archive_url": "https://github.com/skilled-scipkg/OpenFOAM-dev/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/OpenFOAM/OpenFOAM-dev",
+      "homepage_url": "https://openfoam.org",
+      "card": "references/packages/openfoam-dev.md"
+    },
+    {
+      "package_id": "openmc",
+      "title": "OpenMC Monte Carlo Particle Transport",
+      "description": "OpenMC is a Monte Carlo neutron and photon transport package for reactor physics and radiation modeling using continuous energy nuclear data and constructive solid geometry.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "openmc",
+        "monte-carlo",
+        "reactor-physics",
+        "nuclear-transport",
+        "criticality",
+        "radiation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/openmc",
+      "source_archive_url": "https://github.com/skilled-scipkg/openmc/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/openmc-dev/openmc",
+      "homepage_url": "https://docs.openmc.org",
+      "card": "references/packages/openmc.md"
+    },
+    {
+      "package_id": "openmm",
+      "title": "OpenMM Molecular Dynamics Toolkit",
+      "description": "OpenMM is a high-performance molecular dynamics toolkit for biomolecular simulation, offering flexible custom forces and integrators with fast GPU execution through Python and C++ interfaces.",
+      "domains": [
+        "computational_chemistry",
+        "molecular_dynamics"
+      ],
+      "tags": [
+        "molecular-dynamics",
+        "molecular-simulation",
+        "computational-chemistry",
+        "biophysics",
+        "gpu-acceleration"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/openmm",
+      "source_archive_url": "https://github.com/skilled-scipkg/openmm/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/openmm/openmm",
+      "homepage_url": "https://github.com/openmm/openmm",
+      "card": "references/packages/openmm.md"
+    },
+    {
+      "package_id": "openmoc",
+      "title": "OpenMOC Reactor Physics Solver",
+      "description": "OpenMOC is a deterministic method-of-characteristics simulator for neutron transport in nuclear reactors, computing flux, power distribution, and multiplication factors for fixed-source and eigenvalue problems.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "openmoc",
+        "nuclear",
+        "reactor-physics",
+        "neutron-transport",
+        "moc",
+        "core-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/OpenMOC",
+      "source_archive_url": "https://github.com/skilled-scipkg/OpenMOC/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/mit-crpg/OpenMOC",
+      "homepage_url": "https://mit-crpg.github.io/OpenMOC/",
+      "card": "references/packages/openmoc.md"
+    },
+    {
+      "package_id": "openmx",
+      "title": "OpenMX Materials DFT Package",
+      "description": "OpenMX is an open-source DFT package for nano-scale material simulations based on norm-conserving pseudopotentials and pseudo-atomic localized basis functions. It is designed for large-scale parallel electronic-structure calculations with MPI or hybrid MPI/OpenMP execution across bulk, surface, interface, liquid, and low-dimensional materials.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "openmx",
+        "dft",
+        "electronic-structure",
+        "materials-science",
+        "pseudopotentials",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/openmx",
+      "source_archive_url": "https://github.com/skilled-scipkg/openmx/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://www.openmx-square.org/openmx3.9.tar.gz",
+      "homepage_url": "https://www.openmx-square.org/",
+      "card": "references/packages/openmx.md"
+    },
+    {
+      "package_id": "opensees",
+      "title": "OpenSees Earthquake Engineering Simulator",
+      "description": "OpenSees is a finite element platform for nonlinear structural and geotechnical analysis, widely used to model seismic response, time history behavior, and performance based earthquake engineering systems.",
+      "domains": [
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "earthquake-engineering",
+        "structural-mechanics",
+        "finite-element",
+        "seismic-analysis",
+        "civil-engineering"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/OpenSees",
+      "source_archive_url": "https://github.com/skilled-scipkg/OpenSees/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/OpenSees/OpenSees",
+      "homepage_url": "https://github.com/OpenSees/OpenSees",
+      "card": "references/packages/opensees.md"
+    },
+    {
+      "package_id": "opensn",
+      "title": "OpenSn Linear Boltzmann Solver",
+      "description": "OpenSn is a massively parallel scientific simulation engine that solves the linear Boltzmann equation using deterministic discrete-ordinates transport methods.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "neutron-transport",
+        "radiation-transport",
+        "boltzmann-equation",
+        "discrete-ordinates",
+        "hpc",
+        "scientific-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/opensn",
+      "source_archive_url": "https://github.com/skilled-scipkg/opensn/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/Open-Sn/opensn",
+      "homepage_url": "https://open-sn.github.io/opensn/",
+      "card": "references/packages/opensn.md"
+    },
+    {
+      "package_id": "opm-simulators",
+      "title": "OPM Flow Reservoir Simulator",
+      "description": "Open Porous Media simulators provide fully implicit reservoir modeling for black-oil production, CO2 and hydrogen storage, thermal, solvent, and polymer processes using Eclipse-compatible input decks at industrial scale.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "reservoir-simulation",
+        "porous-media",
+        "black-oil",
+        "co2-storage",
+        "hydrogen-storage",
+        "well-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/opm-simulators",
+      "source_archive_url": "https://github.com/skilled-scipkg/opm-simulators/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/OPM/opm-simulators",
+      "homepage_url": "http://www.opm-project.org",
+      "card": "references/packages/opm-simulators.md"
+    },
+    {
+      "package_id": "oqupy",
+      "title": "OQuPy",
+      "description": "Open Quantum Systems in Python package focused on non-Markovian process-tensor methods and environment-driven quantum dynamics.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "open-quantum-systems",
+        "non-markovian",
+        "process-tensor"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/OQuPy",
+      "source_archive_url": "https://github.com/skilled-scipkg/OQuPy/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/tempoCollaboration/OQuPy",
+      "homepage_url": "https://oqupy.readthedocs.io",
+      "card": "references/packages/oqupy.md"
+    },
+    {
+      "package_id": "packmol",
+      "title": "Packmol Molecular Configuration Builder",
+      "description": "Packmol generates initial molecular dynamics coordinates by packing molecules into user-defined regions while satisfying minimum-distance constraints to prevent destabilizing atomic overlaps.",
+      "domains": [
+        "computational_chemistry",
+        "molecular_dynamics"
+      ],
+      "tags": [
+        "molecular-dynamics",
+        "molecule-packing",
+        "initial-configuration",
+        "computational-chemistry",
+        "structure-preparation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/packmol",
+      "source_archive_url": "https://github.com/skilled-scipkg/packmol/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/m3g/packmol",
+      "homepage_url": "http://m3g.github.io/packmol",
+      "card": "references/packages/packmol.md"
+    },
+    {
+      "package_id": "palabos",
+      "title": "Palabos Lattice Boltzmann CFD",
