Data and code for Porubsky and Goldberg, et al., Best practices for making reproducible biochemical models, Cell Systems, 2020

This Git repository contains data and code used in the paper Veronica Porubsky, Arthur Goldberg, Anand Rampadarath, David Nickerson, Jonathan Karr, and Herbert Sauro, Best practices for making reproducible biochemical models, Cell Systems, 2020.

Overview

This Git repository contains code and data that were used to create Table 2, Influence of standards and tools. Reproduce the table by following the instructions below.

Prerequisites

Running this software requires the following prerequisites:

1. pip
2. git
3. Python 3
4. An account to the Google Search API provided by SerpApi. As of June, 2020, free developer trials are available. The 5,000 searches allowed by a trial will be amply sufficient to run this software.
5. Optionally, an NCBI account, which will speed up the program.

Instructions

Clone this repository:

git clone https://github.com/KarrLab/paper_cell_sys__guidelines_4_repro_models_2020.git

Change directory to paper_cell_sys__guidelines_4_repro_models_2020.

Create a file named keys.py. In it define a variable called SERP_API_KEY equal to the API key provided by SerpApi. Optionally, create an NCBI API key , and define a variable called NCBI_API_KEY equal to it keys.py. Be careful to keep keys.py secure.

Run a Python program to prepare the computing environment:

python prepare.py

Run a Python program to reproduce the table's data:

python eval_tool_n_standard_import.py

The table will be updated in two formats. A LaTeX version is provided in evaluated_standards.tex and a tsv version is provided in evaluated_standards.tsv.

Questions or feedback

Contact Arthur Goldberg.