A framework for easy plant model integration

A new tool links models of different languages and scales to create entire plants, fields, or regions in silico.

Thousands of computational models have been created within 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 complex biological processes. However, the technological barriers introduced by differences in model language and data formats has slowed this progress. A new integration system that links models in their diverse, native forms, is presented by Dr. Meagan Lang in a new paper published in in silico Plants.

The yggdrasil (pronounced “ig-druh-sil”) framework was designed for use by domain scientists with limited programming experience. It has an easy to use command line interface that coordinates the parallel execution of models in Python, C, C++, and Matlab on Linux, Mac OS, and Windows operating systems in several data formats. Based on the information contained in the specification files, yggdrasil dynamically establishes a network of asynchronous communication channels, and launches the models in an integration in their own processes. This allows models to complete independent operations in parallel and complete tasks more quickly than models manually integrated in serial. Yggdrasil also performs data format (e.g. scalars, arrays, and tabular data) and unit transformation.

According to Dr. Lang, Research Scientist at National Center for Supercomputing Applications at the University of Illinois, “Although computational models are a powerful tool used throughout biology, many biologists lack formal training in programming or computation. As a result, the models that biologists create, while well suited to answering a particular research question, are not easily adapted for reuse in collaborations outside the context for which they were originally created due to differences in programming languages, data formats, and/or units. By allowing scientists to connect models with minimal modification to the model itself, yggdrasil will allow models to be reused more readily and open up new opportunities for collaboration.”

yggdrasil is an open-source package developed as part of the Crops in Silico initiative to build a complete crop in silico from the level of the genes to the level of the field. The yggdrasil package is available publicly on Github and can be installed using pip or conda. A graphical user interface (GUI) for entering model information, composing integration networks from an existing palette of models, and displaying basic output from an integration run and tools for using yggdrasil to call integrated models as Python functions, allowing users to interactively explore and visualize a model, are currently being developed.

Further reading

Lang, M. (2019). yggdrasil: a Python package for integrating computational models across languages and scales. In Silico Plants, 1(1). https://doi.org/10.1093/insilicoplants/diz001

Marshall-Colon, A., Long, S. P., Allen, D. K., Allen, G., Beard, D. A., Benes, B., … Zhu, X.-G. (2017). Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00786