+      "description": "Palabos is an open-source parallel computational fluid dynamics package implementing the lattice Boltzmann method for simulating complex fluid flows and transport phenomena.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "cfd",
+        "lattice-boltzmann",
+        "fluid-dynamics",
+        "hpc",
+        "multiphase-flow"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/palabos",
+      "source_archive_url": "https://github.com/skilled-scipkg/palabos/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/omalaspinas/palabos",
+      "homepage_url": "https://github.com/omalaspinas/palabos",
+      "card": "references/packages/palabos.md"
+    },
+    {
+      "package_id": "parflow",
+      "title": "ParFlow Watershed Flow Model",
+      "description": "ParFlow is a massively parallel integrated hydrologic model for coupled surface and subsurface watershed flow, simulating overland runoff, groundwater, and land-surface processes across complex terrain.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "hydrology",
+        "watershed",
+        "groundwater",
+        "surface-water",
+        "hpc",
+        "environmental-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/parflow",
+      "source_archive_url": "https://github.com/skilled-scipkg/parflow/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/parflow/parflow",
+      "homepage_url": "http://parflow.org",
+      "card": "references/packages/parflow.md"
+    },
+    {
+      "package_id": "pennylane",
+      "title": "PennyLane",
+      "description": "PennyLane is an open-source Python framework for building and optimizing quantum circuits, hybrid quantum-classical models, and quantum chemistry workflows across simulators and hardware backends.",
+      "domains": [
+        "quantum_chemistry",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "quantum-computing",
+        "quantum-machine-learning",
+        "quantum-chemistry",
+        "python",
+        "variational-algorithms"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pennylane",
+      "source_archive_url": "https://github.com/skilled-scipkg/pennylane/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/PennyLaneAI/pennylane",
+      "homepage_url": "https://pennylane.ai",
+      "card": "references/packages/pennylane.md"
+    },
+    {
+      "package_id": "perceval",
+      "title": "Perceval Photonic Quantum Toolkit",
+      "description": "Perceval is a Python framework for designing, simulating, and executing discrete-variable photonic quantum circuits with linear optics models and Quandela hardware connectivity.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "photonic-quantum",
+        "linear-optics",
+        "fock-states",
+        "quantum-simulation",
+        "quandela"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/Perceval",
+      "source_archive_url": "https://github.com/skilled-scipkg/Perceval/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/Quandela/Perceval",
+      "homepage_url": "https://perceval.quandela.net",
+      "card": "references/packages/perceval.md"
+    },
+    {
+      "package_id": "phono3py",
+      "title": "Phono3py",
+      "description": "phono3py computes anharmonic phonon properties from third-order force constants, enabling lattice thermal conductivity and phonon lifetime simulations for crystalline materials.",
+      "domains": [
+        "materials_science"
+      ],
+      "tags": [
+        "phonons",
+        "anharmonicity",
+        "lattice-dynamics",
+        "thermal-conductivity",
+        "materials-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/phono3py",
+      "source_archive_url": "https://github.com/skilled-scipkg/phono3py/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/phonopy/phono3py",
+      "homepage_url": "http://phonopy.github.io/phono3py/",
+      "card": "references/packages/phono3py.md"
+    },
+    {
+      "package_id": "phonopy",
+      "title": "Phonopy Phonon Lattice Dynamics",
+      "description": "Phonopy computes crystal phonons and vibrational thermodynamic properties from force constants, supporting dispersion, density of states, and finite-displacement lattice-dynamics workflows.",
+      "domains": [
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "phonons",
+        "lattice-dynamics",
+        "solid-state",
+        "materials-simulation",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/phonopy",
+      "source_archive_url": "https://github.com/skilled-scipkg/phonopy/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/phonopy/phonopy",
+      "homepage_url": "http://phonopy.github.io/phonopy/",
+      "card": "references/packages/phonopy.md"
+    },
+    {
+      "package_id": "photutils",
+      "title": "Photutils Astronomical Photometry Toolkit",
+      "description": "Photutils provides robust algorithms for detecting astronomical sources and performing aperture and PSF photometry, with background estimation, segmentation, centroiding, and profile analysis for telescope image data.",
+      "domains": [
+        "astronomy_astrophysics"
+      ],
+      "tags": [
+        "astronomy",
+        "astrophotometry",
+        "source-detection",
+        "aperture-photometry",
+        "psf-photometry",
+        "image-segmentation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/photutils",
+      "source_archive_url": "https://github.com/skilled-scipkg/photutils/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/astropy/photutils",
+      "homepage_url": "https://photutils.readthedocs.io",
+      "card": "references/packages/photutils.md"
+    },
+    {
+      "package_id": "picongpu",
+      "title": "PIConGPU",
+      "description": "PIConGPU performs fully relativistic 3D3V particle-in-cell plasma simulations with self-consistent electromagnetic fields, ionization, radiation diagnostics, and exascale GPU manycore scalability.",
+      "domains": [
+        "electromagnetics",
+        "plasma_particle_simulation",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "plasma-physics",
+        "particle-in-cell",
+        "hpc",
+        "gpu",
+        "electromagnetics",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/picongpu",
+      "source_archive_url": "https://github.com/skilled-scipkg/picongpu/archive/refs/heads/dev.zip",
+      "upstream_repo_url": "https://github.com/ComputationalRadiationPhysics/picongpu",
+      "homepage_url": "https://picongpu.readthedocs.io",
+      "card": "references/packages/picongpu.md"
+    },
+    {
+      "package_id": "plink-ng",
+      "title": "PLINK 2 Genome Association Toolkit",
+      "description": "PLINK-NG provides high-performance whole-genome association and population genetics analyses, supporting large cohort genotype, VCF, and dosage datasets for GWAS, quality control, and relatedness workflows.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "genomics",
+        "gwas",
+        "population-genetics",
+        "bioinformatics",
+        "variant-analysis"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/plink-ng",
+      "source_archive_url": "https://github.com/skilled-scipkg/plink-ng/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/chrchang/plink-ng",
+      "homepage_url": "https://www.cog-genomics.org/plink/2.0/",
+      "card": "references/packages/plink-ng.md"
+    },
+    {
+      "package_id": "precice",
+      "title": "preCICE Coupling Library",
+      "description": "preCICE couples independent simulation solvers for partitioned multi-physics and multi-scale workflows, providing robust communication, data mapping, and acceleration for surface and volume interface exchanges.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "multiphysics",
+        "partitioned-coupling",
+        "cosimulation",
+        "fsi",
+        "multiscale",
