Updates to Scenario 3A

Theme_3_Species_Protection_and_Marine_Habitat_Conservation/README.md

@@ -0,0 +1,3 @@
+# IOOS System Test - Theme 3 - Species Protection and Marine Habitat Conservation
+
+The mission of the NOAA National Marine Fisheries Service is to safeguard the viability of key marine species within the US economic zone. That mission includes conserving sensitive marine habitat and restoring marine habitat that has been degraded by factors such as destructive fishing techniques and water pollution. It also includes monitoring and protecting threatened marine species such as sea turtles and whales. The National Marine Fisheries service includes IOOS data in their assessments of habitat and threatened marine species. Part of the value of integrating species and habitat data into the IOOS system is enabling the resolution of conflicts between human uses of our oceans and the protection of fragile marine habitats and the natural resources that they support. Activities such as mineral extraction and energy siting require the use of a suite of marine habitat and species data in order to ensure that operations comply with marine conservation laws designed to require managers and policy makers to consider the ecological impacts of human activities.

Theme_3_Species_Protection_and_Marine_Habitat_Conservation/Scenario_3A_Assessing_Seabird_Vulnerability_in_the_Bering_Sea/README.md

@@ -2,36 +2,10 @@
 
 ## Scenario 3A - Assessing Seabird Vulnerability in the Bering Sea
 
-### Requirements
+The climate is changing in the Bering Sea and Aleutian Islands region. Residents, stakeholders, scientists, and natural resource managers are all concerned about the impacts of future climate change on important species, systems and habitats. But projections of future climate are uncertain, and different approaches have different strengths and limitations. With variation in projections, and with different impacts depending on species and systems of concern, how can stakeholders and managers realistically anticipate and plan for the impacts of climate change?
 
-1. Using `pip`
-    ```bash
-    pip install -r pip-requirements.txt
-    ```
+Over the past months, an interdisciplinary team of scientists has begun an effort to assess the vulnerability of key resources and ecosystem services including marine mammals, fish and commercial fisheries, terrestrial vegetation, human community sustainability and seabirds. Vulnerability assessment is a well-developed, systematic way to “synthesize and integrate scientific information, quantitative analyses, and expert-derived information in order to determine the degree to which specific resources, ecosystems, or other features of interest are susceptible to the effects of climate change” (USFS 2011). The Aleutian and Bering Climate Vulnerability Assessment (ABCVA) proposed to integrate model projections from two recent climate downscaling approaches; one from the Bering Sea Project, and one from the Spatial Tools for Arctic Mapping and Planning (STAMP). Both of these model outputs were ingested into the AOOS data system and results were shared with a team of 30 leading researchers and managers at the recent Alaska Marine Science Symposium in January. Since then, volunteer teams of expert working groups have begun to develop preliminary vulnerability assessment. Teams have identified specific information gaps and questions of greatest relevance to resource managers and other stakeholders in the region relative to projected changes in climate.
 
-2. Using `conda`
-    ```bash
-    conda install --file pip-requirements.txt
-    ```
-    If you are using environments within conda, be sure to specify it
-    ```bash
-    conda install -n yourenvname --file pip-requirements.txt
-    ```
+One team, focused on seabirds, has identified the need for an analytical process that would allow the the exploration of multiple climate projection data sets. This analytical process, described below, provides an ideal opportunity to evaluate the DMAC system integration capabilities within an existing project with Federal and non-Federal partners and Regional Associations. This project is a collaboration between the Aleutian and Bering Sea Islands Landscape Conservation Cooperative (ABSI LCC), the Alaska Climate Science Center and the Alaska Ocean Observing System (AOOS). It represents approximately a $150,000 investment, contributed in-kind staff time from the three organizations leading the effort, as well as substantial investments of in-kind investments from the 30 members that make up our 5 focal teams. The seabird team, which includes collaborators from Audubon Alaska and the U.S. Fish and Wildlife Service, has identified the need for a change detection analysis using 13 projected climate, and climate-derived, raster data layers within the boundaries of Audubon’s recently established Important Bird Areas (IBAs). Important Bird Areas are zones of high biological productivity and conservation priority for marine bird species extend throughout the Pacific Flyway up the coast of North America, from Mexico to the Gulf of Alaska, through the Bering Sea and into the Arctic Ocean (Smith et al. 2014). Almost 80% of the breeding seabirds within the U.S. are dependent on the Bering Sea and Aleutian Islands making IBAs within our study region especially important. This process will enable access to complex model outputs, and will create new pathways to discover and explore a broad suite of projected model variables that impact seabirds. Pairing this change detection analysis with expert knowledge on seabird ecology will strengthen the ability of managers to proactively plan for seabird monitoring and conservation.
 
