Datanator: Toolkit for discovering and aggregating data for whole-cell modeling

Contents

• Overview
• Installation instructions and documentation
• Testing Datanator
• License
• Development team
• Questions and comments

Overview

Extensive data is needed to build comprehensive predictive models of cells. Although the literature and public repositories contain extensive data about cells, this data is hard to utilize for modeling because it is scattered across a large number of sources; because it is described with inconsistent identifiers, units, and data models; and because there are few tools for finding relevant data for modeling specific species and environmental conditions.

Datanator is a software tool for discovering, aggregating, and integrating the data needed for modeling cells. This includes metabolite, RNA, and protein abundances; protein complex compositions; transcription factor binding motifs; and kinetic parameters. Datanator is particularly useful for building large models, such as whole-cell models, that require large amounts of data to constrain large numbers of parameters.

This package contains the source code for Datanator. The data aggregated with Datanator is available at https://www.datanator.info. The data is also available for download as MongoDB snapshot from Zenodo.

Installation instructions and documentation

Please see the documentation for installation instructions, user instructions, and code documentation.

Note, Datanator only supports Python 3.

If one needs to use the datanator database hosted by Karr Lab, one will need karr_lab_build_config repository saved as .wc in the user home directory.

Testing Datanator

To ensure Datanator works properly, we have developed extensive units tests of every aspect of datanator. We recommend using pytest to run these tests as follows:

python3 -m pytest tests

License

We aim to provide data and tools for working with this data with no additional restrictions beyond those imposed by the third-party data sources and software libraries used to construct Datanator.

The content of the Datanator database is a compilation of data curated by the Datanator Team and data aggregated from third-party databases. The copyrightable content curated by the Datanator Team is released under the Creative Commons 1.0 Universal (CC0) License. The content from third-party databases is available under the licenses summarized here.

The structure of the database is released under the CC0 License. This software is released open-source under the MIT License.

Development team

The model was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, US.

• Yosef Roth
• Zhouyang Lian
• Saahith Pochiraju
• Balazs Szigeti
• Jonathan Karr

Questions and comments

Please contact the Karr Lab with any questions or comments.