+        "solver-coupling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/precice",
+      "source_archive_url": "https://github.com/skilled-scipkg/precice/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/precice/precice",
+      "homepage_url": "https://precice.org/",
+      "card": "references/packages/precice.md"
+    },
+    {
+      "package_id": "psc",
+      "title": "PSC Particle-in-Cell Plasma Simulator",
+      "description": "PSC is a three-dimensional fully electromagnetic particle-in-cell code for kinetic plasma simulations with MPI scaling, GPU acceleration, and patch-based dynamic load balancing.",
+      "domains": [
+        "electromagnetics",
+        "plasma_particle_simulation",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "plasma-physics",
+        "particle-in-cell",
+        "electromagnetics",
+        "kinetic-plasma",
+        "hpc",
+        "gpu"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/psc",
+      "source_archive_url": "https://github.com/skilled-scipkg/psc/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/psc-code/psc",
+      "homepage_url": "https://psc.readthedocs.io/en/latest/",
+      "card": "references/packages/psc.md"
+    },
+    {
+      "package_id": "psi4",
+      "title": "Psi4 Quantum Chemistry",
+      "description": "Psi4 is an open source ab initio quantum chemistry package for high accuracy molecular electronic structure calculations, with performant C++ kernels and Python driven user workflows.",
+      "domains": [
+        "quantum_chemistry",
+        "computational_chemistry",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "quantum-chemistry",
+        "electronic-structure",
+        "ab-initio",
+        "computational-chemistry",
+        "molecular-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/psi4",
+      "source_archive_url": "https://github.com/skilled-scipkg/psi4/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/psi4/psi4",
+      "homepage_url": "http://psicode.org",
+      "card": "references/packages/psi4.md"
+    },
+    {
+      "package_id": "pybinding",
+      "title": "Pybinding Tight Binding Toolkit",
+      "description": "pybinding is a scientific Python library for constructing and solving tight-binding models of crystalline materials to study electronic structure and quantum transport in solid-state systems.",
+      "domains": [
+        "quantum_chemistry"
+      ],
+      "tags": [
+        "computational-physics",
+        "condensed-matter",
+        "tight-binding",
+        "electronic-structure",
+        "quantum-transport"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pybinding",
+      "source_archive_url": "https://github.com/skilled-scipkg/pybinding/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/dean0x7d/pybinding",
+      "homepage_url": "https://pybinding.site",
+      "card": "references/packages/pybinding.md"
+    },
+    {
+      "package_id": "pyfr",
+      "title": "PyFR High-Order CFD Solver",
+      "description": "PyFR is a Python framework for high-order flux-reconstruction simulation of advection-diffusion governing equations on mixed unstructured meshes, optimized for CPUs and GPUs via a templated kernel language.",
+      "domains": [
+        "computational_fluid_dynamics"
+      ],
+      "tags": [
+        "cfd",
+        "pde",
+        "flux-reconstruction",
+        "unstructured-mesh",
+        "gpu-computing"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/PyFR",
+      "source_archive_url": "https://github.com/skilled-scipkg/PyFR/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/PyFR/PyFR",
+      "homepage_url": "https://github.com/PyFR/PyFR",
+      "card": "references/packages/pyfr.md"
+    },
+    {
+      "package_id": "pyhf",
+      "title": "pyhf HistFactory Inference Toolkit",
+      "description": "pyhf provides pure-Python HistFactory statistical models for high-energy physics, enabling likelihood fitting, CLs hypothesis testing, and interval estimation with tensor backends and autodiff support.",
+      "domains": [
+        "high_energy_physics"
+      ],
+      "tags": [
+        "hep",
+        "histfactory",
+        "likelihood",
+        "inference",
+        "cls",
+        "autodiff"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pyhf",
+      "source_archive_url": "https://github.com/skilled-scipkg/pyhf/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scikit-hep/pyhf",
+      "homepage_url": "https://pyhf.readthedocs.io/",
+      "card": "references/packages/pyhf.md"
+    },
+    {
+      "package_id": "pyiron_base",
+      "title": "pyiron Base Workflow Core",
+      "description": "pyiron_base provides core workflow, job orchestration, and HDF5-based data management for large-scale computational materials science studies across local and HPC resources.",
+      "domains": [
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "computational-materials-science",
+        "workflow-management",
+        "hpc",
+        "job-orchestration",
+        "hdf5",
+        "parameter-studies"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pyiron_base",
+      "source_archive_url": "https://github.com/skilled-scipkg/pyiron_base/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/pyiron/pyiron_base",
+      "homepage_url": "https://pyiron-base.readthedocs.io",
+      "card": "references/packages/pyiron_base.md"
+    },
+    {
+      "package_id": "pylcp",
+      "title": "PyLCP Laser Cooling Physics",
+      "description": "pylcp is a Python toolkit for modeling laser-cooling systems by constructing internal Hamiltonians, laser and magnetic-field configurations, and solving optical Bloch equations to compute forces and dynamics.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "laser-cooling",
+        "amo-physics",
+        "quantum-optics",
+        "optical-bloch",
+        "atomic-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pylcp",
+      "source_archive_url": "https://github.com/skilled-scipkg/pylcp/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/JQIamo/pylcp",
+      "homepage_url": "https://github.com/JQIamo/pylcp",
+      "card": "references/packages/pylcp.md"
+    },
+    {
+      "package_id": "pylith",
+      "title": "PyLith Tectonic Deformation Simulator",
+      "description": "PyLith is a finite-element geodynamics package for quasi-static and dynamic simulation of crustal deformation, including earthquake rupture, fault friction, viscoelastic rheology, and volcano-related tectonic processes.",
+      "domains": [
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "geodynamics",
+        "finite-element",
+        "tectonics",
+        "earthquake-modeling",
+        "crustal-deformation",
+        "seismology"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pylith",
+      "source_archive_url": "https://github.com/skilled-scipkg/pylith/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/geodynamics/pylith",
+      "homepage_url": "https://github.com/geodynamics/pylith",
+      "card": "references/packages/pylith.md"
+    },
+    {
+      "package_id": "pynbody",
+      "title": "Pynbody Astrophysical Simulation Analysis",
+      "description": "Python framework for analyzing and visualizing N-body and hydrodynamic astrophysical simulation data, including Gadget, Gasoline, Arepo, N-Chilada, and RAMSES AMR outputs.",
+      "domains": [
+        "astronomy_astrophysics",
+        "computational_fluid_dynamics"
+      ],
+      "tags": [
+        "astrophysics",
+        "cosmology",
+        "nbody",
+        "hydrodynamics",
+        "simulation-analysis",
+        "amr"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pynbody",
+      "source_archive_url": "https://github.com/skilled-scipkg/pynbody/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/pynbody/pynbody",
