ecophysiological models - revisited jeff white usda-ars, alarc, maricopa
TRANSCRIPT
Ecophysiological models- revisited
Jeff White USDA-ARS, ALARC, Maricopa
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Temperature ( C)
Gra
in y
ield
(kg
/ha)
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 SteveShow parallels between the twoComment 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 CO2
based on simulations with ecophysiological models.
Elevated CO2
Ambient CO2
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
iPG2Pproposed workflow
Model Entry
Parameter Estimation
Sensitivity Analysis
Verification
Association Mapping
QTL Visualization
Visualization of Model Outputs
MapMan
eFP Browser
CoGe
NextGen Pipeline
ManualSBML
Format Conversion OpenMI component
DN
A-se
q
RNA-seq
SBML
Opt. method
Biol. data
Environmental data
Problem-specific runs
Biol. dataEnvironmental data
Independent:
Cro
ss v
alid
atio
n o
r b
oo
tstr
ap
pin
g
Parameters to map
Information matrix
Eigen Plot
Other models
Tissu
e
En
viron
.
User defined visual templates
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Graph. Residuals Analysis
Info
rmat
ion
the
ore
tic c
omp
ari
son
s
Model EntryModel Entry
Parameter EstimationParameter Estimation
Sensitivity Analysis
Sensitivity Analysis
VerificationVerification
Association Mapping
Association Mapping
QTL VisualizationQTL Visualization
Visualization of Model Outputs
MapMan
eFP Browser
Visualization of Model Outputs
MapMan
eFP Browser
CoGeCoGe
NextGen Pipeline NextGen Pipeline
ManualManualSBMLSBML
Format ConversionFormat Conversion OpenMI componentOpenMI component
DN
A-se
q
RNA-seq
SBML
Opt. methodOpt. method
Biol. dataBiol. data
Environmental dataEnvironmental data
Problem-specific runs
Biol. dataEnvironmental data
Independent:
Cro
ss v
alid
atio
n o
r b
oo
tstr
ap
pin
g
Parameters to map
Information matrix
Eigen PlotEigen Plot
Other models
Tissu
e
En
viron
.
User defined visual templates
User defined visual templates
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Graph. Residuals Analysis
Graph. Residuals Analysis
Info
rmat
ion
the
ore
tic c
omp
ari
son
s
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
iPG2Pproposed workflow
Model Entry
Parameter Estimation
Sensitivity Analysis
Verification
Association Mapping
QTL Visualization
Visualization of Model Outputs
MapMan
eFP Browser
CoGe
NextGen Pipeline
ManualSBML
Format Conversion OpenMI component
DN
A-se
q
RNA-seq
SBML
Opt. method
Biol. data
Environmental data
Problem-specific runs
Biol. dataEnvironmental data
Independent:
Cro
ss v
alid
atio
n o
r b
oo
tstr
ap
pin
g
Parameters to map
Information matrix
Eigen Plot
Other models
Tissu
e
En
viron
.
User defined visual templates
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Graph. Residuals Analysis
Info
rmat
ion
the
ore
tic c
omp
ari
son
s
Model EntryModel Entry
Parameter EstimationParameter Estimation
Sensitivity Analysis
Sensitivity Analysis
VerificationVerification
Association Mapping
Association Mapping
QTL VisualizationQTL Visualization
Visualization of Model Outputs
MapMan
eFP Browser
Visualization of Model Outputs
MapMan
eFP Browser
CoGeCoGe
NextGen Pipeline NextGen Pipeline
ManualManualSBMLSBML
Format ConversionFormat Conversion OpenMI componentOpenMI component
DN
A-se
q
RNA-seq
SBML
Opt. methodOpt. method
Biol. dataBiol. data
Environmental dataEnvironmental data
Problem-specific runs
Biol. dataEnvironmental data
Independent:
Cro
ss v
alid
atio
n o
r b
oo
tstr
ap
pin
g
Parameters to map
Information matrix
Eigen PlotEigen Plot
Other models
Tissu
e
En
viron
.
User defined visual templates
User defined visual templates
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Graph. Residuals Analysis
Graph. Residuals Analysis
Info
rmat
ion
the
ore
tic c
omp
ari
son
s
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
Model Entry
Parameter Estimation
Sensitivity Analysis
Verification
Association Mapping
QTL Visualization
Visualization of Model Outputs
MapMan
eFP Browser
CoGe
NextGen Pipeline
ManualSBML
Format Conversion OpenMI component
DN
A-se
q
RNA-seq
SBML
Opt. method
Biol. data
Environmental data
Problem-specific runs
Biol. dataEnvironmental data
Independent:
Cro
ss v
alid
atio
n o
r b
oo
tstr
ap
pin
g
Parameters to map
Information matrix
Eigen Plot
Other models
Tissu
e
En
viron
.
User defined visual templates
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Graph. Residuals Analysis
Info
rmat
ion
the
ore
tic c
omp
ari
son
s
Model EntryModel Entry
Parameter EstimationParameter Estimation
Sensitivity Analysis
Sensitivity Analysis
VerificationVerification
Association Mapping
Association Mapping
QTL VisualizationQTL Visualization
Visualization of Model Outputs
MapMan
eFP Browser
Visualization of Model Outputs
MapMan
eFP Browser
CoGeCoGe
NextGen Pipeline NextGen Pipeline
ManualManualSBMLSBML
Format ConversionFormat Conversion OpenMI componentOpenMI component
DN
A-se
q
RNA-seq
SBML
Opt. methodOpt. method
Biol. dataBiol. data
Environmental dataEnvironmental data
Problem-specific runs
Biol. dataEnvironmental data
Independent:
Cro
ss v
alid
atio
n o
r b
oo
tstr
ap
pin
g
Parameters to map
Information matrix
Eigen PlotEigen Plot
Other models
Tissu
e
En
viron
.
User defined visual templates
User defined visual templates
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Eig
en
valu
es
&
vect
ors
Se
nsi
tivity
co
effi
cie
nts
Graph. Residuals Analysis
Graph. Residuals Analysis
Info
rmat
ion
the
ore
tic c
omp
ari
son
s
Workflow boxes & DSSAT tools:Model entryParameter estimationSensitivity analysisVisualization of model inputs & outputsVerificationMissing in workflow boxes:Weather data preparationSoil data preparationManagement data preparationCross-validation data preparation“Generic” applications:
Time seriesSpatial
Missing in DSSATTrue modular model developmentAbility to import sub-modelsApplications for QTL & association mappingLinks to genetic/genomic data
DSSAT4.5Positives• Widely used – “it works”• Promoted standardization of data
via the ICASA standards• Promoted use of systems approaches in researchLimitations• 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.