comparison_5.1_vs_5.2.json

{
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      "disagreements": [
        {
          "repo": "3D-e-Chem/3D-e-Chem-VM",
          "url": "https://github.com/3D-e-Chem/3D-e-Chem-VM",
          "model1_value": "Containers",
          "model2_value": "Builds and releases",
          "model1_overridden": false,
          "model2_overridden": false
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  "override_statistics": {
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  "label_distributions": {
    "gpt-5.1": {
      "actor_unit": {
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        "Individual maintainer": 5,
        "Vendor or commercial entity": 1,
        "Research group or lab": 19,
        "Community or foundation (open source governance)": 1
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        "Application software": 21,
        "Dependency software artifact": 8,
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        "Source repo": 2,
        "Containers": 2
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    "gpt-5.2": {
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        "Application software": 19,
        "Dependency software artifact": 10,
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      "research_role": {
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        "Direct research execution": 16
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        "Package registry": 22,
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        "Source repo": 2,
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    }
  },
  "repositories": [
    {
      "full_name": "0satoken/Eclairs",
      "url": "https://github.com/0satoken/Eclairs",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Installer or binary",
          "distribution_details": null,
          "evidence": [
            "README mentions binaries/installers: \"We will put the download link later (hopefully, in April 2024) on this repository.\"",
            "Author: Ken Osato  Contributors: Takahiro Nishimichi, Francis Bernardeau, and Atsushi Taruya",
            "Then, running `make` creates an executable `eclairs`. The basic usage is `./eclairs [initial parameter file]`"
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": true,
            "distribution_pathway": true
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          "timestamp_utc": "2026-01-22T03:57:42Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Installer or binary",
          "distribution_details": null,
          "evidence": [
            "README mentions binaries/installers: \"We will put the download link later (hopefully, in April 2024) on this repository.\"",
            "Metadata: owner_type is User (owner_login: 0satoken) and README lists a single \"Author: Ken Osato\".",
            "README: \"running `make` creates an executable `eclairs`. The basic usage is `> ./eclairs [initial parameter file]`\" (end-user executable)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:33Z"
        }
      }
    },
    {
      "full_name": "0x0f0f0f/Metatheory.jl",
      "url": "https://github.com/0x0f0f0f/Metatheory.jl",
      "classifications": {
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          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Julia General registry",
          "evidence": [
            "README install command: \"julia> using Pkg; Pkg.add(\"Metatheory\")\"",
            "\"Metatheory.jl is a general purpose term rewriting, metaprogramming and algebraic computation library for the Julia programming language\" (library intended to be used by other Julia code).",
            "\"You can install the stable version: ```julia> using Pkg; Pkg.add(\"Metatheory\")```\" (installation via Julia package registry)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:57:48Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Julia General registry",
          "evidence": [
            "README install command: \"julia> using Pkg; Pkg.add(\"Metatheory\")\"",
            "Metadata: owner_type is \"User\" (owner_login: 0x0f0f0f), suggesting an individually maintained project.",
            "README: \"Metatheory.jl is a general purpose term rewriting, metaprogramming and algebraic computation library for the Julia programming language\" (library intended to be used by other Julia code)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:37Z"
        }
      }
    },
    {
      "full_name": "0xCoto/Virgo",
      "url": "https://github.com/0xCoto/Virgo",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"pip install astro-virgo\"",
            "\"Virgo is an easy-to-use open-source spectrometer and radiometer ... applicable to any radio telescope ... In addition to data acquisition, Virgo also carries out automated analysis of the recorded samples, producing an averaged spectrum, a calibrated spectrum, a dynamic spectrum (waterfall), a time series ...\"",
            "\"Works directly from the command line (`virgo -h`), or as a Python module\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:57:53Z"
        },
        "gpt-5.2": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"pip install astro-virgo\"",
            "Metadata: owner_type is \"User\" (owner_login: 0xCoto), suggesting an individually maintained repository.",