+      "homepage_url": "https://pynbody.readthedocs.io",
+      "card": "references/packages/pynbody.md"
+    },
+    {
+      "package_id": "pysam",
+      "title": "Pysam Genomics I/O",
+      "description": "Python bindings to HTSlib for fast reading, writing, indexing, and querying SAM BAM CRAM and VCF BCF genomics files used in sequencing alignment and variant analysis workflows.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "genomics",
+        "bioinformatics",
+        "sequencing",
+        "htslib",
+        "sam-bam",
+        "vcf-bcf"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pysam",
+      "source_archive_url": "https://github.com/skilled-scipkg/pysam/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/pysam-developers/pysam",
+      "homepage_url": "https://pysam.readthedocs.io/en/latest/",
+      "card": "references/packages/pysam.md"
+    },
+    {
+      "package_id": "pyscf",
+      "title": "PySCF Quantum Chemistry",
+      "description": "PySCF is a Python-based electronic structure and quantum chemistry package for ab initio molecular and periodic calculations, including Hartree-Fock, post-HF, and multireference workflows.",
+      "domains": [
+        "quantum_chemistry",
+        "computational_chemistry",
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "quantum-chemistry",
+        "electronic-structure",
+        "ab-initio",
+        "molecular-modeling",
+        "computational-chemistry",
+        "materials-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/pyscf",
+      "source_archive_url": "https://github.com/skilled-scipkg/pyscf/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/pyscf/pyscf",
+      "homepage_url": "https://github.com/pyscf/pyscf",
+      "card": "references/packages/pyscf.md"
+    },
+    {
+      "package_id": "q-e",
+      "title": "Quantum ESPRESSO",
+      "description": "Quantum ESPRESSO is an open source suite for plane wave density functional theory, phonons, and ab initio molecular dynamics in electronic structure simulations of materials.",
+      "domains": [
+        "quantum_chemistry",
+        "molecular_dynamics",
+        "materials_science"
+      ],
+      "tags": [
+        "quantum-espresso",
+        "dft",
+        "dfpt",
+        "electronic-structure",
+        "materials-simulation",
+        "plane-wave"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/q-e",
+      "source_archive_url": "https://github.com/skilled-scipkg/q-e/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/QEF/q-e",
+      "homepage_url": "https://github.com/QEF/q-e",
+      "card": "references/packages/q-e.md"
+    },
+    {
+      "package_id": "qibo",
+      "title": "Qibo Quantum Simulation and Control",
+      "description": "Qibo is an open-source full-stack framework for building, simulating, and executing quantum circuits, with device-agnostic backends for CPU or GPU simulation and quantum hardware control.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "qibo",
+        "quantum-computing",
+        "quantum-circuits",
+        "quantum-simulation",
+        "hardware-control",
+        "variational-algorithms"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/qibo",
+      "source_archive_url": "https://github.com/skilled-scipkg/qibo/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/qiboteam/qibo",
+      "homepage_url": "https://qibo.science",
+      "card": "references/packages/qibo.md"
+    },
+    {
+      "package_id": "qiskit",
+      "title": "Qiskit Quantum SDK",
+      "description": "Qiskit is an open source quantum computing SDK for building circuits, transpiling to target backends, and evaluating observables with sampler and estimator primitives.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "quantum-computing",
+        "quantum-circuits",
+        "transpiler",
+        "quantum-information",
+        "primitives",
+        "ibm-quantum"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/qiskit",
+      "source_archive_url": "https://github.com/skilled-scipkg/qiskit/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/Qiskit/qiskit",
+      "homepage_url": "https://www.ibm.com/quantum/qiskit",
+      "card": "references/packages/qiskit.md"
+    },
+    {
+      "package_id": "quantica-jl",
+      "title": "Quantica.jl Lattice Quantum Systems",
+      "description": "Quantica.jl is a Julia package for building lattice tight-binding Hamiltonians and computing band structures, Green functions, and transport observables for quantum condensed-matter systems.",
+      "domains": [
+        "quantum_chemistry"
+      ],
+      "tags": [
+        "quantum-physics",
+        "lattice-models",
+        "tight-binding",
+        "condensed-matter",
+        "quantum-transport",
+        "julia"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/Quantica.jl",
+      "source_archive_url": "https://github.com/skilled-scipkg/Quantica.jl/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/pablosanjose/Quantica.jl",
+      "homepage_url": "https://github.com/pablosanjose/Quantica.jl",
+      "card": "references/packages/quantica-jl.md"
+    },
+    {
+      "package_id": "quantumoptics-jl",
+      "title": "QuantumOptics.jl Quantum Dynamics Simulator",
+      "description": "Julia package for numerically simulating closed and open quantum systems, with tools for quantum optics models, operator algebra, and dissipative time evolution.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "quantum-optics",
+        "open-quantum-systems",
+        "julia",
+        "quantum-simulation",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/QuantumOptics.jl",
+      "source_archive_url": "https://github.com/skilled-scipkg/QuantumOptics.jl/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/qojulia/QuantumOptics.jl",
+      "homepage_url": "http://qojulia.org",
+      "card": "references/packages/quantumoptics-jl.md"
+    },
+    {
+      "package_id": "quimb",
+      "title": "Quimb Quantum Tensor Networks",
+      "description": "Quimb is a Python package for quantum information and many-body physics, combining tensor-network algorithms with exact operator methods for entanglement, spectra, and dynamics.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "quantum",
+        "tensor-networks",
+        "many-body",
+        "entanglement",
+        "simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/quimb",
+      "source_archive_url": "https://github.com/skilled-scipkg/quimb/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/jcmgray/quimb",
+      "homepage_url": "http://quimb.readthedocs.io",
+      "card": "references/packages/quimb.md"
+    },
+    {
+      "package_id": "qulacs",
+      "title": "Qulacs Quantum Circuit Simulator",
+      "description": "Qulacs is a high performance C++ and Python library for simulating large noisy and parametric gate based quantum circuits with multithreaded CPU and optional CUDA acceleration for variational quantum computing research.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "quantum",
+        "circuit",
+        "simulation",
+        "variational",
+        "nisq"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/qulacs",
+      "source_archive_url": "https://github.com/skilled-scipkg/qulacs/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/qulacs/qulacs",
+      "homepage_url": "https://github.com/qulacs/qulacs",
+      "card": "references/packages/qulacs.md"
+    },
+    {
+      "package_id": "qutip",
+      "title": "QuTiP Quantum Toolbox",
+      "description": "QuTiP is a Python framework for simulating closed and open quantum system dynamics with Hamiltonians, collapse operators, and time-dependent master-equation solvers used in quantum optics and information research.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "quantum-physics",
+        "open-quantum-systems",
