yggdrasil: a Python package for integrating computational models across languages and scales

Abstract

Thousands of computational models have been created within both the plant biology community and broader scientific communities in the past two decades that have the potential to be combined into complex integration networks capable of capturing more complex biological processes than possible with isolated models. However, the technological barriers introduced by differences in language and data formats have slowed this progress. We present yggdrasil (previously cis_interface), a Python package for running integration networks with connections between models across languages and scales. yggdrasil coordinates parallel execution of models in Python, C, C++, and Matlab on Linux, Mac OS, and Windows operating systems, and handles communication in a number of data formats common to computational plant modelling. yggdrasil is designed to be user-friendly and can be accessed at https://github.com/cropsinsilico/yggdrasil. Although originally developed for plant models, yggdrasil can be used to connect computational models from any domain.