Confluence Retirement

In an effort to consolidate USGS hosted Wikis, the myUSGS Confluence service is targeted for retirement on January 28, 2022. The official USGS Wiki and collaboration space is now SharePoint. Please migrate existing spaces and content to the SharePoint platform and remove it from Confluence at your earliest convenience. If you need any additional information or have any concerns about this change, please contact Thank you for your prompt attention to this matter.

Blog from April, 2020

The CDI Monthly Meeting in March focused on three 2019 CDI-funded projects: a national-scale map of sinkhole subsidence susceptibility; a project that will allow collection of near real-time eDNA surveillance of invasive species or pathogens; and an overview of SEINed - a tool for Screening and Evaluating Invasive and Non-native Data.

Subsidence Susceptibility Map for the Conterminous U.S. Jeanne Jones, USGS 

Jeanne Jones at the Western Geographic Science Center shared progress on the creation of a Subsidence susceptibility Map for the conterminous U.S. that will identify hotspots for sinkholes and areas susceptible to developing sinkholes. Sinkholes can pose major issues by focusing contaminated and/or polluted surface water into groundwater and creating instability in the foundations of buildings and roads. As such, a consistent map for the identification of sinkhole hotspots is vital in order to anticipate and manage risks. 

The goals of this project include creating the first nationwide digital dataset of sinkhole hotspots, incorporating this dataset into the SHIRA (CDI) Risk map for use by DOI emergency agencies, and providing access to the dataset for external use by emergency managers, land use planners, and public works agencies. To meet these goals, the project team used The National Map, the National Hydrography Dataset (NHD), the Yeti supercomputer, and other data.

Jeanne shared challenges and solutions involved with several steps of the process. For instance, data had to be screened visually and manually in order to identify gaps in spatial coverage, and to screen out wetlands, open water, urban areas, and other non-karst landscape features. 

Jeanne also posed a question to the CDI: How does flow accumulation processing with DEMs compare across Arcpy, TauDem, RichDem in terms of speed, consistency of results, max size of raster for high performance computing? You can respond to her at

High-Resolution, Interagency Biosurveillance of Threatened Surface Waters in the United States Sara Eldridge and Elliott Barnhart, USGS

The project presented by Elliott Barnhart tackles the problem of rapid detection and prediction of biological hazards. USGS collects a massive amount of near real time data with stream gauges, but the analysis of this data can take much longer. To solve this problem, the project team created a cloud-hosted digital database that combines all the collected data, and can easily incorporate eDNA and other data streams into models that indicate the presence or absence of organisms. 

Challenges faced during the course of this project included creating effective quality control filters for funneling in data from multiple sources, and linking the benefits and capabilities of several different systems (like the MBARI Environmental Sample Processor, Department of Energy Systems Biology Knowledgebase, and more). 

National Public Screening Tool for Invasive and Non-native Aquatic Species Data Wesley Daniel, USGS

The Nonindigenous Aquatic Species (NAS) is the central repository for spatially referenced accounts of introduced aquatic species. NAS tracks over 1,290 aquatic species and stores over 600,000 observations from across the U.S. and spanning from the 1800's to the present. The SEINeD tool was developed to solve the problem: How does the NAS database get non-native occurrence data from groups not focused on invasive species? The SEINeD tool allows stakeholders to upload a biological dataset (fish, inverts, plants, etc.) collected anywhere in the conterminous US, Alaska, Hawaii, or US Territory that can then be screened for invasive or non-native aquatic species occurrences. 

The SEINed tool helps to filter out inaccuracies due to incorrect taxa and spatial identifications before checking the indigenous status of the species against the sighting location. The tool flags non-native species that are exotic (from other countries/continents), AND non-native species from within the U.S. (for example, rainbow trout native to the west coast on the east coast) The data is then enhanced with the addition of spatial information like hydrological unit codes (HUCs) and returned to the user. The user can then submit the enhanced/corrected CSV to the NAS program.  