+        "quantum-optics",
+        "master-equation",
+        "numerical-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/qutip",
+      "source_archive_url": "https://github.com/skilled-scipkg/qutip/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/qutip/qutip",
+      "homepage_url": "https://qutip.org",
+      "card": "references/packages/qutip.md"
+    },
+    {
+      "package_id": "rdkit",
+      "title": "RDKit Cheminformatics Toolkit",
+      "description": "RDKit is an open-source cheminformatics library for molecular representation, property calculation, fingerprinting, and substructure or similarity search across 2D and 3D chemical workflows.",
+      "domains": [
+        "computational_chemistry",
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "cheminformatics",
+        "computational-chemistry",
+        "molecular-fingerprints",
+        "substructure-search",
+        "drug-discovery"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/rdkit",
+      "source_archive_url": "https://github.com/skilled-scipkg/rdkit/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/rdkit/rdkit",
+      "homepage_url": "https://github.com/rdkit/rdkit",
+      "card": "references/packages/rdkit.md"
+    },
+    {
+      "package_id": "rmg-py",
+      "title": "RMG-Py Reaction Mechanism Generator",
+      "description": "RMG-Py automatically builds detailed chemical kinetic mechanisms and thermochemistry models for combustion, pyrolysis, and atmospheric reaction networks, with Arkane support for pressure-dependent and high-pressure-limit kinetics.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "chemical-kinetics",
+        "reaction-mechanism-generation",
+        "combustion",
+        "thermochemistry",
+        "atmospheric-chemistry",
+        "arkane"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/RMG-Py",
+      "source_archive_url": "https://github.com/skilled-scipkg/RMG-Py/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/ReactionMechanismGenerator/RMG-Py",
+      "homepage_url": "http://reactionmechanismgenerator.github.io/RMG-Py/",
+      "card": "references/packages/rmg-py.md"
+    },
+    {
+      "package_id": "root",
+      "title": "CERN ROOT Data Analysis Framework",
+      "description": "ROOT is CERN's C++ scientific data analysis framework for storing columnar event data, building histograms, fitting models, and producing publication-quality visualizations with interactive and batch workflows.",
+      "domains": [
+        "high_energy_physics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "cern",
+        "hep",
+        "data-analysis",
+        "histogramming",
+        "visualization",
+        "cpp"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/root",
+      "source_archive_url": "https://github.com/skilled-scipkg/root/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/root-project/root",
+      "homepage_url": "https://root.cern",
+      "card": "references/packages/root.md"
+    },
+    {
+      "package_id": "scanpy",
+      "title": "Scanpy Single-Cell Toolkit",
+      "description": "Scanpy is a scalable Python toolkit for preprocessing, visualization, clustering, trajectory inference, and differential expression analysis of single-cell gene expression data.",
+      "domains": [
+        "bioinformatics"
+      ],
+      "tags": [
+        "singlecell",
+        "transcriptomics",
+        "bioinformatics",
+        "rnaseq",
+        "clustering",
+        "trajectory"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/scanpy",
+      "source_archive_url": "https://github.com/skilled-scipkg/scanpy/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scverse/scanpy",
+      "homepage_url": "https://scanpy.readthedocs.io",
+      "card": "references/packages/scanpy.md"
+    },
+    {
+      "package_id": "scikit-allel",
+      "title": "scikit-allel Population Genetics",
+      "description": "Python package for exploratory analysis of large-scale genetic variation data, with tools for genotype arrays, variant statistics, and population genetics workflows.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "population-genetics",
+        "genomics",
+        "variant-analysis",
+        "bioinformatics",
+        "vcf"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/scikit-allel",
+      "source_archive_url": "https://github.com/skilled-scipkg/scikit-allel/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/cggh/scikit-allel",
+      "homepage_url": "https://github.com/cggh/scikit-allel",
+      "card": "references/packages/scikit-allel.md"
+    },
+    {
+      "package_id": "scikit-bio",
+      "title": "scikit-bio Bioinformatics Library",
+      "description": "Community-driven Python bioinformatics library with reusable data structures and algorithms for sequence processing, phylogenetics, microbiome ecology, diversity metrics, ordination, and omic data analysis.",
+      "domains": [
+        "bioinformatics"
+      ],
+      "tags": [
+        "bioinformatics",
+        "omics",
+        "microbiome",
+        "phylogenetics",
+        "sequence-analysis",
+        "community-ecology"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/scikit-bio",
+      "source_archive_url": "https://github.com/skilled-scipkg/scikit-bio/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scikit-bio/scikit-bio",
+      "homepage_url": "https://scikit.bio",
+      "card": "references/packages/scikit-bio.md"
+    },
+    {
+      "package_id": "scqubits",
+      "title": "scqubits superconducting qubit simulator",
+      "description": "scqubits is a Python package for modeling superconducting qubit circuits, computing energy spectra and matrix elements, and analyzing coupled qubit resonator Hilbert spaces for circuit QED research.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "quantum",
+        "superconducting-qubits",
+        "circuit-qed",
+        "quantum-simulation",
+        "qubit-modeling"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/scqubits",
+      "source_archive_url": "https://github.com/skilled-scipkg/scqubits/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scqubits/scqubits",
+      "homepage_url": "https://github.com/scqubits/scqubits",
+      "card": "references/packages/scqubits.md"
+    },
+    {
+      "package_id": "scuff-em",
+      "title": "SCUFF-EM Electromagnetic BEM Suite",
+      "description": "SCUFF-EM is a computational electromagnetics suite for boundary-element simulations of scattering, Casimir interactions, radiative heat transfer, nanophotonics, RF structures, and electrostatics via library and command-line solvers.",
+      "domains": [
+        "electromagnetics"
+      ],
+      "tags": [
+        "computational-physics",
+        "electromagnetics",
+        "boundary-element",
+        "casimir",
+        "nanophotonics",
+        "electrostatics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/scuff-em",
+      "source_archive_url": "https://github.com/skilled-scipkg/scuff-em/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/HomerReid/scuff-em",
+      "homepage_url": "http://www.homerreid.com/scuff-em",
+      "card": "references/packages/scuff-em.md"
+    },
+    {
+      "package_id": "scvi-tools",
+      "title": "scvi-tools Single-Cell Probabilistic Modeling",
+      "description": "scvi-tools provides deep probabilistic models for single-cell and spatial omics, enabling latent representation learning, batch correction, cell type annotation, doublet detection, and multimodal integration within the scverse ecosystem.",
+      "domains": [
+        "bioinformatics"
+      ],
+      "tags": [
+        "single-cell-omics",
+        "spatial-omics",
+        "probabilistic-modeling",
+        "variational-inference",
+        "scverse"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/scvi-tools",
