Metadata-Version: 2.1
Name: optslope
Version: 0.2.0
Summary: OptSlope - A tool for metabolic engineering, based on the OptSlope algorithm
Author-email: Elad Noor <elad.noor@weizmann.ac.il>, "Moritz E. Beber" <midnighter@posteo.net>
License: MIT License
Project-URL: repository, https://gitlab.com/elad.noor/optslope/
Project-URL: documentation, https://gitlab.com/elad.noor/optslope/README.md
Keywords: strain design,gene knockout,optimization,constraint-based
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy~=1.26
Requires-Dist: scipy~=1.12
Requires-Dist: matplotlib~=3.8
Requires-Dist: pandas~=2.2
Requires-Dist: optlang~=1.8
Requires-Dist: cobra~=0.29
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Provides-Extra: development
Requires-Dist: black; extra == "development"
Requires-Dist: isort; extra == "development"
Requires-Dist: flake8; extra == "development"
Requires-Dist: safety; extra == "development"
Requires-Dist: tox; extra == "development"
Requires-Dist: twine; extra == "development"
Provides-Extra: deployment
Requires-Dist: click; extra == "deployment"
Requires-Dist: click-log; extra == "deployment"
Requires-Dist: python-dateutil; extra == "deployment"
Requires-Dist: requests; extra == "deployment"

# OptSlope

[![PyPI version](https://img.shields.io/pypi/v/optslope)](https://badge.fury.io/py/optslppe)
[![Python version](https://img.shields.io/pypi/pyversions/optslope)](https://www.python.org/downloads)
[![MIT license](https://img.shields.io/pypi/l/optslope)](https://mit-license.org/)

[![pipeline status](https://gitlab.com/elad.noor/optslope/badges/develop/pipeline.svg)](https://gitlab.com/elad.noor/optslppe/commits/develop)
[![codecov](https://codecov.io/gl/elad.noor/optslope/graph/badge.svg?token=jUwX9eOqRM)](https://codecov.io/gl/elad.noor/optslope)

A tool for metabolic engineering, based on the OptSlope algorithm.

## Relevant publications:
- Antonovsky, Niv, Shmuel Gleizer, Elad Noor, Yehudit Zohar, Elad Herz, Uri Barenholz, Lior Zelcbuch, et al. “Sugar Synthesis from CO2 in Escherichia Coli.” Cell 166, no. 1 (June 30, 2016): 115–25. https://doi.org/10.1016/j.cell.2016.05.064.
- Gleizer, Shmuel, Roee Ben-Nissan, Yinon M Bar-On, Niv Antonovsky, Elad Noor, Yehudit Zohar, Ghil Jona, et al. “Conversion of Escherichia Coli to Generate All Biomass Carbon from CO2.” Cell 179, no. 6 (November 27, 2019): 1255-1263.e12. https://doi.org/10.1016/j.cell.2019.11.009.
- Aslan, Selçuk, Elad Noor, Sara Benito Vaquerizo, Steffen N. Lindner, and Arren Bar-Even. “Design and Engineering of E. Coli Metabolic Sensor Strains with a Wide Sensitivity Range for Glycerate.” Metabolic Engineering 57 (January 1, 2020): 96–109. https://doi.org/10.1016/j.ymben.2019.09.002.
- Keller, Philipp, Elad Noor, Fabian Meyer, Michael A. Reiter, Stanislav Anastassov, Patrick Kiefer, and Julia A. Vorholt. “Methanol-Dependent Escherichia Coli Strains with a Complete Ribulose Monophosphate Cycle.” Nature Communications 11, no. 1 (October 26, 2020): 5403. https://doi.org/10.1038/s41467-020-19235-5.
- Satanowski, Ari, Beau Dronsella, Elad Noor, Bastian Vögeli, Hai He, Philipp Wichmann, Tobias J. Erb, Steffen N. Lindner, and Arren Bar-Even. “Awakening a Latent Carbon Fixation Cycle in Escherichia Coli.” Nature Communications 11, no. 1 (November 16, 2020): 5812. https://doi.org/10.1038/s41467-020-19564-5.
- Keller, Philipp, Michael A. Reiter, Patrick Kiefer, Thomas Gassler, Lucas Hemmerle, Philipp Christen, Elad Noor, and Julia A. Vorholt. “Generation of an Escherichia Coli Strain Growing on Methanol via the Ribulose Monophosphate Cycle.” Nature Communications 13, no. 1 (September 6, 2022): 5243. https://doi.org/10.1038/s41467-022-32744-9.
