WIP: Examples BESSD

examples/bessd/co2flux/index.rst

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+.. _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<ORNL>` project team consists of:
+
+- `Melanie Mayes (Principal Investigator) <https://www.ornl.gov/staff-profile/melanie-mayes>`_
+- `David Weston (Co-Principal Investigator) <https://www.ornl.gov/staff-profile/david-j-weston>`_
+- `Fernanda Santos (Task Lead) <https://www.ornl.gov/staff-profile/fernanda-santos>`_
+- `John Field <https://www.ornl.gov/staff-profile/john-l-field>`_
+- `Natalie Griffiths <https://www.ornl.gov/staff-profile/natalie-griffiths>`_
+- `Brandon Sloan <https://www.ornl.gov/staff-profile/brandon-p-sloan>`_
+- `Swen Boehm <https://www.ornl.gov/staff-profile/swen-boehm>`_ (:term:`INTERSECT`)
+- `Christian Engelmann <https://www.ornl.gov/staff-profile/christian-engelmann>`_ (:term:`INTERSECT`)
+- `Marshall McDonnell <https://www.ornl.gov/staff-profile/marshall-t-mcdonnell>`_ (:term:`INTERSECT`)
+- `Anees Al Najjar <https://www.ornl.gov/staff-profile/anees-m-al-najjar>`_ (:term:`INTERSECT`)
+- `Nageswara Rao <https://www.ornl.gov/staff-profile/nageswara-s-rao>`_ (:term:`INTERSECT`)
+- `Gregory Watson <https://www.ornl.gov/staff-profile/gregory-r-watson>`_ (Galaxy workflows)
+
+.. toctree::
+   :name: intersect:arch:examples:bessd:co2flux:architecture
+   :maxdepth: 1
+   :caption: Architecture
+
+   pat
+   sos
+   ms

examples/bessd/co2flux/ms.rst

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+.. _intersect:arch:examples:bessd:co2flux:ms:
+
+Microservices Architecture
+--------------------------
+

examples/bessd/co2flux/pat.rst

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+.. _intersect:arch:examples:bessd:co2flux:pat:
+
+Science Use Case Design Patterns
+--------------------------------
+

examples/bessd/co2flux/sos.rst

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+.. _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
+^^^^^^^^^^^^^^^^^^

examples/bessd/index.rst

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+.. _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<VOC>`
+   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<ORNL>` project team consists of:
+
+- `Melanie Mayes (Principal Investigator) <https://www.ornl.gov/staff-profile/melanie-mayes>`_
+- `David Weston (Co-Principal Investigator) <https://www.ornl.gov/staff-profile/david-j-weston>`_
+- `Kelsey Carter (Task Lead) <https://www.ornl.gov/staff-profile/kelsey-r-carter>`_
+- `Fernanda Santos (Task Lead) <https://www.ornl.gov/staff-profile/fernanda-santos>`_
+- `Mengjun Shu (Task Lead) <https://www.ornl.gov/staff-profile/mengjun-shu>`_
+- `Larry York (Task Lead) <https://www.ornl.gov/staff-profile/larry-m-york>`_
+- `Natalie Griffiths <https://www.ornl.gov/staff-profile/natalie-griffiths>`_
+- `Lianhong Gu <https://www.ornl.gov/staff-profile/lianhong-gu>`_
+- `John Field <https://www.ornl.gov/staff-profile/john-l-field>`_
+- Aubrey Fine
+- `Robin Clark <https://www.ornl.gov/staff-profile/robin-j-clark>`_
+- Anand Seethepalli
+- `Christian Salvador <https://www.ornl.gov/staff-profile/christian-mark-g-salvador>`_
+- `Brandon Sloan <https://www.ornl.gov/staff-profile/brandon-p-sloan>`_
+- `Swen Boehm <https://www.ornl.gov/staff-profile/swen-boehm>`_ (:term:`INTERSECT`)
+- `Christian Engelmann <https://www.ornl.gov/staff-profile/christian-engelmann>`_ (:term:`INTERSECT`)
+- `Marshall McDonnell <https://www.ornl.gov/staff-profile/marshall-t-mcdonnell>`_ (:term:`INTERSECT`)
+- `Anees Al Najjar <https://www.ornl.gov/staff-profile/anees-m-al-najjar>`_ (:term:`INTERSECT`)
+- `Nageswara Rao <https://www.ornl.gov/staff-profile/nageswara-s-rao>`_ (:term:`INTERSECT`)
+- `Gregory Watson <https://www.ornl.gov/staff-profile/gregory-r-watson>`_ (Galaxy workflows)
+
+.. toctree::
+   :name: intersect:arch:examples:bessd:objectives
+   :maxdepth: 1
+   :caption: Objectives
+
+   phenotyping/index
+   soilcosm/index
+   co2flux/index

