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
- Install Python and pip
apt-get install python python-pip
- 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
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
The code is released under the MIT license.
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.