            "README: \"Virgo is an easy-to-use open-source spectrometer and radiometer...\" and it \"carries out automated analysis... producing an averaged spectrum, a calibrated spectrum, a dynamic spectrum...\""
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:40Z"
        }
      }
    },
    {
      "full_name": "1054/Crab.Toolkit.michi2",
      "url": "https://github.com/1054/Crab.Toolkit.michi2",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Installer or binary",
          "distribution_details": null,
          "evidence": [
            "README mentions binaries/installers: \"### 1. Download the code\"",
            "\"This is a _Crab_ toolkit for minimumizing chi2 for any 1D model fit, for example, galaxy SED fitting, molecular line ladder fitting.\"",
            "Usage instructions show running commands like `michi2-run-SED-fitting-v5` and `michi2_v05` directly on scientific data files to produce fitting results and plots (e.g., \"The output of michi2 SED fitting will be: ... best-fit parameters, SED and figures.\")."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:57:58Z"
        },
        "gpt-5.2": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Installer or binary",
          "distribution_details": null,
          "evidence": [
            "README mentions binaries/installers: \"### 1. Download the code\"",
            "Metadata: owner_type is \"User\" (owner_login: 1054), suggesting an individually maintained repository.",
            "README describes running end-user commands to perform SED/LVG fitting (e.g., \"michi2-run-SED-fitting-v5\" and \"michi2_v05 ... -obs ... -lib ...\"), indicating an executable research application."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:43Z"
        }
      }
    },
    {
      "full_name": "10XGenomics/bamtofastq",
      "url": "https://github.com/10XGenomics/bamtofastq",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Vendor or commercial entity",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Builds and releases",
          "distribution_details": "GitHub Releases",
          "evidence": [
            "README mentions releases: \"Download the latest release binaries for Linux or Mac from [the releases page](https://github.com/10XGenomics/bamtofastq/releases)\"",
            "\"Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.\"",
            "\"Download the latest release binaries for Linux or Mac from the releases page\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:01Z"
        },
        "gpt-5.2": {
          "actor_unit": "Vendor or commercial entity",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Builds and releases",
          "distribution_details": "GitHub Releases",
          "evidence": [
            "README mentions releases: \"Download the latest release binaries for Linux or Mac from [the releases page](https://github.com/10XGenomics/bamtofastq/releases)\"",
            "Metadata: owner_login is \"10XGenomics\" (Organization), indicating a commercial vendor maintains the repo.",
            "README: \"Tool for converting 10x BAMs ... back to FASTQ files that can be used as inputs to re-run analysis.\""
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:46Z"
        }
      }
    },
    {
      "full_name": "1313e/CMasher",
      "url": "https://github.com/1313e/CMasher",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"$ pip install cmasher\"",
            "\"The CMasher package provides a collection of scientific colormaps and utility functions to be used by different Python packages and projects, mainly in combination with matplotlib\" (indicates it is imported as a component/library).",
            "\"CMasher can now be imported as a package with `import cmasher as cmr`.\" (library-style usage, supports dependency role and direct use in generating plots/results)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:04Z"
        },
        "gpt-5.2": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"$ pip install cmasher\"",
            "Metadata: owner_type is \"User\" (owner_login: 1313e), suggesting an individually maintained repository.",
            "README: \"The CMasher package provides a collection of scientific colormaps and utility functions to be used by different Python packages and projects\" and \"can now be imported as a package with import cmasher as cmr\" (library/dependency)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:51Z"
        }
      }
    },
    {
      "full_name": "1313e/PRISM",
      "url": "https://github.com/1313e/PRISM",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"$ pip install .\"",
            "\"PRISM is a pure Python 3 package that provides an alternative method to MCMC for analyzing scientific models.\"",
            "\"PRISM can now be imported as a package with `import prism`.\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:07Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"$ pip install .\"",
            "Metadata: owner_type is \"User\" (owner_login: 1313e), suggesting an individually maintained repository.",
            "README: \"PRISM is a pure Python 3 package that provides an alternative method to MCMC for analyzing scientific models.\" and example shows importing (\"from prism import Pipeline\"), indicating a reusable library/package."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:55Z"
        }
      }
    },
    {
      "full_name": "18parkky/NanoMnT",
      "url": "https://github.com/18parkky/NanoMnT",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"pip install .\"",