+      "source_archive_url": "https://github.com/skilled-scipkg/scvi-tools/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scverse/scvi-tools",
+      "homepage_url": "http://scvi-tools.org/",
+      "card": "references/packages/scvi-tools.md"
+    },
+    {
+      "package_id": "seissol",
+      "title": "SeisSol Earthquake Wave Simulator",
+      "description": "SeisSol is a high-order discontinuous Galerkin and ADER solver for seismic wave propagation and dynamic earthquake rupture simulations at scale.",
+      "domains": [
+        "computational_fluid_dynamics"
+      ],
+      "tags": [
+        "seismology",
+        "earthquake-dynamics",
+        "wave-propagation",
+        "geophysics",
+        "numerical-pde"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/SeisSol",
+      "source_archive_url": "https://github.com/skilled-scipkg/SeisSol/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/SeisSol/SeisSol",
+      "homepage_url": "http://www.seissol.org",
+      "card": "references/packages/seissol.md"
+    },
+    {
+      "package_id": "sfepy",
+      "title": "SfePy Finite Element PDE Solver",
+      "description": "SfePy is a Python finite element framework for solving coupled PDEs in 1D, 2D, and 3D using weak formulations, configurable problem definition files, and external meshes.",
+      "domains": [
+        "computational_fluid_dynamics",
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "finite-element",
+        "pde",
+        "computational-mechanics",
+        "multiphysics",
+        "numerical-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/sfepy",
+      "source_archive_url": "https://github.com/skilled-scipkg/sfepy/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/sfepy/sfepy",
+      "homepage_url": "http://sfepy.org",
+      "card": "references/packages/sfepy.md"
+    },
+    {
+      "package_id": "sisl",
+      "title": "sisl Electronic Structure Toolkit",
+      "description": "sisl is a Python toolkit for post-processing electronic-structure simulations and building tight-binding and NEGF workflows with LCAO Hamiltonians, transport analysis, and real-space grids.",
+      "domains": [
+        "quantum_chemistry",
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "electronic-structure",
+        "dft",
+        "tight-binding",
+        "negf",
+        "quantum-transport",
+        "materials-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/sisl",
+      "source_archive_url": "https://github.com/skilled-scipkg/sisl/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/zerothi/sisl",
+      "homepage_url": "https://zerothi.github.io/sisl",
+      "card": "references/packages/sisl.md"
+    },
+    {
+      "package_id": "smilei",
+      "title": "Smilei Plasma PIC Simulator",
+      "description": "Smilei is an open-source electromagnetic particle-in-cell code for kinetic plasma simulations, supporting laser-plasma, accelerator, space, and astrophysical applications on modern supercomputers.",
+      "domains": [
+        "electromagnetics",
+        "plasma_particle_simulation",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "plasma-physics",
+        "particle-in-cell",
+        "electromagnetics",
+        "computational-physics",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/Smilei",
+      "source_archive_url": "https://github.com/skilled-scipkg/Smilei/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/SmileiPIC/Smilei",
+      "homepage_url": "https://smileipic.github.io/Smilei",
+      "card": "references/packages/smilei.md"
+    },
+    {
+      "package_id": "snakemake",
+      "title": "Snakemake Workflow Manager",
+      "description": "Snakemake is a Python based workflow management system for reproducible and scalable scientific data pipelines that execute on local machines, HPC clusters, grids, and cloud environments.",
+      "domains": [
+        "bioinformatics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "workflow",
+        "pipelines",
+        "reproducibility",
+        "bioinformatics",
+        "hpc",
+        "orchestration"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/snakemake",
+      "source_archive_url": "https://github.com/skilled-scipkg/snakemake/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/snakemake/snakemake",
+      "homepage_url": "https://snakemake.github.io",
+      "card": "references/packages/snakemake.md"
+    },
+    {
+      "package_id": "specfem3d-globe",
+      "title": "SPECFEM3D Globe",
+      "description": "SPECFEM3D Globe is a 3D spectral-element solver for simulating global and continental-scale seismic wave propagation in Earth, Mars, and Moon models.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "seismology",
+        "geodynamics",
+        "wave-propagation",
+        "spectral-element",
+        "earth-science",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/specfem3d_globe",
+      "source_archive_url": "https://github.com/skilled-scipkg/specfem3d_globe/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/SPECFEM/specfem3d_globe",
+      "homepage_url": "https://specfem.org",
+      "card": "references/packages/specfem3d-globe.md"
+    },
+    {
+      "package_id": "specutils",
+      "title": "Specutils Astronomical Spectroscopy",
+      "description": "Specutils provides shared data models and analysis utilities for astronomical spectra, supporting spectral extraction, line measurements, continuum handling, and interoperable spectroscopy workflows in Python astronomy.",
+      "domains": [
+        "astronomy_astrophysics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "astronomy",
+        "spectroscopy",
+        "astrophysics",
+        "spectral-analysis",
+        "python"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/specutils",
+      "source_archive_url": "https://github.com/skilled-scipkg/specutils/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/astropy/specutils",
+      "homepage_url": "http://specutils.readthedocs.io/en/latest/",
+      "card": "references/packages/specutils.md"
+    },
+    {
+      "package_id": "spglib",
+      "title": "Spglib Crystal Symmetry Toolkit",
+      "description": "Spglib provides robust crystal symmetry analysis to determine space groups, symmetry operations, and standardized cells from atomic coordinates, supporting crystallography, materials modeling, and solid-state simulation workflows.",
+      "domains": [
+        "materials_science",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "crystallography",
+        "materials-science",
+        "crystal-symmetry",
+        "space-groups",
+        "solid-state",
+        "atomistic",
+        "structure-analysis"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/spglib",
+      "source_archive_url": "https://github.com/skilled-scipkg/spglib/archive/refs/heads/develop.zip",
+      "upstream_repo_url": "https://github.com/spglib/spglib",
+      "homepage_url": "https://spglib.readthedocs.io/en/latest/",
+      "card": "references/packages/spglib.md"
+    },
+    {
+      "package_id": "squidpy",
+      "title": "Squidpy Spatial Omics Analysis",
+      "description": "Squidpy is a Python toolkit for scalable spatial single-cell and spatial omics analysis, combining tissue image feature extraction, spatial statistics, neighborhood graphs, and interactive exploration.",
+      "domains": [
+        "bioinformatics",
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "spatial-omics",
+        "single-cell",
+        "bioinformatics",
+        "spatial-transcriptomics",
+        "tissue-imaging",
+        "scverse"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/squidpy",
+      "source_archive_url": "https://github.com/skilled-scipkg/squidpy/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scverse/squidpy",
+      "homepage_url": "https://squidpy.readthedocs.io/en/stable/",