examples/bessd/phenotyping/index.rst

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+.. _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)<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<VOC>` 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)<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)<SNP>` 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<ORNL>` project team consists of:
+
+- `Melanie Mayes (Principal Investigator) <https://www.ornl.gov/staff-profile/melanie-mayes>`_
+- `David Weston (Co-Principal Investigator) <https://www.ornl.gov/staff-profile/david-j-weston>`_
+- `Kelsey Carter (Task Lead) <https://www.ornl.gov/staff-profile/kelsey-r-carter>`_
+- `Mengjun Shu (Task Lead) <https://www.ornl.gov/staff-profile/mengjun-shu>`_
+- `Lianhong Gu <https://www.ornl.gov/staff-profile/lianhong-gu>`_
+- Anand Seethepalli
+- `Christian Salvador <https://www.ornl.gov/staff-profile/christian-mark-g-salvador>`_
+- `Swen Boehm <https://www.ornl.gov/staff-profile/swen-boehm>`_ (:term:`INTERSECT`)
+- `Christian Engelmann <https://www.ornl.gov/staff-profile/christian-engelmann>`_ (:term:`INTERSECT`)
+- `Marshall McDonnell <https://www.ornl.gov/staff-profile/marshall-t-mcdonnell>`_ (:term:`INTERSECT`)
+- `Anees Al Najjar <https://www.ornl.gov/staff-profile/anees-m-al-najjar>`_ (:term:`INTERSECT`)
+- `Nageswara Rao <https://www.ornl.gov/staff-profile/nageswara-s-rao>`_ (:term:`INTERSECT`)
+- `Gregory Watson <https://www.ornl.gov/staff-profile/gregory-r-watson>`_ (Galaxy workflows)
+
+.. toctree::
+   :name: intersect:arch:examples:bessd:phenotyping:architecture
+   :maxdepth: 1
+   :caption: Architecture
+
+   pat
+   sos
+   ms

examples/bessd/phenotyping/ms.rst

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+.. _intersect:arch:examples:bessd:phenotyping:ms:
+
+Microservices Architecture
+--------------------------
+

examples/bessd/phenotyping/pat.rst

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+.. _intersect:arch:examples:bessd:phenotyping:pat:
+
+Science Use Case Design Patterns
+--------------------------------
+

examples/bessd/phenotyping/sos.rst

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+.. _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
+^^^^^^^^^^^^^^^^^^

examples/bessd/soilcosm/index.rst

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+.. _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<ORNL>` project team consists of:
+
+- `Melanie Mayes (Principal Investigator) <https://www.ornl.gov/staff-profile/melanie-mayes>`_
+- `David Weston (Co-Principal Investigator) <https://www.ornl.gov/staff-profile/david-j-weston>`_
+- `Larry York (Task Lead) <https://www.ornl.gov/staff-profile/larry-m-york>`_
+- `John Field <https://www.ornl.gov/staff-profile/john-l-field>`_
+- Aubrey Fine
+- `Robin Clark <https://www.ornl.gov/staff-profile/robin-j-clark>`_
+- Anand Seethepalli
+- `Brandon Sloan <https://www.ornl.gov/staff-profile/brandon-p-sloan>`_
+- `Swen Boehm <https://www.ornl.gov/staff-profile/swen-boehm>`_ (:term:`INTERSECT`)
+- `Christian Engelmann <https://www.ornl.gov/staff-profile/christian-engelmann>`_ (:term:`INTERSECT`)
+- `Marshall McDonnell <https://www.ornl.gov/staff-profile/marshall-t-mcdonnell>`_ (:term:`INTERSECT`)
+- `Anees Al Najjar <https://www.ornl.gov/staff-profile/anees-m-al-najjar>`_ (:term:`INTERSECT`)
+- `Nageswara Rao <https://www.ornl.gov/staff-profile/nageswara-s-rao>`_ (:term:`INTERSECT`)
+- `Gregory Watson <https://www.ornl.gov/staff-profile/gregory-r-watson>`_ (Galaxy workflows)
+
+.. toctree::
+   :name: intersect:arch:examples:bessd:soilcosm:architecture
+   :maxdepth: 1
+   :caption: Architecture
+
+   pat
+   sos
+   ms

examples/bessd/soilcosm/ms.rst

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+.. _intersect:arch:examples:bessd:soilcosm:ms:
+
+Microservices Architecture
+--------------------------
+

examples/bessd/soilcosm/pat.rst

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+.. _intersect:arch:examples:bessd:soilcosm:pat:
+
+Science Use Case Design Patterns
+--------------------------------
+