Table 1.

Existing tools and resources for integrative and multi-scale modeling.

	Resource	Description	Citation
Frameworks	Cactus	Problem solving framework that enables parallel computation across scales.	Goodale et al., 2003
	SemGen	Tool to automate modular composition and decomposition of biosimulation models	Gennari et al., 2011; Neal et al., 2015
	FLAME	Agent-based modeling system that scales from laptops to HPC and parallel super computing	Holcombe et al., 2006; Kiran et al., 2010
	OpenMI	Software for independent model exchange at run time.	Moore and Tindall, 2005
	Swift	Parallel scripting system for many task workflows.	Wilde et al., 2011
	VLab/L-studio	Modeling and simulation of plant development from genes to ecosystems	Prusinkiewicz, 2004
	OpenAlea	Visualization and modeling of plant architecture.	Pradal et al., 2008
Model/data repositories	PlaSMo	Database for plant growth models and interface,	Tindal et al., 2010
	BioModels	Database with biochemical and non-biochemical models, MIRIAM compliant	Chelliah et al., 2015
	GEO	Data repository for high throughput genomic datasets, utilizing MIAME standards	Edgar et al., 2002
	CyVerse	Repository for tools for developing data storage pipeline	Hanlon et al., 2015; Merchant et al., 2016
Semantic reconciliation	SBOL	Standard synthetic biology open language	Roehner et al., 2016
	JSim	Utilizes mathematical modeling language for writing models and annotation	Butterworth et al., 2013
	COMBINE	Initiative to develop a set of interoperable and non-overlapping standards for modeling	Hucka et al., 2003