+      "card": "references/packages/squidpy.md"
+    },
+    {
+      "package_id": "starry",
+      "title": "starry stellar and exoplanet mapper",
+      "description": "starry provides fast analytic models of stellar and exoplanet surface maps to generate and fit transit, eclipse, and phase light curves.",
+      "domains": [
+        "astronomy_astrophysics"
+      ],
+      "tags": [
+        "astronomy",
+        "exoplanets",
+        "stellar",
+        "lightcurve",
+        "mapping",
+        "sphericalharmonics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/starry",
+      "source_archive_url": "https://github.com/skilled-scipkg/starry/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/rodluger/starry",
+      "homepage_url": "https://starry.readthedocs.io",
+      "card": "references/packages/starry.md"
+    },
+    {
+      "package_id": "strawberryfields",
+      "title": "Strawberry Fields Continuous-Variable Quantum Toolkit",
+      "description": "Strawberry Fields is a Python platform for designing, simulating, and optimizing continuous-variable photonic quantum circuits, including near-term algorithms and execution pathways for quantum optical hardware.",
+      "domains": [
+        "electromagnetics"
+      ],
+      "tags": [
+        "quantum-computing",
+        "photonics",
+        "continuous-variable",
+        "quantum-optics",
+        "circuit-simulation",
+        "bosonic-systems"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/strawberryfields",
+      "source_archive_url": "https://github.com/skilled-scipkg/strawberryfields/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/XanaduAI/strawberryfields",
+      "homepage_url": "https://xanadu.ai",
+      "card": "references/packages/strawberryfields.md"
+    },
+    {
+      "package_id": "su2",
+      "title": "SU2 Open-Source CFD Suite",
+      "description": "SU2 is an open-source C++ suite for computational fluid dynamics, multiphysics PDE simulation, and adjoint-driven aerodynamic shape optimization for engineering analysis and design.",
+      "domains": [
+        "computational_fluid_dynamics"
+      ],
+      "tags": [
+        "cfd",
+        "aerodynamics",
+        "multiphysics",
+        "pde",
+        "optimization",
+        "simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/SU2",
+      "source_archive_url": "https://github.com/skilled-scipkg/SU2/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/su2code/SU2",
+      "homepage_url": "https://su2code.github.io",
+      "card": "references/packages/su2.md"
+    },
+    {
+      "package_id": "sunny-jl",
+      "title": "Sunny.jl Magnetic Materials Modeling",
+      "description": "Sunny.jl models magnetic materials with symmetry-aware Hamiltonians, quantum spin excitations, finite-temperature spin dynamics, and fitting to neutron or X-ray scattering data.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "magnetism",
+        "spin-waves",
+        "spin-dynamics",
+        "quantum-materials",
+        "scattering"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/Sunny.jl",
+      "source_archive_url": "https://github.com/skilled-scipkg/Sunny.jl/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/SunnySuite/Sunny.jl",
+      "homepage_url": "https://sunnysuite.github.io/Sunny.jl/",
+      "card": "references/packages/sunny-jl.md"
+    },
+    {
+      "package_id": "sw4",
+      "title": "SW4 Seismic Waves Solver",
+      "description": "SW4 is a high-order solver for 3D seismic wave propagation with free-surface and absorbing boundaries, supporting point-force and moment-tensor earthquake source modeling.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "sw4",
+        "seismology",
+        "geophysics",
+        "seismic-modeling",
+        "elastic-waves",
+        "finite-difference",
+        "earthquake-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/sw4",
+      "source_archive_url": "https://github.com/skilled-scipkg/sw4/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/geodynamics/sw4",
+      "homepage_url": "https://github.com/geodynamics/sw4",
+      "card": "references/packages/sw4.md"
+    },
+    {
+      "package_id": "swift",
+      "title": "SWIFT Astrophysical Simulation Engine",
+      "description": "SWIFT is a high-performance astrophysics engine for cosmological particle simulations, combining gravity and smoothed particle hydrodynamics with fine-grained tasking across large HPC systems.",
+      "domains": [
+        "astronomy_astrophysics",
+        "computational_fluid_dynamics",
+        "workflow_provenance",
+        "robotics_physics"
+      ],
+      "tags": [
+        "astrophysics",
+        "cosmology",
+        "hydrodynamics",
+        "sph",
+        "gravity",
+        "hpc"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/SWIFT",
+      "source_archive_url": "https://github.com/skilled-scipkg/SWIFT/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/SWIFTSIM/SWIFT",
+      "homepage_url": "http://www.swiftsim.com",
+      "card": "references/packages/swift.md"
+    },
+    {
+      "package_id": "tdnegf",
+      "title": "TDNEGF Hybrid Quantum Transport",
+      "description": "TDNEGF-Hybrid provides one-time TDNEGF ODE simulation of open quantum devices, evolving reduced density matrices and auxiliary states to compute time-resolved charge and spin transport observables.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "tdnegf",
+        "quantum-transport",
+        "nonequilibrium-greens-function",
+        "spintronics",
+        "open-quantum-systems"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/TDNEGF",
+      "source_archive_url": "https://github.com/skilled-scipkg/TDNEGF/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/Jalil199/TDNEGF",
+      "homepage_url": "https://github.com/Jalil199/TDNEGF",
+      "card": "references/packages/tdnegf.md"
+    },
+    {
+      "package_id": "tenpy",
+      "title": "TeNPy Tensor Network Python",
+      "description": "TeNPy is a tensor-network simulation library for strongly correlated quantum many-body systems, with readable yet extensible implementations of DMRG, TEBD, and related matrix-product-state algorithms for physics research.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "tensor-networks",
+        "quantum-many-body",
+        "dmrg",
+        "tebd",
+        "matrix-product-states",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/tenpy",
+      "source_archive_url": "https://github.com/skilled-scipkg/tenpy/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/tenpy/tenpy",
+      "homepage_url": "https://github.com/tenpy/tenpy",
+      "card": "references/packages/tenpy.md"
+    },
+    {
+      "package_id": "thermo",
+      "title": "Thermo Chemical Engineering Thermodynamics",
+      "description": "Python package for chemical engineering thermodynamics and phase equilibrium, providing pure component and mixture property models, transport correlations, and rigorous flash calculation workflows.",
+      "domains": [
+        "workflow_provenance"
+      ],
+      "tags": [
+        "thermodynamics",
+        "chemicalengineering",
+        "phaseequilibrium",
+        "vle",
+        "flashcalculation",
+        "mixtureproperties"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/thermo",
+      "source_archive_url": "https://github.com/skilled-scipkg/thermo/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/CalebBell/thermo",
+      "homepage_url": "https://github.com/CalebBell/thermo",
+      "card": "references/packages/thermo.md"
+    },
+    {
+      "package_id": "tkwant",
+      "title": "Tkwant Time-Dependent Quantum Transport",
+      "description": "Tkwant is a Python package for simulating time-dependent quantum dynamics of mesoscopic systems and serves as the time-dependent extension of Kwant for open quantum transport problems.",
