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Code associated with the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnology
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This repository provides the code used to generate the figures and tables in the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnology.

The code performs the following functions:

  • Downloads the BioModels database (Release 30)
  • Parses all of downloaded SBML files for both the curated and non-curated models
  • Uses heuristics to try to determine the mathematical type (flux balance analysis, logical, stochastic) of each model
  • Extracts all of the model-level annotations (e.g. taxon, pathway, reference) of each model
  • Inserts all of the model metadata (id, name, mathematical type, annotations) into a sqlite database
  • Exports all of the model mdetadata to an Excel file
  • Analyze the metadata and generate the figures and tables for the review paper

How to run this code


  • Pip
  • Python

Run the code

pip install -r requirements.txt
python paper_2018_curr_opin_biotechnol/

View the results

All of the results will be stored in the directory paper_2018_curr_opin_biotechnol/data.

How to cite this code

Check back in 2018


The code is released under the MIT license.

Development team

This code was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.

Questions and comments

Please contact the Karr Lab with any questions or comments.

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