Chloe and Demeter are the code components of our crop management system for our maize research.

• Chloe: a set of Perl scripts to process raw data; generate tags, labels, and barcodes; and miscellaneous crop management tasks. These files have a .perl suffix.

• Demeter: a declarative, Prolog database for crop, genetic, and phenotype data; associated data provenance; and code for pedigree generation, crop planning, and management of field work. These files have a .pl suffix, since I started writing Prolog before Perl.

Both rely entirely on open-source tools. Mobile device-specific tools (free or very cheap) are used for data capture. Chloe applies to both the whole system and the Perl component (a little operator overloading).

Chloe implements ideas I advocated some time ago in Ten simple rules for experiments' provenance, PLoS Computational Biology, 11: e1004384 (2015).

There are four forms of documentation:

• procedure.org, my running notebook on different ways to use Chloe, with step-by-step instructions;
• chloe.org is the most extensive documentation and user guide;
• a poster at the 2019 Maize Genetics Conference; and
• a bioRxiv preprint.

Please cite this work as:

Chloe: Flexible, Efficient Data Provenance and Management (2020) Toni Kazic bioRxiv 2020.01.28.923763; doi: https://doi.org/10.1101/2020.01.28.923763

Comments and pull requests are welcome, especially for the documentation. Please use the Github issue machinery for reporting issues, rather than emailing me. I can guide you in adapting the code for your work: you don't need to know much about writing code to get started.

Note that dates are in the form day.month.year.

Toni Kazic, 7.10.2024