gekim 0.7.7

Generalized Kinetic Modeler: A Python package for modeling arbitrary kinetic schemes.

GeKiM (Generalized Kinetic Modeler)

Description

GeKiM (Generalized Kinetic Modeler) is a Python package designed for creating, interpreting, and modeling arbitrary kinetic schemes. Schemes are defined by the user in a dictionary of species and transitions, which is used to initialize an instance of the System class. Choose (or make) and initialize a simulator for the instance and run it. Field-specific practices are found in gekim/fields.

Installation

With pip:

pip install gekim

Or directly from the source code:

git clone https://github.com/kghaby/GeKiM.git
cd GeKiM
pip install --editable . 

Usage

Here is a basic example of how to use GeKiM to create and simulate a kinetic system:

import gekim as gk
from gekim.fields.bio.enzyme.inhib import irrev as ii 

# Define your kinetic scheme in a configuration dictionary
concI0,concE0 = 100,1
scheme = {
    'species': {
        "I": {"y0": concI0, "label": "I"},
        "E": {"y0": concE0, "label": "E"},
        "EI": {"y0": 0, "label": "EI"},
        "E-I": {"y0": 0, "label": "E-I"},
    },    
    'transitions': {
        "kon": {"k": 0.01, "source": ["E","2I"], "target": ["EI"]},
        "koff": {"k": 0.1, "source": ["EI"], "target": ["E","2I"]},
        "kinact": {"k": 0.01, "source": ["EI"], "target": ["E-I"]}, # irreversible step
    }
}

# Initialize a system with your schematic dictionary
system = gk.System(scheme, quiet=False)

# Choose a simulator and go
#   In this example we're doing a deterministic 
#   simulation of the concentrations of each species over time.
sim = system.set_simulator(gk.simulators.ODESolver)
sim.simulate() # Note the lack of time-scale input. It's predicted!

# Fit the data to experimental models to extract mock-experimental measurements
t = system.simout["t"]
final_state = system.species["E-I"].simout["y"]
all_bound = system.sum_species_simout(blacklist=["E","I"])

fit_output = ii.kobs_uplim_fit_to_occ_final_wrt_t(
    t, final_state, 
    nondefault_params={"Etot":{"value":concE0, "vary":False}})

For more detailed examples, please refer to the examples directory.

Documentation

Documentation pages are pending, but the functions have docstrings.

Example Jupyter Notebooks where GeKiM has been applied to model and analyze irreversible enzyme inhibition:

1. Covalent kinetics with rapid intermediates (2025)
2. Covalent kinase activity probes (2025)

Contributing

If you have suggestions or want to contribute code, please feel free to open an issue or a pull request.

License

GeKiM is licensed under MIT.

Contact

[e-mail]

Citation

If you use this software, please cite:

Ghaby, K.; Roux, B. Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States. J. Chem. Inf. Model. 2025. https://doi.org/10.1021/acs.jcim.5c00952