-### Helper methods
-
-Some helper functions have been abstracted into the file called `utilities.py`
-so the IPython notebook can maintain a certain degree of readability.
-
-
-**Note:** If your HDF5 and/or NETCDF4 libraries are in uncommon locations, you
-may need to specify the paths when installing netCDF4.
-```bash
-HDF5_DIR=/your/path/to/hdf5 NETCDF4_DIR=/your/path/to/netcdf4 PIP_OR_CONDA_INSTALL_COMMAND
-```
-
-**Note:** If your `gdal-config` binary is in an uncommon location, you may need
-to specify the path when installing.
-```bash
-PATH=/your/path/to/gdal/bin:$PATH PIP_OR_CONDA_INSTALL_COMMAND
-```
+Opportunities to replicate and adapt the workflow processes established by the IOOS System Integration Test could include any other regions where user-defined polygons and IOOS held model projects can be used to define statistical reports for IOOS resources using open-source computing resources. Other examples include using a very similar process to explore the projection space with IBAs in California using the same types of models, or marine mammal distribution areas and how they relate to projections of food sources (e.g., foraging areas associated with rookeries for northern fur seals and Steller sea lions have similarly been identified by NOAA managers). The proposed IPython Notebooks could also be used to explore projected changes in the marine ecosystem and how they relate to Essential Fish Habitat maps.

Theme_3_Species_Protection_and_Marine_Habitat_Conservation/Scenario_3A_Assessing_Seabird_Vulnerability_in_the_Bering_Sea/Scenario_3A_Important_Bird_Area_Polygon_Analysis/README.md

@@ -0,0 +1,44 @@
+# IOOS System Test - Theme 3 - Species Protection and Marine Habitat Conservation
+
+## Scenario 3A - Assessing Seabird Vulnerability in the Bering Sea
+
+### Important Bird Area Polygon Analysis
+
+Given a WFS server with an Important Bird Area polygon, can we discover and query
+oceanographic and meteorological information inside of the polygon and run
+an analysis of the data with some amazing graphs and stories to tell?
+
+
+#### Requirements
+
+1. Using `pip`
+    ```bash
+    pip install -r pip-requirements.txt
+    ```
+
+2. Using `conda`
+    ```bash
+    conda install --file pip-requirements.txt
+    ```
+    If you are using environments within conda, be sure to specify it
+    ```bash
+    conda install -n yourenvname --file pip-requirements.txt
+    ```
+
+#### Helper methods
+
+Some helper functions have been abstracted into the file called `utilities.py`
+so the IPython notebook can maintain a certain degree of readability.
+
+
+**Note:** If your HDF5 and/or NETCDF4 libraries are in uncommon locations, you
+may need to specify the paths when installing netCDF4.
+```bash
+HDF5_DIR=/your/path/to/hdf5 NETCDF4_DIR=/your/path/to/netcdf4 PIP_OR_CONDA_INSTALL_COMMAND
+```
+
+**Note:** If your `gdal-config` binary is in an uncommon location, you may need
+to specify the path when installing.
+```bash
+PATH=/your/path/to/gdal/bin:$PATH PIP_OR_CONDA_INSTALL_COMMAND
+```