https://github.com/ginkgobioworks/geckopy

Enzyme-constrained genome-scale models in python
https://github.com/ginkgobioworks/geckopy

data-integration enzyme-constraints kinetics omics proteomics systems-biology thermodynamics

Last synced: 2 months ago
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Enzyme-constrained genome-scale models in python

• Host: GitHub
• URL: https://github.com/ginkgobioworks/geckopy
• Owner: ginkgobioworks
• License: apache-2.0
• Created: 2021-03-09T16:22:54.000Z (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2023-10-25T08:39:05.000Z (about 1 year ago)
• Last Synced: 2024-05-02T05:43:16.070Z (8 months ago)
• Topics: data-integration, enzyme-constraints, kinetics, omics, proteomics, systems-biology, thermodynamics
• Language: Python
• Homepage: https://geckopy.readthedocs.io/en/latest/
• Size: 4.84 MB
• Stars: 23
• Watchers: 6
• Forks: 4
• Open Issues: 6
• Metadata Files:
  • Readme: README.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        
geckopy

=======

.. image:: https://github.com/ginkgobioworks/geckopy/actions/workflows/main.yml/badge.svg

   :target: https://github.com/ginkgobioworks/geckopy/actions

   :alt: CI build

**G**\ enome-scale model **E**\ nzyme **C**\ onstraints, using **K**\ inetics and 

**O**\ mics in **py**\ thon.

By combining kcats and proteomics measurement, geckopy allows for improving

the modeling capabilities in genome-scale models.

..

   Based on `Sánchez et al., 2017`_.

   Citing geckopy: `Carrasco et al., 2023`_.

Check https://github.com/SysBioChalmers/GECKO for the matlab counterpart.

Overview

--------

Load a model.

.. code-block:: python

   import geckopy

   model = geckopy.io.read_sbml_ec_model("tests/data/eciML1515.xml.gz")

   model.optimize()

Add copy number experimental data.

.. code-block:: python

   import pandas as pd

   from geckopy.experiment import from_copy_number

   raw_proteomics = pd.read_csv("tests/data/ecoli_proteomics_schmidt2016S5.tsv")

   exp_model = from_copy_number(

       model,

       index=raw_proteomics["uniprot"],

       cell_copies=raw_proteomics["copies_per_cell"],

       stdev=raw_proteomics["stdev"],

       vol=2.3,

       dens=1.105e-12,

       water=0.3,

   )

   exp_model.optimize()

Add pool constraint.

.. code-block:: python

   # add some molecular weights to the proteins if the model does not have them

   for prot in ec_model.proteins:

       prot.mw = 330

   exp_model.constrain_pool(

       p_measured=12.,

       sigma_saturation_factor=0.8,

       fn_mass_fraction_unmeasured_matched=0.2,

   )

   print(exp_model.optimize())

   print(exp_model.protein_pool_exchange)

Build the documentation

-----------------------

To build the documentation locally, run 

.. code-block:: shell

  cd docs

  pip install -r requirements.txt

  make ipy2rst  # if there are notebooks for the docs at docs/notebooks

  make html

License

-------

Copyright 2021 Ginkgo Bioworks.

Licensed under Apache License, Version 2.0, (LICENSE_ or

http://www.apache.org/licenses/LICENSE-2.0).

Contribution

~~~~~~~~~~~~

Unless you explicitly state otherwise, any contribution intentionally submitted

for inclusion in the work by you, as defined in the Apache-2.0 license, shall 

be licensed as above, without any additional terms or conditions.

.. _Sánchez et al., 2017: https://dx.doi.org/10.15252/msb.20167411

.. _Carrasco et al., 2023: https://doi.org/10.1128/spectrum.01705-23

.. _LICENSE: ./LICENSE

.. _virtualenv: https://pypi.python.org/pypi/virtualenv