Confluence Retirement

Due to the feedback from stakeholders and our commitment to not adversely impact USGS science activities that Confluence supports, we are extending the migration deadline to January 2023.

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is targeted for retirement. 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 myusgs@usgs.gov. Thank you for your prompt attention to this matter.

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  1. Based on recent USGS guidance, will this call be moved off of Zoom to Teams?
    1. Leslie: We are testing external participation now and will keep the CDI informed of tech choice. Anyone interested in testing or discussing further, get in touch with me!
  2. Would you be able to see if you have any "surprising" new users as a result of the tool, or do you have ideas of how to learn if you do?
    1. The package is not officially released on GitHub but we are working on it, and there will be a publication in Journal of Open Source Software. Hope we see people fork code, can incorporate user modifications back into the main branch. Hoping the user community picks this up and makes it into a bigger and better toolbox.
  3. What was your process for identifying your main users and their needs?
    1. Our center is part of a USGS network meant to work with natural resource management partners to help understand climate adaptation science. We have worked quite extensively with Fish and Wildlife Service and National Park Service over 7 years on supporting their science needs. We saw inefficiencies in the workflow, and commonalities existed in the data requested, but we were starting from the ground up whenever we had to provide it. Anyone doing research across continental US can use it, so hoping to expand past initial stakeholders.
  4. Is the climate reanalysis data included so that historical climate (and weather) can be downloaded too?
    1. Yes, it can do historical and future comparisons.
  5. Could you say more about the Journal of Open Source Software?
    1. Open review process; way to release new tools that are allowing people access to new data. Write-ups for publication are pretty short; description of the package/software, what problem it solves, and how you are contributing (not doing something that is already done). Goes through peer review process and is released as a publication. Nice way to get the tool out to a broader community.
  6. Is it possible to include a vignette that uses the software in a JOSS publication?
    1. Will find that out and get back to you.
  7. Is "edge computing" the same as "data proximate analysis"? Can you explain it a bit more?
    1. No (don't know what data proximate analysis is). Edge computing is putting some sort of internet-connected device (like RaspberryPIs) at the edge, in the environment its meant to be in. Camera on the bank of a river, phone in your pocket, etc.
    Can a user trigger the camera remotely? Or, based on water surface elevation?
    1. Yes. You can trigger the RaspberryPI to record video based on an external trigger. If it's an internet-connected PI, you can hrhouse : I am assuming the working definition of "data proximate analysis" just means you run the analysis of the data "near" where the data sits. For instance, running a cloud-based application against data that resides on-premise would not be data proximate analysis. Edge computing, which means you are running jobs "next: to devices in-situ where the data is collected would be "data proximate analysis". In other words, edge computing is a subset of data proximate analysis.
  8. Can a user trigger the camera remotely? Or, based on water surface elevation?
    1. Yes. You can trigger the RaspberryPI to record video based on an external trigger. If it's an internet-connected PI, you can query another streamgage or other sensor and trigger that way. In the process of testing some other methods.
  9. How do you handle security with IoT? Are these RaspberryPIs protected since they have AWS credentials to upload the data? Is there a DMZ for video uploads?
    1. We are developing a stig for RaspberryPIs. We enforce how people set up modems in the field so it is unreachable from the outside world.
  10. Are you using raspberri Pi camera?
    1. Yes. We use many different cameras. Rely on security web cameras that are NDAA compliant cameras.
  11. Can you elaborate a bit on Infrastructure as Code practices you're using for this IoT project? You mentioned that you had to create infrastructure first
    Have you looked at how your community standard will translate to the biological data standard: Darwin Core?
    1. Foundry is the infrastructure. Code is Python-based.
  12. How many IoT RPis cameras are there. Do they provide constant video feed?
    1. Two cameras enabled IoT. 20-40 connected cameras not on IoT.
  13. Is that RPi stig available anywhere?
  14. What happens to the video stream after processing? Is it archived somewhere?
