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Science Ambassador Blog: Promoting Aquavit Science Gateway and Preparing for Implementation of a Water Quality Portal Interface

One of five 2019 SGCI Science Ambassadors, Jack Smith, a research scientist at Marshall University in Huntington, WV, and Cyberinfrastructure Coordinator for West Virginia Science and Research, attended the 11th National Monitoring Conference in Denver, CO, March 25-29, 2019, to promote the Aquavit science gateway. He also spent time with the EPA Water Quality Portal team as he prepares to implement a Water Quality Portal interface into Aquavit in collaboration with the GeoEDF project, which was recently awarded a $4.5 million NSF grant. Below he reports on his activities as a 2019 Science Ambassador. 

By Jack Smith

Introduction

This SGCI Science Ambassadors program allows an awardee, especially a gateway developer, like myself, to take a deeper dive into a science discipline supported by the gateway that may be different than their own to help build a better bridge between the gateway platform and the science it supports. It also provides an opportunity to extend the awardee’s network of resources, especially the human kind, that can be drawn upon in further advancing their gateway, promoting its use, and broadening its impact – to become a better ambassador for the science supported by the gateway as well as the gateway itself.

Gateway Project: Aquavit

Aquavit is a HUBzero-based collaboration portal hosted at Marshall University. It was initially developed to support an NSF-funded (EPSCoR RII Track 1) project called the Appalachian Freshwater Initiative (AFI) that focuses on water quality research across 3 West Virginia institutions (WV University, Marshall University, and WV State University) involving new sensor development, monitoring of streams and lakes, and modeling the fate and transport of contaminants. It also now supports the SENSE project, another EPSCoR (Track 2) project also focused on water quality, but with an emphasis on harmful algae bloom (HABs). The SENSE project is spread across 2 states (WV and KY) and 3 institutions (Marshall University, University of Kentucky, and Murray State University).

Both of these projects collect and process a lot of water quality data, using both discrete sampling and continuous monitoring. Both seek a way to share their data with the larger research community while also using data from external sources in their modeling. The approach taken for this was to use the EPA/USGS Water Quality Portal (WQP) for downloading external data as needed, develop a local repository for staging and vetting project-collected data along with downloaded data (for use in modeling), and then use the EPA Water Quality eXchange (WQX) to eventually upload data to the WQP for broader use. 

SGCI and Purdue as Partners

To help with this development, we applied for and received Extended Developer Support (EDS) support from the SGCI. This EDS project involved people from the HUBzero and MyGeoHub teams at Purdue, with whom I had worked with previously on an XSEDE Campus Champions Fellows project and met again at the first SGCI Science Gateways Bootcamp (now called Gateway Focus Week). In addition, I was a Co-PI on an NSF CSSI grant application along with the GABBs and MyGeoHub teams at Purdue, which was recently awarded $4.5 million. This grant includes our effort at Marshall to develop modular data connectors and processors for the proposed GeoEDF framework (a.k.a. GABBs 2.0) to further facilitate access to WQP and WQX from within the HUBzero/GABBs environment beyond Aquavit. So, the SGCI and Purdue have been and continue to be a consistent and critical partner in our efforts.

New Science Discipline: Water Quality Monitoring

It turns out that water quality monitoring is a new field for our small team at Marshall, especially for me. Our backgrounds and experiences are in computational science (modeling and simulation across a variety of science disciplines), high-performance computing (HPC), advanced scientific visualization, and the development of virtual collaboration environments. So our primary role on the AFI and SENSE projects was to provide assistance in the development and sharing of modeling tools for surface water systems, especially the transportation and fate of contaminants in freshwater streams in Appalachia. The HUBzero platform helps facilitate that. Although hinted at in the project’s Data Management Plan, the addition of a WQP/WQX data portal to HUBzero to support the collection and sharing of water quality data was mostly an unplanned (and unbudgeted) effort. This is why the SGCI, and now the GeoEDF project, have been such godsends to this effort.

