pbalancing 3.0.0a1

Parameter balancing of metabolic models in systems biology

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

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:

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.

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.