The SEINed tool launches May 4thWatch the NAS website for updates. 

See the recording and slides at the March Monthly Meeting page.

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You can get to all of these groups and sign up for mailing lists on the CDI Collaboration Area wiki page.

3/2/20 Metadata Reviewers - sharing metadata creation practices for data and software

The Metadata Reviewers group discussed (1) At your office, how much do you create a single metadata record for? Individual data files, items in a database, collections of data, whole data releases, or what? (2) What about metadata for software or code? How can we prepare to think together about that, maybe on our next phone call? Should we invite a speaker? Bring in reference materials? Bring in good examples?

Link highlight: Data Management Training resources on the USGS Data Management Website

See other notes, links, and take-aways on the Metadata Reviewers Meetings Page! Contact: Lightsom, Frances L.

Training relevant to metadata creation is on the USGS Data Management Website!

3/3/20 Fire Science Update

At the March Fire Science Community of Practice meeting, Paul Steblein gave a fire science update. An FY2021 Request for Proposals will be issued this summer from the Joint Fire Science Program. Anna Stull presented on fire deployment requirements. Geoff Plumlee presented on the Department of Defense (DoD) Joint Artificial Intelligence Center (JAIC), Humanitarian Assistance and Disaster Relief (HADR) National Mission Initiative (NMI). During and post fire what can USGS be doing to link topography, mineralogy, debris flow, revegetation, invasive species? Rachel Loehman presented on the status and next steps of the USGS Fire Science Strategic Plan, and she is a new co-lead with Paul for the Fire Science CoP!

Past activity can be viewed at the Fire Science wiki page. Contact: Steblein, Paul Francis 

Recent wildland fire activity is shared at the Fire Science Community of Practice Meetings. 

3/9/20 Data Management - How do we convince them?

The Data Management Working Group again welcomed Science Gateways Community Institute trainers Claire Stirm and Juliana Casavan to host a working session on Communicating Data Value Propositions to Scientists. I found the concepts to be useful for communicating anything in general when trying to get "buy-in." Although some of us may be uncomfortable with the term "marketing," I think we may relate to the lessons of verbiage, graphics, actions, and strategies for trying to get buy-in for whatever we are working on.

Slides and recording are posted at the wiki meeting page. Contacts: Langseth, Madison Lee and Hutchison, Vivian B.

Slide from the "Communicating Data Value Propositions to Scientists" presentation.

3/12/20 Semantic Web - biodiversity in the world's oceans

Summary provided by Lightsom, Frances L.

Topic:  A practical example of semantic technology in action: assessing the status of biodiversity in the world’s oceans

Sky Bristol (USGS Core Science Systems, presented a big use case, in which semantic standards are needed to enable integration of multiple large datasets of ocean biological and ecological observations to understand effects of human activities on ocean ecosystems, as well as the sustainability of human uses of ocean resources. Several groups are working on ontologies that provide standard terms for the biota, ecosystem components, and relationships. A next step will be normalizing all the data with ontologies. This is an opportunity to assist with real world semantic web work.

See more at the Semantic Web meetings page.

A slide from Sky Bristol's presentation on a practical example of semantic technology - biodiversity in the world's oceans.

3/12/20 Tech Stack - provision of rapid response during Australian bushfires

Following the ESIP Theme "Putting Data to Work," the Tech Stack group had a presentation on the Discrete Global Grid System's use during the Australian bushfires.

From the abstract: The devastation caused by the Australian Bushfires highlighted the need for a new approach for rapid data integration. The total burnt area during Autumn-Summer 2019-2020 is 72,000 square miles, which is an equivalent to a half of Montana or North Dakota and Delaware areas combined. Rapid response in provision of information on areas affected by the bushfires was required to support evaluation of the impact, and also planning the recovery process and support for families, businesses and the environment. This presentation will discuss application of the Discrete Global Grid System (DGGS) in bringing together diverse complex information from multiple sources to support the response process. 