The new Science Ambassadors program offered yet one more opportunity for the SGCI to help advance our effort. One of the goals of this program is to help bridge the gap between gateway development and the science discipline it supports. This program allowed me to take a deeper dive into the unknown world of water quality monitoring – to learn more about their tools, methods, protocols, standards, best practices, common use cases, etc. More importantly, it allowed me to become a freshman member of the water quality monitoring community and begin to build a network of colleagues that wouldn’t normally be at my disposal. This was especially important in getting to know key players within the relevant government agencies, like the EPA and USGS.

A West Virginia University field trip participant uses an electrofishing backpack for a fish survey. Fish surveys
take place during environmental DNA samplings to help determine the sensitivity of eDNA genetic assays.

Travel: NWQMC Monitoring Conference

For my travel assistance under the Science Ambassadors program, I chose to attend the annual NWQMC Monitoring Conference held in Denver in May of 2019. This conference also offered several workshops and tutorials in addition to the usual mix of plenary sessions, keynote speakers, panel discussions, and several parallel tracks of technical presentations, demos and breakout sessions. There was also a concurrent expo with a wide array of vendors and agencies represented, including booths for the EPA and USGS offering demos of WQP, the WQX Web portal, and several WQP-based tools.

I attended a full-day hands-on pre-conference workshop on WQP and WQX, including the new REST API, which was instructed by key representatives (and developers) from the EPA and USGS. I participated in a breakout session dedicated to WQP and WQX and their use outside the EPA and USGS. I met with several of the EPA and USGS representatives throughout the conference and at their booths to discuss the AFI and SENSE projects, our Aquavit portal, the new GeoEDF project and its proposed framework, and our effort to develop a WQX/WQP data portal based on this framework with an accompanying WQX-compatible database for local staging and analysis of data.

I had the opportunity to hear more about the Interoperable Watershed Network (IWN) effort by the EPA, following their recent pilot project, to address continuously monitored (real-time sensor) data. The GeoEDF proposal includes interfacing with the IWN as it matures into an EPA-supported component of WQX and WQP. I also learned about the “Internet of Water” (IoW) effort that appears to be a driving force for cooperation among both government and non-government agencies.

I was introduced to several other tools and development resources, many of which interface with the WQP API, such as: “How’s My WaterWay?” 2.0 (EPA); WQP Discovery Tool, an R Shiny app (EPA); new NLDI (Network-Linked Data Index) web services from USGS; EGRET R package (USGS); USGS-R on GitHub.

Learnings and Follow-up

Some key learnings from the NWQMC conference were:

  • The WQP API is being broadly used by other tools and services, like the NLDI web services from the USGS and those mentioned above.
  • The WQX Web portal API is reducing major hurdles in uploading data and eliminating the need for exchange nodes and commercial software.
  • The IWN effort by the EPA appears to be evolving into real tools and protocols for handling continuously monitored data.
  • The EPA and USGS WQP/WQX people are very willing to collaborate.
  • The NWQMC community is a great source for learning best practices in water quality monitoring.
  • The independent “Internet of Water” effort is quickly becoming a driving force for cooperation among a disparate array of entities involved in water quality.

Following the NWQMC conference, I have taken the following actions to stay connected and advance our effort:

  • Regularly attend monthly calls of EPA WQX group.
  • Regularly attend seminars by the NWQMC.
  • Invited representatives from EPA (Dwane Young) and USGS (Jim Kreft) to the first GeoEDF Stakeholder meeting this fall at Purdue.
  • Started building Jupyter Notebooks built on libraries (R and Python) and web services learned about at this conference and sharing them on Aquavit, which serves as both research and educational tools.

Conclusion

The Science Ambassadors program has proven to be yet one more tool in SGCI’s arsenal for helping gateway developers be successful in bringing the tools of science, the data it needs, and the data it produces, closer to the community they serve. This computational chemist and gateway developer is not yet an expert at water quality monitoring, but he now feels more comfortable, somewhat more competent, and much better resourced in this new community he serves - thanks to this program.


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