diff --git a/examples/bessd/co2flux/co2flux.png b/examples/bessd/co2flux/co2flux.png new file mode 100644 index 0000000..b591217 Binary files /dev/null and b/examples/bessd/co2flux/co2flux.png differ diff --git a/examples/bessd/co2flux/index.rst b/examples/bessd/co2flux/index.rst new file mode 100644 index 0000000..1c27b51 --- /dev/null +++ b/examples/bessd/co2flux/index.rst @@ -0,0 +1,42 @@ +.. _intersect:arch:examples:bessd:co2flux: + +Automated CO\ :sub:`2` Flux Measurement +======================================= + +The goal within this objective is to reduce uncertainties associated with the +impacts of thermal extremes on terrestrial soil C cycling by developing and +deploying an automated CO\ :sub:`2` flux measurement system within an +instrumented field-scale experiment to allow for near real-time analysis of +data and feedback to field experimental designs +(:numref:`intersect:arch:examples:bessd:co2flux:co2flux`). + +.. figure:: co2flux.png + :name: intersect:arch:examples:bessd:co2flux:co2flux + :align: center + :width: 600 + + Conceptual diagram of the overall work and data flow. + +The :term:`Oak Ridge National Laboratory` project team consists of: + +- `Melanie Mayes (Principal Investigator) `_ +- `David Weston (Co-Principal Investigator) `_ +- `Fernanda Santos (Task Lead) `_ +- `John Field `_ +- `Natalie Griffiths `_ +- `Brandon Sloan `_ +- `Swen Boehm `_ (:term:`INTERSECT`) +- `Christian Engelmann `_ (:term:`INTERSECT`) +- `Marshall McDonnell `_ (:term:`INTERSECT`) +- `Anees Al Najjar `_ (:term:`INTERSECT`) +- `Nageswara Rao `_ (:term:`INTERSECT`) +- `Gregory Watson `_ (Galaxy workflows) + +.. toctree:: + :name: intersect:arch:examples:bessd:co2flux:architecture + :maxdepth: 1 + :caption: Architecture + + pat + sos + ms diff --git a/examples/bessd/co2flux/ms.rst b/examples/bessd/co2flux/ms.rst new file mode 100644 index 0000000..4cb67f0 --- /dev/null +++ b/examples/bessd/co2flux/ms.rst @@ -0,0 +1,5 @@ +.. _intersect:arch:examples:bessd:co2flux:ms: + +Microservices Architecture +-------------------------- + diff --git a/examples/bessd/co2flux/pat.rst b/examples/bessd/co2flux/pat.rst new file mode 100644 index 0000000..7b0f9a9 --- /dev/null +++ b/examples/bessd/co2flux/pat.rst @@ -0,0 +1,5 @@ +.. _intersect:arch:examples:bessd:co2flux:pat: + +Science Use Case Design Patterns +-------------------------------- + diff --git a/examples/bessd/co2flux/sos.rst b/examples/bessd/co2flux/sos.rst new file mode 100644 index 0000000..c1afa99 --- /dev/null +++ b/examples/bessd/co2flux/sos.rst @@ -0,0 +1,51 @@ +.. _intersect:arch:examples:bessd:co2flux:sos: + +System-of-Systems Architecture +------------------------------ + +.. _intersect:arch:examples:bessd:co2flux:sos:physical: + +Physical View +============= + + +.. _intersect:arch:examples:bessd:co2flux:sos:logical: + +Logical View +============ + + +.. _intersect:arch:examples:bessd:co2flux:sos:data: + +Data View +========= + + +.. _intersect:arch:examples:bessd:co2flux:sos:operational: + +Operational View +================ + + +.. _intersect:arch:examples:bessd:co2flux:sos:user: + +User View +========= + + +.. _intersect:arch:examples:bessd:co2flux:sos:standards: + +Standards View +============== + + +.. _intersect:arch:examples:bessd:co2flux:sos:standards:internal: + +Internal Standards +^^^^^^^^^^^^^^^^^^ + + +.. _intersect:arch:examples:bessd:co2flux:sos:standards:external: + +External Standards +^^^^^^^^^^^^^^^^^^ diff --git a/examples/bessd/index.rst b/examples/bessd/index.rst new file mode 100644 index 0000000..7fc3903 --- /dev/null +++ b/examples/bessd/index.rst @@ -0,0 +1,75 @@ +.. _intersect:arch:examples:bessd: + +Multi-scale Biological and Environmental Solutions for a Sustainable Earth +========================================================================== + +The 10-year grand challenge in biological and environmental systems science is +to mitigate the existential threats of disturbance and climate change on +natural and managed ecosystems. This challenge can be best addressed by +designing a flexible and multi-scale