FluxPyt Code
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| File | Date | Author | Commit |
|---|---|---|---|
| .spyproject | 2019-08-20 |
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[2818e4] misc |
| docs | 2017-11-24 |
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[09988e] added all chenges to branch sym_mids |
| fluxpyt | 2021-05-21 |
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[8fd0ac] misc comment deleted |
| .coveragerc | 2017-10-14 |
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[0a6127] Initial commit |
| .gitignore | 2017-10-15 |
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[67c019] html docs removed from .gitignore |
| AUTHORS.rst | 2017-10-14 |
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[0a6127] Initial commit |
| CHANGES.rst | 2018-02-28 |
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[d2cb9c] changed CHANGE.rst |
| LICENSE.txt | 2017-10-14 |
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[f63eca] first commit |
| README.rst | 2021-02-03 |
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[ba0464] changed README.rst |
| setup.cfg | 2021-02-03 |
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[759b0d] edited version name |
| setup.py | 2019-07-06 |
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[d8647a] changed setup.py |
Read Me
fluxpyt
This package is developed to perform stationary 13C metabolic flux analysis calculations for estimation of intracellular flux distribution. FluxPyt is written in python3. The anaconda package list is provided in the requirements.txt file.
The package was developed as a part of PhD work of Desai Trunil Shamrao at:
Systems Biology for Biofuels Group Group Leader, Dr. Shireesh Srivastava International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi.
Acknowledgements
The PhD fellowship of Trunil is funded by the Council for Scientific and Industrial Research (CSIR). The project is funded by Department of Biotechnology (DBT)
The author specially thanks Ahmad for being there to discuss issues and to help get rid of few bugs.
Installation ( for Windows):
These directions are written for Windows users who are not familiar with Python programming.
Download and install Anaconda distribution (version 3.4.4.0 was used in this tutorial).
Open an Anaconda command prompt. Click on Windows start button. Type 'anaconda'. A link to open Anaconda command promt will be shown.
Type following commands to create new environment in Anaconda for running fluxpyt:
conda create -n fluxpyt_env python=3.6.1 numpy=1.12.1 scipy=0.19.0 sympy=1.0
activate fluxpyt_env
conda install -c conda-forge lmfit
conda install -c sjpfenninger glpk
conda install csvkit=0.9.1
conda install matplotlib=2.0.2
conda install pandas=0.20.1
conda install spyder
Install FluxPyt from source code in development mode:
Extract the .zip file.
CD to 'fluxpyt' folder.
Type following:
pip install -e .
Changelog
Version 0.1.7
- Added net_flux_cal.py. Bootstrap calls it to calculate CIs for net fluxes of the reversible reactions.
Version 0.1.6
- Solved some bugs
Version 0.1.5
-Lower bounds and upper bounds of each reaction can be assigned by user. Note: User defined bounds will affect the final solution only if they affect the bounds of free fluxes. -Initial values of free flux parameters selected ome by one by performing flux variability for each free flux taking into account the previously selected value for other free fluxes.
Version 0.1.4
-Cleared code to largely follow PEP 8 guidelines.
Version 0.1.4
-Minor changes
Version 0.1.3
-Changed installation directions in README.rst
Version 0.1.2
-Changed installation directions in README.rst
Version 0.1.1
-Project setup created by Pyscaffold.
-Generated documentation using Sphinx
Version 0.1
-Initial release
Note
This project has been set up using PyScaffold 2.5.8. For details and usage information on PyScaffold see http://pyscaffold.readthedocs.org/.