            "\"A collection of Python scripts for (1) correcting sequencing errors within STR regions from Oxford Nanopore (ONT) sequencing data and (2) genotyping monoallelic STR regions.\"",
            "\"NanoMnT requires Krait output files as inputs\" and commands like `estimateLociCoverage`, `getAlleleTable`, `getLocusTable`, and `findInformativeLoci` directly process sequencing/BAM data to generate analysis tables and MSI-related metrics."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:11Z"
        },
        "gpt-5.2": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"pip install .\"",
            "Metadata: owner_type is \"User\" (owner_login: 18parkky), with no README indication of an institution, lab, or foundation maintaining it.",
            "README: \"A collection of Python scripts for (1) correcting sequencing errors within STR regions... and (2) genotyping monoallelic STR regions.\" (end-user analysis scripts/commands)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:58Z"
        }
      }
    },
    {
      "full_name": "21cmfast/21cmFAST",
      "url": "https://github.com/21cmfast/21cmFAST",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "conda-forge",
          "evidence": [
            "README install command: \"conda install -c conda-forge 21cmFAST\"",
            "\"This is the official repository for ``21cmFAST``: a semi-numerical code that is able to produce 3D cosmological realisations of many physical fields in the early Universe.\"",
            "\"21cmFAST has been widely used, for example, by the Murchison Widefield Array (MWA), LOw-Frequency ARray (LOFAR) and Hydrogen Epoch of Reionization Array (HERA), to model the large-scale cosmological 21-cm signal.\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:16Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "conda-forge",
          "evidence": [
            "README install command: \"conda install -c conda-forge 21cmFAST\"",
            "Metadata: owner_type is Organization (21cmfast), indicating a project/group rather than an individual maintainer.",
            "README: \"A semi-numerical cosmological simulation code for the radio 21-cm signal\" and \"produce 3D cosmological realisations...\" (end-user simulation application)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:01Z"
        }
      }
    },
    {
      "full_name": "21cmfast/21cmEMU",
      "url": "https://github.com/21cmfast/21cmEMU",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Network service",
          "distribution_details": null,
          "evidence": [
            "README indicates network usage: \"See `the documentation <https://21cmemu.readthedocs.io/en/latest/>`_ for tutorials and API.\"",
            "\"An emulator of 21cmFAST summaries. Emulate the following summary statistics: * 21-cm power spectrum ...\" (domain-specific scientific emulator, used in research).",
            "PyPI badges and links: \"https://img.shields.io/pypi/v/py21cmemu.svg\" with target \"https://pypi.org/project/py21cmemu/\" (indicates distribution as a Python package via PyPI, i.e., dependency library)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:19Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Network service",
          "distribution_details": null,
          "evidence": [
            "README indicates network usage: \"See `the documentation <https://21cmemu.readthedocs.io/en/latest/>`_ for tutorials and API.\"",
            "(metadata) owner_type: Organization; owner_login: 21cmfast",
            "README: \"An emulator of 21cmFAST summaries.\""
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:05Z"
        }
      }
    },
    {
      "full_name": "2decomp-fft/2decomp-fft",
      "url": "https://github.com/2decomp-fft/2decomp-fft",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Community or foundation (open source governance)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Source repo",
          "distribution_details": null,
          "evidence": [
            "\"This README contains basic instructions for building and installing the 2DECOMP&FFT library, more detailed instructions about installation and linking to the library within an external project\"",
            "\"Please have a look at HOWTO.md and at the examples ... for how to use the library with your application\"",
            "\"The development of 2DECOMP&FFT occurs on Github, with release versions on the `main` branch.\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T03:58:22Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Source repo",
          "distribution_details": null,
          "evidence": [
            "Metadata: repo owner_type is Organization (2decomp-fft), indicating an organizational maintainer rather than an individual.",
            "README: \"building and installing the 2DECOMP&FFT library\" and \"linking to the library within an external project\" / \"use the library with your application\" (library meant to be depended on).",
            "README provides CMake build/install-from-source instructions (cmake configure/build/install) and does not mention a package registry, container image, or downloadable installer/binary."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T04:00:08Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/3D-e-Chem-VM",
      "url": "https://github.com/3D-e-Chem/3D-e-Chem-VM",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Infrastructure",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Containers",
