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1. CovertLab/WholeCell CovertLab/WholeCell Public

   Mycoplasma genitalium whole-cell model

   MATLAB 121 41

2. biosimulations/biosimulations biosimulations/biosimulations Public

   A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

   TypeScript 40 14

3. biosimulators/Biosimulators biosimulators/Biosimulators Public

   Registry of containerized biosimulation tools that support a standard command-line interface

   Python 13

4. KarrLab/de_sim KarrLab/de_sim Public

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

   Python 32 5

5. KarrLab/datanator KarrLab/datanator Public

   Toolkit for discovering and aggregating data for whole-cell modeling

   Python 15 3

6. deeporiginbio/deeporigin-client deeporiginbio/deeporigin-client Public

   Deep Origin CLI and Python client

   Python 9