CONOPS – Advanced Application for Mosquito-Borne Disease Early Warning
=====================================================================

CONOPS is a DestinE Advanced Application and Service (AAS) that provides early-warning indicators for
mosquito abundance and mosquito-borne disease risk, using Earth Observation, climate reanalysis and
machine learning models.

This documentation is primarily a **user manual**: it explains how to run analyses, interpret results,
and download outputs. Technical integration and operational topics are available in a separate section.

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What you can do with CONOPS
---------------------------

With CONOPS you can:

* Select an Area of Interest (e.g., NUTS region; and/or custom AOI if available in the UI)
* Choose a time period (monthly or custom range within the mosquito season)
* Run the available models:
  * **MAMOTH** – mosquito abundance indicators
  * **DVI** – mosquito-borne disease risk indicators
* Visualize results on the map and explore layers/legends
* Download outputs for further use in GIS or analysis tools

Typical outputs include gridded maps (1x1 or 2×2 km) and summary indicators for the selected area and period.

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Quickstart
----------

1. Open **CONOPS** from the DestinE Services catalogue and sign in.
2. On the main page, select your **Area of Interest**.
3. Select the **time period** (month or custom range).
4. Choose the **model** (MAMOTH or DVI) and any available options.
5. Click **Run / Submit** to create an order.
6. Monitor the order status until it is **Completed**.
7. Open **Results** to view the map outputs and charts.
8. Use **Download / Export** to retrieve outputs.

.. figure:: _static/conops-guide-1.png
   :alt: CONOPS home page
   :width: 90%

   CONOPS home page.

.. figure:: _static/conops-guide-2.png
   :alt: Select area and time period
   :width: 90%

   Select an area and time period.

.. figure:: _static/conops-guide-3.png
   :alt: Choose model and submit an order
   :width: 90%

   Choose a model and submit an order.

.. figure:: _static/conops-guide-4.png
   :alt: View results and download outputs
   :width: 90%

   View results and download outputs.

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How to use the web application
------------------------------

Select an Area of Interest
^^^^^^^^^^^^^^^^^^^^^^^^^^

* Use the available selector (e.g., NUTS regions) to define the area for analysis.
* If the UI supports custom AOIs, draw or upload your geometry following the UI instructions.

Choose a time period
^^^^^^^^^^^^^^^^^^^^

* Choose a month (recommended for standard workflows), or
* Define a custom time range when supported.

Run a model
^^^^^^^^^^^

* **MAMOTH** provides mosquito abundance indicators.
* **DVI** provides mosquito-borne disease risk indicators.

After selecting inputs, click **Run / Submit** to create an order.

Track orders
^^^^^^^^^^^^

Orders typically progress through states such as **Queued**, **Running**, and **Completed** (or **Failed**).
If an order fails, consult :doc:`faq` for common causes and recommended actions.

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Understanding results
---------------------

Results are provided at **1x1/2×2 km** spatial resolution for the selected area and period.

To interpret a result:

* Use the map **legend** to understand the indicator scale
* Review any available **explanation/quality** layers in the UI
* Compare different months or areas using consistent settings

If your workflow requires scientific interpretation (thresholds, confidence, limitations),
see :doc:`results` and :doc:`glossary`.

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Data sources
------------

CONOPS currently ingests data exclusively from the **DestinE Data Lake (DEDL)**:

* Sentinel-2
* Landsat 7 / 8 / 9
* ERA5 reanalysis products

Digital Twin datasets are not integrated at this stage.

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Documentation
-------------

.. toctree::
   :maxdepth: 2
   :caption: User manual

   user_guide
   results
   export
   faq
   glossary

.. toctree::
   :maxdepth: 2
   :caption: Operations & integration (service admins)

   architecture
   data_pipeline
   iam
   monitoring
   verification
   release_process
   operations

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Contact and support
-------------------

For service access issues, usage questions, or incident reporting, follow the DestinE support process
and contact the designated Service Desk / Client Administrators defined for your organization.