          "distribution_details": null,
          "evidence": [
            "\"3D-e-Chem-VM: Structural cheminformatics research infrastructure in a freely available Virtual Machine\"",
            "\"Scripts to create a Vagrant box using packer and ansible.\"",
            "\"vagrant init nlesc/3d-e-chem\" and references to publishing the box on Vagrant Cloud indicate distribution as a virtual machine image/box rather than via source or a package registry."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T03:58:24Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Infrastructure",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Builds and releases",
          "distribution_details": null,
          "evidence": [
            "Metadata: owner_type is Organization and owner_login is \"3D-e-Chem\", indicating a project/group rather than an individual.",
            "README: \"Scripts to create a Vagrant box using packer and ansible.\" (creates a VM environment).",
            "README: \"Publish box on https://app.vagrantup.com/nlesc/boxes/3d-e-chem\" and upload the generated \".box\" file (distribution via built VM box release artifact)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T04:00:11Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-gpcrdb",
      "url": "https://github.com/3D-e-Chem/knime-gpcrdb",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"KNIME plugin for retrieving data from https://gpcrdb.org, GPCRdb website contains data, web tools and diagrams for G protein-coupled receptors (GPCRs).\"",
            "\"Steps to get GPCRDB nodes inside KNIME\" followed by KNIME GUI installation steps, indicating an end-user plugin application rather than a library dependency."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:29Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: owner_type is Organization (3D-e-Chem), indicating a group/project rather than an individual maintainer.",
            "README: \"KNIME plugin for retrieving data from https://gpcrdb.org\" and installation is via KNIME 'Install new software' (end-user plugin usage)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:14Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-klifs",
      "url": "https://github.com/3D-e-Chem/knime-klifs",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"KNIME nodes for retrieving data from KLIFS (https://klifs.net/). KLIFS is a structural kinase-ligand interaction database.\"",
            "\"Steps to get KLIFS nodes inside KNIME: ... 6. Select KLIFS knime nodes 7. Install software & restart\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:31Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "(metadata) owner_type: Organization; owner_login: 3D-e-Chem (appears to be a research-group identity rather than an individual)",
            "README: “KNIME nodes for retrieving data from KLIFS (https://klifs.net/). KLIFS is a structural kinase-ligand interaction database.” (end-user KNIME extension used to obtain research data)"
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:17Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-kripodb",
      "url": "https://github.com/3D-e-Chem/knime-kripodb",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn package\"",
            "\"KNIME nodes for KripoDB\" – provides domain-specific KNIME nodes as a tool used directly in workflows, i.e. an application extension rather than a generic library.",
            "\"Steps to get KripoDB nodes inside KNIME\" followed by KNIME update site URL and installation steps – indicates users install and run this as an end-user tool within KNIME for workflows (direct research use)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:34Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn package\"",
            "(metadata) owner_type: Organization; owner_login: 3D-e-Chem (appears to be a named research team/project rather than an individual)",
            "README: \"[KNIME] nodes for KripoDB\" and \"Steps to get KripoDB nodes inside KNIME\" (end-user nodes installed and run in KNIME)"
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:21Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-molviewer",
      "url": "https://github.com/3D-e-Chem/knime-molviewer",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"KNIME node which launches a web browser with a molecule viewer powered by NGL.\"",
            "\"If you are using KNIME workflows with large molecules and you want to view them in 3D then the molviewer nodes are able to handle this.\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:37Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: owner_type is Organization (3D-e-Chem), suggesting a group/project rather than an individual maintainer.",
            "README: Described as a “KNIME node” that “launches a web browser with a molecule viewer” and “Adds nodes to KNIME to visualize proteins, small molecules and pharmacophores,” indicating an end-user tool (application) used within KNIME workflows."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:25Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-pharmacophore",
      "url": "https://github.com/3D-e-Chem/knime-pharmacophore",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"[KNIME] plugin with nodes to convert and align pharmacophores.\"",
