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MeLoDy Lab - Tool Repositories

Popular repositories

  1. dyse_wm dyse_wm Public

    The Dynamic System Explanation (DySE) Framework contains tools for building, simulating, and verifying qualitative models, built by the Mechanisms and Logic of Dynamics (MeLoDy) Lab at the Universi…

    Python 1 2

  2. CLARINET CLARINET Public

    CLARINET (CLARIfying NETworks) is a tool that equips modelers with a fast and reliable assistant to select the most relevant knowledge about the systems being modeled using graph-based approaches a…

    Python 1

  3. TernaryBody TernaryBody Public

    Jupyter Notebook 1 1

  4. ACCORDION ACCORDION Public

    ACCORDION (ACCelerating and Optimizing model RecommenDatIONs) is a novel tool and methodology for rapid model assembly by automatically extending and evaluating dynamic network models with the info…

    Python

  5. FIDDLE FIDDLE Public

    FIDDLE (Finding Interactions using Diagram Driven modeL Extension) is a tool to automatically assemble or extend models with the knowledge extracted from published literature. The two main methods …

    Python

  6. VIOLIN VIOLIN Public

    VIOLIN (Validating Interactions Of Likely Importance to the Network) is a tool used to automatically classify and judge literature-extracted interactions curated from machine readers by comparing t…

    Python

Repositories

Showing 10 of 10 repositories
  • VIOLIN Public

    VIOLIN (Validating Interactions Of Likely Importance to the Network) is a tool used to automatically classify and judge literature-extracted interactions curated from machine readers by comparing them to existing models. This comparison can help identify key interactions for model extension.

    Python 0 MIT 0 0 0 Updated May 3, 2024
  • BioRECIPE Public

    The standard format of model spreadsheet used by MeLoDy Lab

    Python 0 1 4 0 Updated May 2, 2024
  • CLARINET Public

    CLARINET (CLARIfying NETworks) is a tool that equips modelers with a fast and reliable assistant to select the most relevant knowledge about the systems being modeled using graph-based approaches and literature occurrence metadata.

    Python 1 MIT 0 0 0 Updated Apr 16, 2024
  • TernaryBody Public
    Jupyter Notebook 1 MIT 1 0 0 Updated Apr 16, 2024
  • DiSH Public
    Python 0 MIT 0 0 0 Updated Mar 13, 2024
  • ACCORDION Public

    ACCORDION (ACCelerating and Optimizing model RecommenDatIONs) is a novel tool and methodology for rapid model assembly by automatically extending and evaluating dynamic network models with the information published in literature.

    Python 0 MIT 0 0 0 Updated Mar 1, 2024
  • FLUTE Public

    FLUTE (The FiLter for Understanding True Events) - A tool for identifying high-confidence machine reading interactions through comparison to publicly available interaction databases.

    Python 0 0 0 0 Updated Mar 21, 2023
  • FIDDLE Public

    FIDDLE (Finding Interactions using Diagram Driven modeL Extension) is a tool to automatically assemble or extend models with the knowledge extracted from published literature. The two main methods developed as part of FIDDLE are called Breadth First Addition (BFA) and Depth First Addition (DFA), and they are based on network search algorithms.

    Python 0 MIT 0 0 0 Updated Feb 28, 2023
  • melodylab Public

    A placeholder repo to host the summary page of all tools' readthedocs, the readthedocs page of each tools will be a subproject to this repo. melodylab.readthedocs.io is registered.

    0 0 0 0 Updated Feb 8, 2023
  • dyse_wm Public

    The Dynamic System Explanation (DySE) Framework contains tools for building, simulating, and verifying qualitative models, built by the Mechanisms and Logic of Dynamics (MeLoDy) Lab at the University of Pittsburgh.

    Python 1 MIT 2 0 0 Updated Jan 4, 2023

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