WIP: Examples AutoFlows

examples/autoflows/index.rst

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+.. _intersect:arch:examples:autoflows:
+
+Autonomous Continuous Flow Reactor Synthesis
+============================================
+
+There is a critical need for efficient scale-up of atom precise
+synthesis products to quantities that enable full characterization of
+the structure-composition-property relationships and for scalable
+deployment of important material for key applications. Coupled with new
+instrumentation design, robotics, and in-operando interconnected
+analytical tools, automation, intelligent discovery of synthesis
+pathways is feasible and can potentially bridge the gap for scale-up of
+new materials. :term:`AutoFlowS`
+(:numref:`intersect:arch:examples:autoflows:autoflows`) is a system
+targeting this capability using an autonomous continuous flow chemistry
+framework that translates high-quality lead molecules and materials to
+quantities that meet scalability demands. At its core the continuous
+flow synthesis platform can design its own viable synthesis pathway to a
+particular molecule or material and then autonomously carry it out.
+Ultimately the goal is to enable enhanced automation of all aspects of
+the scientific discovery process: from hypotheses generation to the
+design of experiments to testing hypotheses to execution of physical
+experiments to the analysis and interpretation of the results.
+
+The :term:`Oak Ridge National Laboratory<ORNL>` project team consists of:
+
+- `Rigoberto Advincula (Principal Investigator) <https://www.ornl.gov/staff-profile/rigoberto-c-advincula>`_
+
+.. figure:: autoflows.png
+   :name: intersect:arch:examples:autoflows:autoflows
+   :align: center
+   :width: 800
+
+   An autonomous continuous flow reactor synthesis science use case
+
+.. toctree::
+   :name: intersect:arch:examples:autoflows:architecture
+   :maxdepth: 1
+   :caption: Architecture
+
+   pat
+   sos
+   ms

examples/autoflows/ms.rst

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+.. _intersect:arch:examples:autoflows:ms:
+
+Microservices Architecture
+--------------------------
+

examples/autoflows/pat.rst

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+.. _intersect:arch:examples:autoflows:pat:
+
+Science Use Case Design Patterns
+--------------------------------
+
+The :term:`AutoFlowS` science use case implements the Design of Experiments
+strategic pattern (:numref:`intersect:arch:examples:autoflows:pat:strategic`),
+as a continuous flow reactor performs experiments, experiment results
+are analyzed, and subsequent experiments are performed based on analysis
+results. At the strategic pattern level of abstraction, the individual
+pattern components are as follows:
+
+-  The experiment design plan describes the goal, which is the desired
+   chemical compound, and the logic necessary to craft subsequent
+   experiments towards achieving the goal.
+
+-  The experiment planner could be the SME who could be substituted by a
+   machine learning or deep learning model implemented in the SnapDragon
+   control software which would decide on the next experiment plan given
+   the experiment results from past experiments.
+
+-  The experiment plan would be the sequence of predetermined steps and
+   associated parameters necessary to run the current experiment. The
+   predetermined steps include the parameters for the programmable
+   valves to release the correct amounts of the desired reactant
+   chemicals from the vials, parameters to control the reaction in the
+   reactor, parameters for characterizing the synthesized chemical
+   compound, and safety related feedback instructions.
+
+-  The SnapDragon software is the experiment controller, communicating
+   with and controlling the pumps, reactor, and analytical tools.
+
+-  The test performed in an experiment characterizes the synthesized
+   chemical compound.
+
+-  The experiment result is a combination of the sample characterization
+   results.
+
+.. figure:: pat/strategic.png
+   :name: intersect:arch:examples:autoflows:pat:strategic
+   :align: center
+
+   Design of Experiments strategic pattern for the \gls{:term:`AutoFlowS`}
+   science use case
+
+The experiment is a complex sequence of steps involving multiple
+instruments i.e., reactant vials and tools), actuators (i.e., pumps and
+valves), sensors (i.e., analytical tools), etc. Thus, the Experiment
+itself could be considered a Multi-Experiment Workflow strategic pattern
+or a sequence of Experiment Control strategic patterns
+(:numref:`intersect:arch:examples:autoflows:pat:strategic-workflow`). Examples
+of steps that constitute the Multi-Experiment Workflow strategic pattern
+include the control of the pumps for reactants, controlling the reactor,
+and each of the individual characterization steps such as the infrared
+spectroscopy, Raman spectroscopy, non-magnetic resonance imaging,
+fluorescence imaging, quartz crystal micro-balance measurements,
+viscosity meters, etc. Many of these steps could potentially be
+performed in parallel since the chemical product can be channeled to
+different analytical tools simultaneously.
+
+.. figure:: pat/strategic-workflow.png
+   :name: intersect:arch:examples:autoflows:pat:strategic-workflow
+   :align: center
+
+   Design of Experiments strategic pattern for the :term:`AutoFlowS`
+   science use case, using the Multi-Experiment Workflow strategic
+   pattern.
+
+The :term:`AutoFlowS` science use case implements the Local Design of
+Experiments architectural pattern
+(:numref:`intersect:arch:examples:autoflows:pat:architectural`), as all
+components (planner, controller(s), synthesis station(s), and
+characterization station(s)) are local, i.e., in close physical and
+logical proximity with no significant latency (for communication or
+sample movement) to remote components. The experiment itself could be
+considered a Local Multi-Experiment Workflow architectural pattern using
+a sequence of Local Experiment Control architectural patterns
+(:numref:`intersect:arch:examples:autoflows:pat:architectural-workflow`). In
+this case, there is a significant overlap of the different components,
+as the same shared storage is being used, for example.
+
+.. figure:: pat/architectural.png
+   :name: intersect:arch:examples:autoflows:pat:architectural
+   :align: center
+
+   Local Design of Experiments architectural pattern for the
+   :term:`AutoFlowS` science use case
+
+.. figure:: pat/architectural-workflow.png
+   :name: intersect:arch:examples:autoflows:pat:architectural-workflow
+   :align: center
+
+   Local Design of Experiments architectural pattern for the
+   :term:`AutoFlowS` science use case, using the Local Multi-Experiment
+   Workflow architectural pattern