            "\"Steps to get the Pharmacophore KNIME nodes inside KNIME: ... Install software\" (indicates end-user functionality inside KNIME for domain tasks)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:40Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: owner_type is Organization and owner_login is \"3D-e-Chem\" (suggesting a lab/project team rather than an individual).",
            "README: \"[KNIME] plugin with nodes to convert and align pharmacophores.\" (end-user KNIME nodes used to perform a domain task)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:29Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-plants",
      "url": "https://github.com/3D-e-Chem/knime-plants",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"KNIME nodes to configure, run and analyze PLANTS protein-ligand docking\"",
            "\"Included in PLANTS nodes plugin is the PLANTS executable with academic license\" and \"To use these nodes in a commercial manner you need to acquire a valid license yourself and configure the PLANTS node to use the commercial executable.\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:43Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: GitHub owner is an Organization (3D-e-Chem), suggesting maintenance by a research project/group rather than an individual.",
            "README: \"KNIME nodes to configure, run and analyze PLANTS protein-ligand docking\" (end-user nodes used to run/analyze docking)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:33Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-python-node-archetype",
      "url": "https://github.com/3D-e-Chem/knime-python-node-archetype",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn archetype:generate -DarchetypeGroupId=nl.esciencecenter \\\"",
            "\"Generates KNIME workflow node skeleton repository with sample code. The node executes a Python script which is included in the skeleton.\"",
            "\"The [Maven archetype] will generate a multi-module project with the following structure\" and usage via `mvn archetype:generate` indicates it is tooling to scaffold projects, not a library imported at runtime."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:46Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn archetype:generate -DarchetypeGroupId=nl.esciencecenter \\\"",
            "Metadata: repo owner is organization \"3D-e-Chem\" (owner_type: Organization).",
            "README: \"The archetype is hosted on a BinTray repository\" and shows adding a Maven repository URL plus installing via `mvn archetype:generate` with `-DarchetypeGroupId`/`-DarchetypeArtifactId`."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:38Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-python-wrapper",
      "url": "https://github.com/3D-e-Chem/knime-python-wrapper",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"Abstract Python wrapper KNIME node and helpers. Used for development of KNIME nodes calling Python scripts.\"",
            "\"Nodes derived from this repo will have a Python script included in their jar file and the dialog of the node will contain no source code text area.\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:50Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: owner_type is Organization (3D-e-Chem), indicating a group/project rather than an individual maintainer.",
            "README: \"Abstract Python wrapper KNIME node and helpers. Used for development of KNIME nodes calling Python scripts.\" (library/tooling consumed by other KNIME node projects)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:41Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-silicos-it",
      "url": "https://github.com/3D-e-Chem/knime-silicos-it",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"KNIME nodes and example workflows for software made by Silicos-it like shape-it to align molecules based on shape and align-it to align molecules based on their pharmacophore.\"",
            "\"Steps to get the Silicos-it KNIME node inside KNIME: 1. Goto Help > Install new software ... menu ... 6. Install software\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:53Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: owner_type is Organization (3D-e-Chem), suggesting a lab/project team rather than an individual.",
            "README: \"KNIME nodes and example workflows ... like shape-it to align molecules ... and align-it to align molecules based on their pharmacophore.\" (end-user scientific workflow functionality)"
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:44Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-sstea",
      "url": "https://github.com/3D-e-Chem/knime-sstea",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"KNIME node to calculate subfamily specific two entropy analysis (ss-TEA) score.\"",
            "\"Steps install ss-TEA KNIME node: ... Fill text fields with `https://3d-e-chem.github.io/updates/5.1/` ... Install software & restart\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:55Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: GitHub owner is an Organization (3D-e-Chem), suggesting a project/group-maintained research software effort rather than an individual.",
            "README: \"KNIME node to calculate subfamily specific two entropy analysis (ss-TEA) score.\" (a user-run analysis node within KNIME, i.e., an end-user application component)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:47Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-sygma",
