Installation

BiGG_SABIO is installed in a command prompt, Powershell, Terminal, or Anaconda Command Prompt via pip:

pip install bigg_sabio

__init__()

The scraping is initiated through four arguments:

import bigg_sabio
bgsb = bigg_sabio.SABIO_scraping(bigg_model_path, bigg_model_name = None, export_model_content = False, verbose = False)

• bigg_model_path str: specifies the path to the JSON file of the BiGG model that will be parsed.

• bigg_model_name str: specifies the name of the BiGG model, which will be used to identify the model and name the output folder directory, where None defaults the name of the file from the bigg_model_path parameter.

• export_model_content bool: specifies where parsed information about the BiGG model will be of the SBML file for the BiGG model that will be simulated.

• verbose & printing bool: specifies whether simulation details (which is valuable for trobuleshooting) and results, respectively, will be printed.

complete()

The complete scraping process is concisely conducted through a single function, which references the object variables that are defined through the __init__() function:

import bigg_sabio
bgsb = bigg_sabio.SABIO_scraping(bigg_model_path, bigg_model_name = None, export_model_content = False, verbose = False)
bgsb.complete()

scrape_bigg_xls()

This function is the first step in BiGG_SABIO workflow, where a Selenium WebDriver is directed through the advanced search options of SABIO and proceeds to download all of the search results that match annotations from the BiGG model. These numerous XLS files, at the end of the scraping process, are concatenated into a spreadsheet with the duplicate rows are removed to yield a complete CSV file of the SABIO kinetics data for the respective BiGG model. The identities and values for each parameter are subsequently scraped, and assembled and downloaded as a separate JSON file.

to_fba()

This is the final step in BiGG_SABIO workflow, where the complete assemblage of SABIO kinetics data is refined into a structure that is amenable with the dFBAy module.

Executing the individual functions

The individual functions can be executed through the following sequence:

import bigg_sabio
bgsb = bigg_sabio.SABIO_scraping(bigg_model_path, bigg_model_name = None, export_model_content = False, verbose = False)
bgsb.scrape_bigg_xls()
bgsb.to_fba()

# Scrape data for a BiGG model
from bigg_sabio import SABIO_scraping
bgsb = SABIO_scraping(bigg_model_path, bigg_model_name = None, export_model_content = False, verbose = False)
print(dir(bgsb))