Slides and recording on the joint CDI Tech Stack and ESIP IT&I webinars on the ESIP page. Contact: Blodgett, David L.

Slide from the DGGS and Australian bushfires presentation.

3/16/20 Ignite Open Innovation Forum - volcanic hazards and problem-based learning

Jefferson Chang presented on Using Volcanic Hazards in Hawai‘i as a STEM Platform in Problem-Based Learning.

From the abstract: We use emerging technology to empower youth in a problem-based learning approach during a summer-long course. With guidance from HVO scientists, students essentially adopt the hazards mission of the USGS. Students not only aid in the volcano monitoring efforts on Hawai‘i Island, but also (1) take ownership of their own learning, (2) increase their capacity in STEM, and (3) engage the local community and address its needs.

See more at the Open Innovation wiki site. Contact: Liu, Sophia

Slide from Jefferson Chang's presentation at the Ignite Open Innovation Forum.

3/17 - 3/18/20 ICEMM - Interagency Collaborative for Environmental Modeling and Monitoring public meeting - Integrated Modeling, Monitoring, and Working with Nature.

The ICEMM group held its 2020 Public Meeting (March 17-18, 2020) at USGS Headquarters, Reston, VA.  The theme was Integrated Modeling, Monitoring, and Working with Nature.

Selected presentation titles: Engineering with nature for sustainable systems; Building smarter water systems through improved sensors, autonomy, and data processing; Black swans, disappearing lakes, and the societal value of integrated modeling and monitoring; Integrated water prediction at the USGS; Next generation integrated modeling of water availability in the Delaware River Basin and beyond.

Links: Agenda.  Abstracts and Biographical Information. Description of the meeting.  

Please contact Unknown User (  by email ( for further information or questions.

Slide from Branko Kerkez's presentation on Building smarter water systems.

3/18/20 Usability Resource Review Posting - using web analytics to inform how our web pages and tools are being used

From Sophie Hou, Hou, Chung Yi (Contractor) :

For March, I have prepared a resource review to address questions relating to the “How can we use Google Analytics DataStudio to inform how our online tools are used?” topic posted to the forum.

Using analytics to inform how our web pages/tools are being used

Please note that although Google Analytics is referenced in the original question and in my resource review, there are other options. If you have used tools other than Google Analytics, please could you share the information/experience through the usability listserv?

Behavior flow snapshot from the resource: How to use the behavior flow report to improve your webpage user experience.

3/19/20 Risk Community of Practice - situation assessment, stakeholder alignment, prototyping, and strategic planning

From the Risk CoP wiki: This was part 2 of a series of training webinars provided by Impact360 Alliance on human-centered design thinking and inclusive problem solving. During this webinar, participants took a deeper dive into six of the tools from Impact360's Toolkit360. Toolkit360 includes six tools for collaboratively understanding wicked problems and six tools for collaboratively generating strategies to solve wicked problems. The twelve tools bridge the "problem space" and "solution space" using situation assessment, stakeholder alignment, prototyping, and strategic planning.

Access the slides and recording, and handouts at the Risk Meetings page (must log in as a CDI member, join here if you're not a member yet). Contact: Ludwig, Kristin A.

I appreciated the clear steps for the different tools in the toolkit, for example for [Re]Assess.

3/26/20 Software Development - using the cloud to support geophysical research

Kirstie Haynie, a Mendenhall post-doc at the USGS, is exploring how to use the cloud to support geophysical research. She presented from a geophysicist's point of view, running the Slab2 model in the cloud. With the goal of operationalization of Slab2, she demonstrated the process of using CloudFormation templates for reproducibility, automation, and long term success.

Get to more resources on the Software Dev Cluster wiki page. Contacts: Ladino, Cassandra C.Guy, Michelle , Newson, Jeremy K.

Subduction zones via Slab2 at the software dev cluster meeting!

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