+      "domains": [
+        "quantum_chemistry",
+        "plasma_particle_simulation"
+      ],
+      "tags": [
+        "time-dependent-quantum-transport",
+        "non-equilibrium",
+        "tight-binding",
+        "mesoscopic-physics",
+        "nanoelectronics",
+        "keldysh-formalism"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/tkwant",
+      "source_archive_url": "https://github.com/skilled-scipkg/tkwant/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://gitlab.kwant-project.org/kwant/tkwant",
+      "homepage_url": "https://tkwant.kwant-project.org/",
+      "card": "references/packages/tkwant.md"
+    },
+    {
+      "package_id": "tvb-root",
+      "title": "The Virtual Brain Core",
+      "description": "The Virtual Brain main codebase provides neuroscience tools for whole-brain network simulation, multimodal data analysis, and framework components for workflows, storage, and visualization.",
+      "domains": [
+        "bioinformatics",
+        "computational_neuroscience",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "neuroscience",
+        "brain-simulation",
+        "connectomics",
+        "neuroinformatics",
+        "computational-neuroscience"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/tvb-root",
+      "source_archive_url": "https://github.com/skilled-scipkg/tvb-root/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/the-virtual-brain/tvb-root",
+      "homepage_url": "https://thevirtualbrain.org",
+      "card": "references/packages/tvb-root.md"
+    },
+    {
+      "package_id": "uproot5",
+      "title": "Uproot5 ROOT I/O",
+      "description": "Uproot5 is a pure Python library for reading and writing CERN ROOT files, especially TTrees, and streaming high-energy physics event data into array and dataframe workflows without C++ ROOT.",
+      "domains": [
+        "high_energy_physics",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "hep",
+        "root",
+        "ttree",
+        "columnar",
+        "particle-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/uproot5",
+      "source_archive_url": "https://github.com/skilled-scipkg/uproot5/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/scikit-hep/uproot5",
+      "homepage_url": "https://uproot.readthedocs.io",
+      "card": "references/packages/uproot5.md"
+    },
+    {
+      "package_id": "vampire",
+      "title": "VAMPIRE Atomistic Spin Dynamics Simulator",
+      "description": "VAMPIRE is an atomistic spin dynamics code for simulating magnetic materials, enabling finite-temperature magnetism, hysteresis, ultrafast dynamics, and spin-transport studies at atomic resolution.",
+      "domains": [
+        "molecular_dynamics",
+        "materials_science"
+      ],
+      "tags": [
+        "magnetism",
+        "spin-dynamics",
+        "atomistic-simulation",
+        "materials-science",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/vampire",
+      "source_archive_url": "https://github.com/skilled-scipkg/vampire/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/richard-evans/vampire",
+      "homepage_url": "https://github.com/richard-evans/vampire",
+      "card": "references/packages/vampire.md"
+    },
+    {
+      "package_id": "wannier_tools",
+      "title": "WannierTools Topological Materials Toolkit",
+      "description": "WannierTools analyzes Wannier tight binding Hamiltonians to compute topological invariants, surface spectra, Weyl and Dirac features, Berry properties, and transport observables in quantum materials.",
+      "domains": [
+        "quantum_chemistry",
+        "finite_element_engineering"
+      ],
+      "tags": [
+        "topological-materials",
+        "tight-binding",
+        "electronic-structure",
+        "wannier",
+        "condensed-matter",
+        "surface-states"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/wannier_tools",
+      "source_archive_url": "https://github.com/skilled-scipkg/wannier_tools/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/quanshengwu/wannier_tools",
+      "homepage_url": "http://www.wanniertools.org",
+      "card": "references/packages/wannier_tools.md"
+    },
+    {
+      "package_id": "warpx",
+      "title": "WarpX PIC Plasma Simulator",
+      "description": "WarpX is a high-performance electromagnetic and electrostatic particle-in-cell simulator for plasma and accelerator modeling, with mesh refinement, boosted-frame techniques, and scalable CPU and GPU execution on supercomputers.",
+      "domains": [
+        "electromagnetics",
+        "plasma_particle_simulation",
+        "workflow_provenance"
+      ],
+      "tags": [
+        "plasma-physics",
+        "particle-in-cell",
+        "accelerator-physics",
+        "electromagnetics",
+        "electrostatics",
+        "hpc-simulation"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/warpx",
+      "source_archive_url": "https://github.com/skilled-scipkg/warpx/archive/refs/heads/development.zip",
+      "upstream_repo_url": "https://github.com/BLAST-WarpX/warpx",
+      "homepage_url": "https://blast-warpx.github.io",
+      "card": "references/packages/warpx.md"
+    },
+    {
+      "package_id": "wrf",
+      "title": "WRF Weather Forecasting Model",
+      "description": "WRF is an open source mesoscale numerical weather prediction system for atmospheric research and operational forecasting, including regional climate downscaling, severe weather studies, and nested domain simulations.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "wrf",
+        "atmospheric-modeling",
+        "numerical-weather-prediction",
+        "mesoscale",
+        "regional-climate",
+        "weather-forecasting"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/WRF",
+      "source_archive_url": "https://github.com/skilled-scipkg/WRF/archive/refs/heads/master.zip",
+      "upstream_repo_url": "https://github.com/wrf-model/WRF",
+      "homepage_url": "https://github.com/wrf-model/WRF",
+      "card": "references/packages/wrf.md"
+    },
+    {
+      "package_id": "xtb",
+      "title": "xTB Extended Tight-Binding Quantum Chemistry",
+      "description": "xTB is a semiempirical extended tight-binding quantum chemistry package for fast molecular energies, structures, frequencies, and conformational analyses across large systems with broad element coverage.",
+      "domains": [
+        "quantum_chemistry",
+        "computational_chemistry"
+      ],
+      "tags": [
+        "quantum-chemistry",
+        "semiempirical",
+        "tight-binding",
+        "molecular-modeling",
+        "computational-chemistry"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/xtb",
+      "source_archive_url": "https://github.com/skilled-scipkg/xtb/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/grimme-lab/xtb",
+      "homepage_url": "https://xtb-docs.readthedocs.io/",
+      "card": "references/packages/xtb.md"
+    },
+    {
+      "package_id": "yt",
+      "title": "yt Volumetric Simulation Analysis",
+      "description": "yt is a Python library for physically meaningful analysis and visualization of volumetric simulation data across structured and unstructured meshes, particles, and adaptive mesh refinement datasets.",
+      "domains": [
+        "computational_science"
+      ],
+      "tags": [
+        "scientific-visualization",
+        "simulation-analysis",
+        "volumetric-data",
+        "amr",
+        "computational-physics"
+      ],
+      "knowledge_url": "https://github.com/skilled-scipkg/yt",
+      "source_archive_url": "https://github.com/skilled-scipkg/yt/archive/refs/heads/main.zip",
+      "upstream_repo_url": "https://github.com/yt-project/yt",
+      "homepage_url": "http://yt-project.org",
+      "card": "references/packages/yt.md"
+    }
+  ]
+}