Ecophysiological models - revisited Jeff White USDA-ARS, ALARC, Maricopa

Objectives Remind/inform people of basic capabilities of ecophysiological models and associated tools Compare an existing model + software shell (DSSAT) to the iPlant G-to-P Modeling Workflow proposed by Steve  Show parallels between the two  Comment on lessons from a DSSAT-type approach Identify opportunities for iPlant

Fourth Assessment Report of IPCC. Response of wheat yields (%) to global warming and elevated CO 2 based on simulations with ecophysiological models. Elevated CO 2 Ambient CO 2

Management Phenology Photosynthesis Respiration Partitioning Water & N balance Senescence Maturity? Output Final output Yes No Initial inputs: start date, cultivar, soil, fertilizers … Daily inputs: weather, management, pests... Simplified* flow diagram *CSM has > 270 routines

Relative effect of temperature on leaf photosynthesis for wheat. Source: P. Bindraban, 1997

Simulated vs observed growth of winter wheat at Manhattan, Kansas

iPG2P proposed workflow

DSSAT4.5 Over 25 crop species Large user base 15+ years Over 100 countries Public and private sector Numerous training events Developed through collaboration among US and other universities, international centers, etc. Partially supported through software license ($200 per copy) Other models & shells exist! 

DSSAT4.5 is a shell Dataset preparation Runs cumpliant models such as Cropping Systems Model Tools for model applications: Parameter estimation Cross-validation Sensitivity analysis Time series analysis Spatial analysis

iPG2P proposed workflow

Tools for parameter estimation: - GenCalc - GLUE

Two tools for sensitivity analysis: - Embedded in CSM model ( a legacy tool) - DSSAT Sensitivity Analysis V 4.5

Tools for visualization: - GBuild - EasyGrapher - Others incorporate graphics: weather, seasonal analysis, etc.

Simulated response of common bean to elevated temperature for 96 combinations of alleles at six loci

iPG2P proposed workflow compared to DSSAT Workflow boxes & DSSAT tools: Model entry Parameter estimation Sensitivity analysis Visualization of model inputs & outputs Verification Missing in workflow boxes: Weather data preparation Soil data preparation Management data preparation Cross-validation data preparation “Generic” applications: Time series Spatial Missing in DSSAT True modular model development Ability to import sub-models Applications for QTL & association mapping Links to genetic/genomic data

DSSAT4.5 Positives Widely used – “it works” Promoted standardization of data via the ICASA standards Promoted use of systems approaches in research Limitations Models are only partially modular Source code is not truly open - Scares off contributors - Painfully inefficient for software maintenance Diverse GUIs for tools – confusing to users One person maintains one tool – high risk for users Tools have overlapping functionality – confusing to users Incomplete documentation – confusing & frustrating Main GUI is inefficient for many applications – more frustration

Key opportunities for iPG2P C.I. Open, modular framework for modeling from pathway/organ scales to whole plant scale Generic tools for:  Model development at different scales  Model evaluation  Dataset preparation – relates to data integration  Model applications Parameter estimation Time series analyses (e.g., multiple years or seasons)  Visualization is required throughout (and in numerous layouts) G-to-P tools  Association and QTL mapping  Genetic data as inputs to models (parameter estimation) Keys to success:  Open source – requires training for crop modeling community  Guidelines on “look and feel” or GUI  Learn from or adapt features of existing tools (not just DSSAT)  Tests cases that challenge multiple facets of the IPG2P C.I.