    1. You can do whatever you want with the video stream artifacts. That is up to the owner of the system.
  15. Can you comment about any "disagreements" that came up on the submission form when you got input from your community?
    1. Earliest iteration was just a CSV file, and more work would be done to vet data. Idea for pre-submission survey came up as input from the community. Lots of conversations about controls, that controls were in place, making sure we had questions that vetted the assay that was being run, making sure people were taking multiple samples from the field. Wanted to be as inclusive as possible, while maintaining a high level of quality. 
  16. Is the eDNA data being used to validate/reinforce other species detection/occurrence data in NAS?
    1. Not specifically, but can work to the ability to do that. NAS does a lot of work to vet photos/data that come in.
  17. can you talk a bit more about spatial controls? links to NHD?
    1. This data layer is not going to be linked to anything, but this is one of the types of areas that might help to inform broader understanding of species distribution. We are interested in ways to pair eDNA with covariates.
    1. Yes, they are similar. There's going to be a lot of overlap, and would like to make it overlap as much as possible. hrhouse : The Infrastructure as code environment just means that the environment is implemented typically via Cloud Formation scripts which can be easily be replicated as needed. This is a key principle in how the CHS environment is architected and presented. That is the only way we can support the environment at scale, and is really a best practice. The sensor processing system, like all other systems in CHS, are required to adhere to this basic design principle. So the good news is we can support such systems at scale, and the customer can also scale their own work as well. The bad news is as Frank mentioned, it does take a new level of skill set to understand what needs to be done to work within that framework. The CHS program provides a base environment, but the customers also have an obligation to build out systems without those boundaries in this manner. We recognize how this limits adoption, and are working to bring on some support engineers who can work with customers to help them.
  18. How many IoT RPis cameras are there. Do they provide constant video feed?
    1. Two cameras enabled IoT. 20-40 connected cameras not on IoT.
  19. Is that RPi stig available anywhere?
  20. What happens to the video stream after processing? Is it archived somewhere?
    1. You can do whatever you want with the video stream artifacts. That is up to the owner of the system.
  21. Can you comment about any "disagreements" that came up on the submission form when you got input from your community?
    1. Earliest iteration was just a CSV file, and more work would be done to vet data. Idea for pre-submission survey came up as input from the community. Lots of conversations about controls, that controls were in place, making sure we had questions that vetted the assay that was being run, making sure people were taking multiple samples from the field. Wanted to be as inclusive as possible, while maintaining a high level of quality. 
  22. Is the eDNA data being used to validate/reinforce other species detection/occurrence data in NAS?
    1. Not specifically, but can work to the ability to do that. NAS does a lot of work to vet photos/data that come in.
  23. can you talk a bit more about spatial controls? links to NHD?
    1. This data layer is not going to be linked to anything, but this is one of the types of areas that might help to inform broader understanding of species distribution. We are interested in ways to pair eDNA with covariates.
  24. Have you looked at how your community standard will translate to the biological data standard: Darwin Core?
    1. Yes, they are similar. There's going to be a lot of overlap, and would like to make it overlap as much as possible. 


Other comments from the chat

From Sophia Liu : I think we need a “Lending Lab of Low-Cost Instruments and Sensors” as an off shoot of what the USGS HIF provides but bringing together these low-cost sometimes disruptive innovations leveraging IOT and other sensors that we can maybe push out to the public for crowdsourcing or citizen science projects.

From Abby Benson : Jason you might consider looking at the Hydrolink Tool do link the eDNA occurrences to the NHD.

From Jake Weltzin : check out the hydro-link tool for snapping a sample location to NHD(+) network

Page properties
hiddentrue


Date
2020-04-08
Presentation Title(s)
Open-source and open-workflow Climate Scenarios Toolbox for adaptation planning
Develop Cloud Computing Capability at Streamgages using Amazon Web Services GreenGrass IoT Framework for Camera Image Velocity Gaging
Establishing standards and integrating environmental DNA (eDNA) data into the USGS Nonindigenous Aquatic Species database
Speaker(s)

Aparna Bamzai, USGS

Frank Engel, USGS

Jason Ferrante, USGS


...