      "url": "https://github.com/3D-e-Chem/knime-sygma",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"The SyGMa KNIME nodes for the Systematic Generation of potential Metabolites.\" (domain-specific KNIME nodes for metabolite generation)",
            "\"Steps to get the SyGMa KNIME nodes inside KNIME: ... Fill text fields with the `https://3d-e-chem.github.io/updates/5.1` update site url. ... Select the node ... Install software\" (installed as an application extension via update site)"
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:58:59Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: repo owner is organization '3D-e-Chem' (owner_type: Organization).",
            "README: \"The SyGMa KNIME nodes for the Systematic Generation of potential Metabolites.\""
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:50Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/knime-testflow",
      "url": "https://github.com/3D-e-Chem/knime-testflow",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "\"This plugin is available in the `https://3d-e-chem.github.io/updates` update site.\"",
            "\"To make use of in a Tycho based project add to the `<repositories>` tag of the `pom.xml` file the following\" (showing it is added as a dependency in other projects)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:01Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn verify\"",
            "Metadata: GitHub owner is an Organization (3D-e-Chem), indicating institutional/project ownership rather than an individual.",
            "README: \"This repo gives you another option run a test workflow inside of a Junit @Test method declaration.\" (a plugin/library used from JUnit tests, i.e., consumed as a dependency)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:00:56Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/kripodb",
      "url": "https://github.com/3D-e-Chem/kripodb",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"pip install -U setuptools\"",
            "\"Library to interact with Kripo fragment, fingerprint, pharmacophore and similarity data files.\"",
            "Installation via pip from GitHub: \"pip install git+https://github.com/3D-e-Chem/kripodb.git\" and usage as a CLI: \"kripodb --help\" and commands like \"kripodb similar sim_all.h5 3kxm_K74_frag1 --cutoff 0.45\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:04Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"pip install -U setuptools\"",
            "Metadata: owner_type is Organization and owner_login is \"3D-e-Chem\" (suggesting a lab/project team rather than an individual).",
            "README: \"Library to interact with Kripo fragment, fingerprint, pharmacophore and similarity data files.\" and provides a CLI (e.g., \"kripodb --help\", \"kripodb similar ...\")."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:01:01Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/sygma",
      "url": "https://github.com/3D-e-Chem/sygma",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Containers",
          "distribution_details": null,
          "evidence": [
            "README container command: \"docker run 3dechem/sygma c1ccccc1O\"",
            "\"SyGMa is a python library for the **Sy**\\ stematic **G**\\ eneration of potential **M**\\ et\\ **a**\\ bolites.\"",
            "Example shows library-style use: \"import sygma\" and constructing a Scenario to generate a metabolic tree and scores."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:08Z"
        },
        "gpt-5.2": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Containers",
          "distribution_details": null,
          "evidence": [
            "README container command: \"docker run 3dechem/sygma c1ccccc1O\"",
            "Metadata: owner_type is Organization (3D-e-Chem), suggesting a project/group rather than an individual maintainer.",
            "README: \"SyGMa is a python library\" and example shows `import sygma`, indicating it is intended to be used as a reusable package/dependency."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:01:05Z"
        }
      }
    },
    {
      "full_name": "3D-e-Chem/tycho-knime-node-archetype",
      "url": "https://github.com/3D-e-Chem/tycho-knime-node-archetype",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn archetype:generate -DarchetypeGroupId=nl.esciencecenter \\\"",
            "\"Generates KNIME workflow node skeleton repository with sample code.\"",
            "\"The archetype is hosted on a GitHub packages repository (https://github.com/orgs/3D-e-Chem/packages?repo_name=tycho-knime-node-archetype).\""
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:10Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Dependency software artifact",
          "research_role": "Research-support tooling",
          "distribution_pathway": "Package registry",
          "distribution_details": "Maven/Gradle ecosystem",
          "evidence": [
            "README shows dependency/install info: \"mvn archetype:generate -DarchetypeGroupId=nl.esciencecenter \\\"",
            "Metadata: repository owner is organization \"3D-e-Chem\" (owner_type: Organization).",
            "README: \"Generates KNIME workflow node skeleton repository with sample code.\" (a Maven archetype used by other projects)."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:01:08Z"
        }
      }
    },
    {
      "full_name": "3d-pli/fastpli",
