Metadata-Version: 2.1
Name: pbalancing
Version: 3.0.0a1
Summary: Parameter balancing of metabolic models in systems biology
Home-page: https://gitlab.com/elad.noor/parameter-balancing/
Download-URL: https://pypi.org/project/pbalancing/
Author: Timo Lubitz, Elad Noor, Wolfram Liebermeister
Author-email: elad.noor@weizmann.ac.il, wolfram.liebermeister@gmail.com
License: MIT
Project-URL: Source Code, https://gitlab.com/elad.noor/parameter-balancing/
Project-URL: Bug Tracker, https://gitlab.com/elad.noor/parameter-balancing/-/issues
Keywords: parameter balancing,bayesian inference,multivariate Gaussian distribution
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
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 :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy (~=1.22)
Requires-Dist: cvxpy (~=1.2)
Requires-Dist: scipy (~=1.8)
Requires-Dist: python-libsbml (~=5.19)
Requires-Dist: sbtab (~=1.0)
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'
Provides-Extra: development
Requires-Dist: black (~=22.1) ; extra == 'development'
Requires-Dist: isort (~=5.10) ; extra == 'development'
Requires-Dist: flake8 (~=4.0) ; extra == 'development'
Requires-Dist: safety (~=1.10) ; extra == 'development'
Requires-Dist: tox (~=3.24) ; extra == 'development'
Requires-Dist: twine (~=3.8) ; extra == 'development'
Provides-Extra: test
Requires-Dist: pytest ; extra == 'test'
Requires-Dist: pytest-cov ; extra == 'test'
Requires-Dist: pytest-raises ; extra == 'test'
Requires-Dist: pytest-allclose ; extra == 'test'

# Parameter Balancing: Standalone Version

Parameter balancing is a tool for metabolic modeling in systems biology. It is implemented in Python and its code underlies the PEP8 guidelines. It can either be downloaded and used from command-line as is or embedded in your own Python3 projects. In both cases, you will be required to install Python packages to make the scripts work.

## Parameter balancing on the command-line

Parameter balancing can be employed on the command-line by
```bash
python -m scripts.parameter_balancing.py model.xml
```

where `model.xml` corresponds to the path of your SBML model. It is also possible to provide further input files, such as
an SBtab parameter files (`.tsv`), an SBtab prior information file (`.tsv`), and an SBtab options file (`.tsv`) for the
configuration of parameter balancing. Providing complete file information would look like this:

```bash
python -m scripts.parameter_balancing.py model.xml --sbtab_data data_file.tsv --sbtab_prior prior_file.tsv --sbtab_options options_file.tsv
```

You can create a log file by setting the flag -l, you can use pseudo values to account for a lack of data by setting the flag -p, you can watch program outputs on your command-line by setting the flag -v. Information on the SBtab format can be found on `www.sbtab.net`, more information on the mentioned file types can be found in the parameter balancing manual in this repository's `examples/pb_manual.pdf`, and example files can be found in `examples/example_files/`.

## Embedding parameter balancing in your Python package

You can also embed the modules of parameter balancing in your own Python workflow.

```python
from pbalancing import parameter_balancing_wrapper

balanced_sbml, balanced_sbtab = parameter_balancing_wrapper(
  sbml,
  sbtab_data,
  sbtab_prior,
  sbtab_options,
  verbose,
  no_pseudo_values,
  output_name,
  pb_log
)
```

### Input arguments
  - `sbml` - path to SBML file, REQUIRED)
  - `sbtab_data` - path to SBtab data file (OPTIONAL)
  - `sbtab_prior` - path to SBtab prior file (OPTIONAL)
  - `sbtab_options` - path to SBtab options file (OPTIONAL)
  - `verbose` - Boolean, enable messages on command-line (OPTIONAL)
  - `no_pseudo_values` - Boolean, disable usage of pseudo values (OPTIONAL)
  - `output_name` - name for the output files (OPTIONAL)
  - `pb_log` - Boolean, enable writing of a log file (OPTIONAL)

### Output parameters
  - `balanced_sbml` - SBML file object with balanced content
  - `balanced_sbtab` - SBtab object with balanced content

## Citation and Contact

If you use parameter balancing, please cite http://pubs.acs.org/doi/abs/10.1021/jp108764b for details.

If you are encountering trouble with any of the above, please file a bug report in GitLab. You can also feel free to file feature requests in the same manner.


