Past Awardee

Plants in silico: A multi-scale modeling platform

Amy Marshall-Colon

College: Liberal Arts and Sciences
Award year: 2015-2016

Individual models are limited in their ability to provide a holistic view of plant or ecosystem response to global change. However, this limitation can be addressed by integrative, multi-scale modeling, which will allow: i) identification and explanation of hidden/unknown parameters that can be targeted for experimental study; ii) simulation to design an ideal plant capable of withstanding future environmental challenges; iii) synergy among expertise at different levels of plant biology, engineering, math and computation. Plants in silico (Psi) is proposed as a modeling platform to provide a quantitative knowledge framework where the implications of a discovery at one level can be examined at the whole plant or even crop or natural ecosystem levels. This requires a paradigm shift from the development of disparate models to a community effort where experts in each domain co-develop models as modules of a larger Psi framework. Psi will therefore generate new insights into plant biology as well as new modalities for collaboration and integration among plant biologists, engineers, and computer scientists.

For this to be accomplished we must establish a virtual laboratory for such collaborations to occur, and we propose to achieve this through three specific aims:

Aim 1. Data sharing, storage and management: Create a virtual laboratory for curation of existing and future mechanistic models at different levels of organization for various plant species and the rapid sharing of data among collaborators.

Aim 2. Data synthesis: Develop a suite of tools for preprocessing and processing pipelines that will annotate models, translate model semantics, and apply standardized ontologies and vocabulary to model components.

Aim 3. Data visualization: create a web interface to access models and tools and visualize model outputs as easy to interpret graphs, tables, animated simulations of plant growth and ecosystem interactions. Here, we propose to lay the initial foundation of these aims by building the Psi framework through a new collaboration with the NCSA and the National Data Service (NDS).