observation-experiment-modeling +integration framework for integrated laboratory, greenhouse, and field +experiments. Integrating currently independent capabilities in cross-scale +experimental systems and modeling enables efficient, economical, and +enlightening studies across a range of temporal and spatial scales, in natural +and managed ecosystems. Such studies ensure sustainable life on Earth with +clean energy and resilient biological, environmental, and human systems. + +This project develops an exemplar multi-scale observation-experiment-modeling +platform that leverages :term:`INTERSECT` federated ecosystem to address two +key questions: 1) how can plant genotypes be used to predict resilience to +increased temperature due to climate change, and 2) how can soil greenhouse gas +emissions be impacted by resilient plant traits? It collects and transfers data +from multi-scale laboratory, greenhouse, and field manipulation studies for +modeling simulations in the :term:`INTERSECT` federated ecosystem to predict +genes underlying plant resilience traits, and the effect of those genes on soil +C dynamics under enhanced warming. The results enable feedback experiment +steering and design, with the long-term goal for live feedback to experimental +manipulations in future studies. + +The overarching objective is to develop capabilities for a multi-scale +observation-experiment-modeling integration framework, enabled by the +:term:`INTERSECT` federated ecosystem to facilitate data transfer, analysis, +simulation, and experiment steering and design. This project has the following +3 :ref:`intersect:arch:examples:bessd:objectives`: + +- :ref:`intersect:arch:examples:bessd:phenotyping`: Discovering the genetics of + resilient plant traits by integrating high-frequency phenotyping with + measurements of photosynthesis and :term:`volatile organic compound` + emissions. +- :ref:`intersect:arch:examples:bessd:soilcosm`: Towards an automated soil + microcosm with model-experiment feedback. +- :ref:`intersect:arch:examples:bessd:co2flux`: Integrating automated + CO\ :sub:`2` flux measurement systems into field-scale experiments to reduce + uncertainties in C-flux responses to thermal extremes. + +The :term:`Oak Ridge National Laboratory` project team consists of: + +- `Melanie Mayes (Principal Investigator) `_ +- `David Weston (Co-Principal Investigator) `_ +- `Kelsey Carter (Task Lead) `_ +- `Fernanda Santos (Task Lead) `_ +- `Mengjun Shu (Task Lead) `_ +- `Larry York (Task Lead) `_ +- `Natalie Griffiths `_ +- `Lianhong Gu `_ +- `John Field `_ +- Aubrey Fine +- `Robin Clark `_ +- Anand Seethepalli +- `Christian Salvador `_ +- `Brandon Sloan `_ +- `Swen Boehm `_ (:term:`INTERSECT`) +- `Christian Engelmann `_ (:term:`INTERSECT`) +- `Marshall McDonnell `_ (:term:`INTERSECT`) +- `Anees Al Najjar `_ (:term:`INTERSECT`) +- `Nageswara Rao `_ (:term:`INTERSECT`) +- `Gregory Watson `_ (Galaxy workflows) + +.. toctree:: + :name: intersect:arch:examples:bessd:objectives + :maxdepth: 1 + :caption: Objectives + + phenotyping/index + soilcosm/index + co2flux/index diff --git a/examples/bessd/phenotyping/index.rst b/examples/bessd/phenotyping/index.rst new file mode 100644 index 0000000..ff18480 --- /dev/null +++ b/examples/bessd/phenotyping/index.rst @@ -0,0 +1,57 @@ +.. _intersect:arch:examples:bessd:phenotyping: + +High-frequency Phenotyping with Genome-based Photosynthesis and Volatile Organic Compound Modeling +================================================================================================== + +The goal within this objective is to integrate high-frequency :term:`Advanced +Plant Phenotyping Laboratory (APPL)` data collection and model driven +insights with the :term:`INTERSECT` federated ecosystem to advance bioenergy +feedstock development and ecosystem prediction. The approach tests the +hypothesis that a deeper genomic understanding can greatly improve trait +prediction and enhance earth system photosynthesis modelling. Central to this +strategy is the utilization of an existing