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@KarrLab

Karr whole-cell modeling lab

Developing whole-cell computational models to predict and engineer biology.

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  1. de_sim de_sim Public

    Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling

    Python 34 5

  2. latex-grant latex-grant Public

    LaTeX classes for formatting scientific documents, including US federal grant proposals.

    TeX 24 10

  3. gdoc_down gdoc_down Public

    Command line programs to save Google documents to text and LaTeX files

    Python 17 2

  4. intro_to_wc_modeling intro_to_wc_modeling Public

    Whole-cell modeling tutorials

    Python 16 4

  5. datanator datanator Public

    Toolkit for discovering and aggregating data for whole-cell modeling

    Python 15 3

  6. wc_rules wc_rules Public

    Rule-based modeling for whole-cell models.

    Python 10 3

Repositories

Showing 10 of 66 repositories
  • obj_tables Public

    Tools for creating and reusing high-quality spreadsheets

    KarrLab/obj_tables’s past year of commit activity
    Python 8 MIT 2 25 0 Updated Aug 18, 2025
  • wc_utils Public

    Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others

    KarrLab/wc_utils’s past year of commit activity
    Python 1 MIT 1 5 0 Updated Aug 18, 2025
  • test_wc_lang_test_io Public
    KarrLab/test_wc_lang_test_io’s past year of commit activity
    0 0 0 0 Updated Aug 18, 2025
  • test_wc_kb_test_io Public
    KarrLab/test_wc_kb_test_io’s past year of commit activity
    0 0 0 0 Updated Aug 18, 2025
  • wc_kb Public

    Tools for building databases of experimental data for constructing whole-cell models

    KarrLab/wc_kb’s past year of commit activity
    Python 4 MIT 5 12 0 Updated Aug 15, 2025
  • karr_lab_build_utils Public

    Utilities for testing Python code and its downstream dependencies, submitting coverage reports, conducting static analyses, and generating documenation

    KarrLab/karr_lab_build_utils’s past year of commit activity
    Python 0 MIT 0 2 0 Updated Aug 7, 2025
  • pkg_utils Public

    Utilities for packaging Python code

    KarrLab/pkg_utils’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jul 18, 2025
  • wc_model_gen Public

    Framework for systematically and scalably designing whole-cell models from large datasets

    KarrLab/wc_model_gen’s past year of commit activity
    Python 6 MIT 2 9 0 Updated Jan 20, 2025
  • wc_sim Public

    A multi-algorithmic simulator for whole-cell models

    KarrLab/wc_sim’s past year of commit activity
    Jupyter Notebook 6 MIT 2 36 0 Updated Jan 15, 2025
  • datanator_rest_api Public

    A OAS3 compliant REST API for the Datanator integrated database

    KarrLab/datanator_rest_api’s past year of commit activity
    Python 0 MIT 3 7 1 Updated Oct 18, 2022
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