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Code associated with our 2018 review in Current Opinion in Systems Biology
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.gitignore
README.md
europe_pmc_query.txt
get_author_emails.py
make_figures.py
requirements.txt
survey_invitations.xlsx
survey_responses-edited.xlsx
survey_responses-raw.xlsx

README.md

Code for "A blueprint for human whole-cell modeling"

This repository provides the code for "A blueprint for human whole-cell modeling" by Szigeti et al.

The code performs the following functions:

  • Generates part of the email list used for the biomodeling community survey reported in the paper
    • Uses the Europe PMC webservice to find articles about biomodeling
    • Extracts the author emails and ORCIDs and citation counts from the returned results
    • Groups the articles by author (common email and/or ORCID)
    • Counts the number of articles and sums the citations for each author
    • Saves the results to a TSV file
  • Analyzes the invited investigators and the survey responses
    • Generates several supplementary figures

How to install this code

  1. Install Python and pip
    apt-get install python python-pip
    
  2. Install the require PyPI packages
    pip install -r requirements.txt
    

How to run this code

python get_author_emails.py
python make_figures.py

The first script generates part of the list of investigators that we invited to participate in the survey and saves this list to investigators.tsv. The second script analyzes the survey invitations in survey_invitations.xlsx and survey responses in survey_responses-edited.xlsx and saves several figures to figures/.

How to cite this code

Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC & Karr JR†. A blueprint for human whole-cell modeling. Curr Opin Syst Biol 7, 8–15 (2018). doi: 10.1016/j.coisb.2017.10.005

License

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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