Confluence Retirement

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is scheduled for retirement on January 27th, 2023. 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.
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Thanks to April Clyburne-Sherin for answering the following questions from the OSF viewpoint.

  1. How might OSF fit into a workflow that uses USGS repositories for data publication (such as USGS ScienceBase, or NWIS)? The OSF provides a place to centralize the organization of a collaborative research project by connecting common research services and tracking changes over time. This lowers the barrier to documentation and organization of complex projects. When you are ready to use an external USGS repository, you will easily find all the materials you need for data publication in one place. Many of these repositories that are not yet integrated with the OSF still allow you to provide Related External Resources to your data submission, which is a great place to include the GUID for public OSF projects. Providing your OSF project GUIC alongside publications is a simple way to improve transparency and context for your publications!

  2. How is OSF different from other workflow software such as Taverna, Kepler, etc.? Taverna and Keplar are great tools that allow researchers to track the provenance of their data and manage their workflow. If you are using software that tracks provenance, eases documentation, without leaving gaps as you move from one research service to another, then you have a connected workflow already. The OSF is useful to fill in gaps in research services and is most useful to those who have workflows that cannot be contained within one software application.

  3. How can OSF save me time? Generally takes large amounts of time to document. The OSF connects research services together and has built in version control. By centralizing your workflow and tracking your changes, you will find the most recent version of your materials quickly and reduce conflicts in versions from collaborators. It also makes on-boarding and off-boarding more efficient by ensuring that materials do not leave with lab mates, and that new lab members have access to all materials in one, centralized location.

  4. Can OSF document processing, analysis and results? All changes to your code, data, and outputs are automatically tracked by the OSF. The OSF does not currently allow for data processing and analysis to be run within the OSF itself. However, you can upload the outputs of other services, such as Docker or Jupyter notebooks, to document these changes using the built-in version control.

  5. What are some best practices for documenting scientific workflow for new/exploratory methods in data processing and analysis?Taverna and Kepler can help you document your processing and analyses steps. The OSF allows you to create a project that provide the necessary context and insight into the new methods, including a component to organize the literature that underlies the method, a component for the materials and outputs, a wiki to provide important information and links to related content, and registrations to mark important steps in the discovery process so you can refer to them later in publications. 

  6. Would like to understand who 'owns' legally data that is posted on the site. Does it still belong to the scientist??? It seems like this service could be vulnerable to FOIA /legal challenges and/or security issues. COS and the OSF do not require any rights to data posted on the site - the ownership always remains with the original owner. 

  7. The question came to mind that there would be security issues for USGS researchers to use this systemAs for security, it is a top priority of the OSF and I am happy to answer security concerns if they are able to elaborate on their security needs. 

  8. How does OSF fit with USGS data and software policy? It seems like what was presented might be contrary to USGS policy. CDI: Use of OSF may fit better with some USGS researchers than others, or as they say, "Your mileage may vary." For instance, collaborations with outside partners could benefit from use of tools that were not built specifically for USGS and greatly improve efficiency. On the other hand, some USGS researchers work with sensitive information that is not appropriate for external tools. Even if you feel you will not be able to use the OSF, we hope that the concepts of reproducibility and documentation of scientific workflow that were presented, and the demonstration of those through the OSF were useful as we all think about our own practices. If there are questions about specific points from the USGS policy, please do start the conversation with the CDI coordinators at cdi@usgs.gov and we can try to address these in future meetings.


Participant responses to "why are you attending this training" could be grouped into the following categories:

  1. To learn about the Open Science Framework (OSF). Yes, this will definitely be covered.
  2. To learn about workflow in general and strategies for improving workflow documentation or reproducibility. Yes, this should be covered.
  3. To learn about USGS policy. This will not be covered in this training, however, we will try to compile specific questions and find answers. 
  4. To learn about USGS tools for workflow. The Open Science Framework (OSF) is not a USGS product, but we arranged for this training because it is a widely-used tool that we think will be useful for our community to learn about. For USGS products related to data management, a few great places to start are (1) The Data Release Workbench (2) The USGS Data Management Website.
  5. To learn information to spread to other scientific researchers at one's center.

 

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