      "url": "https://github.com/3d-pli/fastpli",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Research group or lab",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Source repo",
          "distribution_details": null,
          "evidence": [
            "\"Fiber Architecture Simulation Toolbox for 3D-PLI (fastpli) is a toolbox for polarized light imaging (PLI) with three main purposes\" followed by modules and tutorials showing it is run as an end-user toolbox, not just a library dependency.",
            "Installation instructions emphasize cloning and building from GitHub: \"git clone --recursive https://github.com/3d-pli/fastpli.git\" and then \"make fastpli\" and \"pip3 install .\", indicating primary distribution via the source repository.",
            "\"fastPLI is an open source toolbox for modeling nerve fibers, simulating them in a 3D-PLI microscope and the signal processing developed by the fiber architecture group at the Forschungszentrum Jülich\" showing it directly performs domain-specific simulations and analyses for research."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T03:59:14Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Source repo",
          "distribution_details": null,
          "evidence": [
            "(Actor unit) README: \"signal processing developed by the fiber architecture group at the Forschungszentrum Jülich - INM1\" (institutional affiliation)",
            "(Supply chain / research role) README: \"is a toolbox for polarized light imaging (PLI)\" with modules for \"Simulation - simulation of 3D-Polarized Light Imaging (3D-PLI)\" and \"analysis of 3D-PLI results\"",
            "(Distribution) README installation instructs: \"git clone --recursive https://github.com/3d-pli/fastpli.git\" then \"make fastpli\" and \"pip3 install .\" (install from cloned source)"
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": false,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T04:01:12Z"
        }
      }
    },
    {
      "full_name": "3fon3fonov/exostriker",
      "url": "https://github.com/3fon3fonov/exostriker",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "“**Developer** * Trifon Trifonov, MPIA Heidelberg. * with contributions by …” (single named lead developer with contributors)",
            "“The Exo-Striker analyzes exoplanet orbitals, performs N-body simulations, and models the RV stellar reflex motion… It offers a broad range of tools for detailed analysis of transit and Doppler data…” (end-user analysis/simulation application for research)",
            "PyPI badge and link: “[![PyPI - Version](https://img.shields.io/pypi/v/exostriker?logo=pypi)](https://pypi.org/project/exostriker/)” indicating distribution via the PyPI package registry"
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": false,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T03:59:19Z"
        },
        "gpt-5.2": {
          "actor_unit": "Institution (university, lab, government research organization)",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "Metadata: owner_type is \"User\" (owner_login: 3fon3fonov), and README lists a single \"Developer\" (Trifon Trifonov) with additional contributors, consistent with an individual maintainer.",
            "README: \"The Exo-Striker analyzes exoplanet orbitals, performs N-body simulations, and models the RV stellar reflex motion...\" indicating an end-user research application that directly produces scientific analyses.",
            "README shows PyPI distribution via badge/link: \"PyPI - Version\" pointing to https://pypi.org/project/exostriker/ (and usage via CLI/module: \"$ exostriker\" / \"$ python3.11 -m exostriker\")."
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": true,
            "research_role": false,
            "distribution_pathway": false
          },
          "timestamp_utc": "2026-01-22T04:01:16Z"
        }
      }
    },
    {
      "full_name": "3top1a/biotools-linter",
      "url": "https://github.com/3top1a/biotools-linter",
      "classifications": {
        "gpt-5.1": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"$ pip install -r required.txt\"",
            "\"This is a rule-based linter for the bio.tools database. The script searches the bio.tools API for a given tool name and checks various properties...\" (end users run the linter as a program).",
            "Installation instructions emphasize cloning and running from the git repository: \"Clone this git repository\" and then run via `python3 linter/cli.py` and `cargo run` (source-based usage)."
          ],
          "model": "gpt-5.1",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T03:59:22Z"
        },
        "gpt-5.2": {
          "actor_unit": "Individual maintainer",
          "supply_chain_role": "Application software",
          "research_role": "Direct research execution",
          "distribution_pathway": "Package registry",
          "distribution_details": "PyPI",
          "evidence": [
            "README install command: \"$ pip install -r required.txt\"",
            "Metadata: owner_type is \"User\" (owner_login: 3top1a), suggesting an individually maintained repository.",
            "README: \"This is a rule-based linter for the bio.tools database.\""
          ],
          "model": "gpt-5.2",
          "overrides_applied": {
            "actor_unit": false,
            "research_role": true,
            "distribution_pathway": true
          },
          "timestamp_utc": "2026-01-22T04:01:19Z"
        }
      }
    }
  ]
}