experiment involving 500 Populus +trichocarpa genotypes. This existing study includes dozens of plant growth +traits and focuses on difficult to measure leaf-level photosynthesis rates and +:term:`volatile organic compound` emissions —- especially isoprene, by +using both manual techniques and the :term:`APPL` platform (component C in +:numref:`intersect:arch:examples:bessd:phenotyping:phenotyping`). Two modeling +services are employed that encompass :term:`genome-wide association studies +(GWAS)`/genomic predictions along with a process-based Earth system +physiological model. This will enable the association of approximately 8 +million :term:`single nucleotide polymorphisms (SNPs)` to plant traits and +provide the ability to scale genes to leaf to whole plant productivity in a +unified observation-experiment-simulation framework (components D and E in +:numref:`intersect:arch:examples:bessd:phenotyping:phenotyping`). + +.. figure:: phenotyping.png + :name: intersect:arch:examples:bessd:phenotyping:phenotyping + :align: center + :width: 500 + + Conceptual diagram of the overall work and data flow, integrating + experiments with the :term:`INTERSECT` federated ecosystem. + +The :term:`Oak Ridge National Laboratory` project team consists of: + +- `Melanie Mayes (Principal Investigator) `_ +- `David Weston (Co-Principal Investigator) `_ +- `Kelsey Carter (Task Lead) `_ +- `Mengjun Shu (Task Lead) `_ +- `Lianhong Gu `_ +- Anand Seethepalli +- `Christian Salvador `_ +- `Swen Boehm `_ (:term:`INTERSECT`) +- `Christian Engelmann `_ (:term:`INTERSECT`) +- `Marshall McDonnell `_ (:term:`INTERSECT`) +- `Anees Al Najjar `_ (:term:`INTERSECT`) +- `Nageswara Rao `_ (:term:`INTERSECT`) +- `Gregory Watson `_ (Galaxy workflows) + +.. toctree:: + :name: intersect:arch:examples:bessd:phenotyping:architecture + :maxdepth: 1 + :caption: Architecture + + pat + sos + ms diff --git a/examples/bessd/phenotyping/ms.rst b/examples/bessd/phenotyping/ms.rst new file mode 100644 index 0000000..27e6cd3 --- /dev/null +++ b/examples/bessd/phenotyping/ms.rst @@ -0,0 +1,5 @@ +.. _intersect:arch:examples:bessd:phenotyping:ms: + +Microservices Architecture +-------------------------- + diff --git a/examples/bessd/phenotyping/pat.rst b/examples/bessd/phenotyping/pat.rst new file mode 100644 index 0000000..5e66f72 --- /dev/null +++ b/examples/bessd/phenotyping/pat.rst @@ -0,0 +1,5 @@ +.. _intersect:arch:examples:bessd:phenotyping:pat: + +Science Use Case Design Patterns +-------------------------------- + diff --git a/examples/bessd/phenotyping/phenotyping.png b/examples/bessd/phenotyping/phenotyping.png new file mode 100644 index 0000000..7cce3dc Binary files /dev/null and b/examples/bessd/phenotyping/phenotyping.png differ diff --git a/examples/bessd/phenotyping/sos.rst b/examples/bessd/phenotyping/sos.rst new file mode 100644 index 0000000..0135f44 --- /dev/null +++ b/examples/bessd/phenotyping/sos.rst @@ -0,0 +1,51 @@ +.. _intersect:arch:examples:bessd:phenotyping:sos: + +System-of-Systems Architecture +------------------------------ + +.. _intersect:arch:examples:bessd:phenotyping:sos:physical: + +Physical View +============= + + +.. _intersect:arch:examples:bessd:phenotyping:sos:logical: + +Logical View +============ + + +.. _intersect:arch:examples:bessd:phenotyping:sos:data: + +Data View +========= + + +.. _intersect:arch:examples:bessd:phenotyping:sos:operational: + +Operational View +================ + + +.. _intersect:arch:examples:bessd:phenotyping:sos:user: + +User View +========= + + +.. _intersect:arch:examples:bessd:phenotyping:sos:standards: + +Standards View +============== + + +.. _intersect:arch:examples:bessd:phenotyping:sos:standards:internal: + +Internal Standards +^^^^^^^^^^^^^^^^^^ + + +.. _intersect:arch:examples:bessd:phenotyping:sos:standards:external: + +External Standards +^^^^^^^^^^^^^^^^^^ diff --git a/examples/bessd/soilcosm/index.rst b/examples/bessd/soilcosm/index.rst new file mode 100644 index 0000000..3dd3046 --- /dev/null +++ b/examples/bessd/soilcosm/index.rst @@ -0,0 +1,52 @@ +.. _intersect:arch:examples:bessd:soilcosm: + +SoilCosm Galaxy +=============== + +The goal within this objective is to advance understanding of controls on soil +carbon storage and greenhouse gas production using a soil microcosm system +linked to a predictive model framework. This project will expand the +capabilities of SoilCosms, an automated monitoring of soil incubation +experiments, involving continuous measurement of greenhouse gases. Gas +analyzers will be combined into a testbed hardware design where near real-time +monitoring is used to guide discrete sampling events for characterization of +soil carbon and microbiology pools based on forecasting methods and anomaly +detection. SoilCosm data will be contextualized by comparing to a simple soil +carbon simulation model (DayCent model) using the :term:`INTERSECT` federated +ecosystem and Galaxy workflows +(:numref:`intersect:arch:examples:bessd:soilcosm:soilcosm`). + +.. figure:: soilcosm.png + :name: intersect:arch:examples:bessd:soilcosm:soilcosm + :align: center + :width: 600 + + Conceptual diagram of the overall work and data flow, integrating + experiments with the :term:`INTERSECT` federated ecosystem and Galaxy + workflows. + +The :term:`Oak Ridge National Laboratory` project team consists of: + +- `Melanie Mayes (Principal Investigator) `_ +- `David Weston (Co-Principal Investigator) `_ +- `Larry York (Task Lead) `_ +- `John Field `_ +- Aubrey Fine +- `Robin Clark `_ +- Anand Seethepalli +- `Brandon Sloan `_ +- `Swen Boehm `_ (:term:`INTERSECT`) +- `Christian Engelmann `_ (:term:`INTERSECT`) +- `Marshall McDonnell `_ (:term:`INTERSECT`) +- `Anees Al Najjar `_ (:term:`INTERSECT`) +- `Nageswara Rao `_ (:term:`INTERSECT`) +- `Gregory Watson `_ (Galaxy workflows) + +.. toctree:: + :name: intersect:arch:examples:bessd:soilcosm:architecture + :maxdepth: 1 + :caption: Architecture + + pat + sos + ms diff --git a/examples/bessd/soilcosm/ms.rst b/examples/bessd/soilcosm/ms.rst new file mode 100644 index 0000000..866552f --- /dev/null +++ b/examples/bessd/soilcosm/ms.rst @@ -0,0 +1,5 @@ +.. _intersect:arch:examples:bessd:soilcosm:ms: + +Microservices Architecture +-------------------------- + diff --git a/examples/bessd/soilcosm/pat.rst b/examples/bessd/soilcosm/pat.rst new file mode 100644 index 0000000..cea1fda --- /dev/null +++ b/examples/bessd/soilcosm/pat.rst @@ -0,0 +1,5 @@ +.. _intersect:arch:examples:bessd:soilcosm:pat: + +Science Use Case Design Patterns +-------------------------------- + diff --git a/examples/bessd/soilcosm/soilcosm.png b/examples/bessd/soilcosm/soilcosm.png new file mode 100644 index 0000000..eebed6f Binary files /dev/null and b/examples/bessd/soilcosm/soilcosm.png differ diff --git a/examples/bessd/soilcosm/sos.rst b/examples/bessd/soilcosm/sos.rst new file mode 100644 index 0000000..3bb81b9 --- /dev/null +++ b/examples/bessd/soilcosm/sos.rst @@ -0,0 +1,51 @@ +.. _intersect:arch:examples:bessd:soilcosm:sos: + +System-of-Systems Architecture +------------------------------ + +.. _intersect:arch:examples:bessd:soilcosm:sos:physical: + +Physical View +============= + + +.. _intersect:arch:examples:bessd:soilcosm:sos:logical: + +Logical View +============ + + +.. _intersect:arch:examples:bessd:soilcosm:sos:data: + +Data View +========= + + +.. _intersect:arch:examples:bessd:soilcosm:sos:operational: + +Operational View +================ + + +.. _intersect:arch:examples:bessd:soilcosm:sos:user: + +User View +========= + + +.. _intersect:arch:examples:bessd:soilcosm:sos:standards: + +Standards View +============== + + +.. _intersect:arch:examples:bessd:soilcosm:sos:standards:internal: + +Internal Standards +^^^^^^^^^^^^^^^^^^ + + +.. _intersect:arch:examples:bessd:soilcosm:sos:standards:external: + +External Standards +^^^^^^^^^^^^^^^^^^ diff --git a/examples/index.rst b/examples/index.rst index c6755c4..9f635bd 100644 --- a/examples/index.rst +++ b/examples/index.rst @@ -34,3 +34,4 @@ use cases are addressed by the architecture, including how the :caption: Architecture Examples Catalog aam/index + bessd/index