The 2022 Fall Alaska Fisheries Science Center Openscapes Cohort

About

The 2022 Fall Openscapes cohort training took place over 5 remote calls from October 5 to November 30, 2022. Cohort calls focused on 1) establishing open science mindset and introducing psychological safety (call 1 digest), 2) publishing and project management on GitHub (call 2 digest), 3) instituting team culture and data strategies (call 3 digest), 4) nurturing open science communities and coding strategies (call 4 digest), and 5) developing each team’s path forward as they continue their open science journeys after Openscapes training (call 5 digest). Participants’ GitHub usernames are provided within each team description to connect them to their Openscapes work. 

The Marine Mammal Lab/RSST Lab Manual team

The Marine Mammal Lab/RSST Lab Manual team focused their efforts on developing lab manuals for their teams. This team includes Katie Luxa, Erin Moreland, Kim Shelden, Nancy Friday, Cynthia Christman and Joanna Magner. 

This cross-division collaboration gave the participants a wider-ranging perspective and an understanding of the universal problems different teams experience. Their lab manual covers on-/off-boarding, outreach, lab safety, field safety, travel, time and attendance, and employee resources. This lab manual was developed by referencing other lab manuals (e.g., Fay lab manual) and with the team’s new skills in Quarto, GitHub repo and project management, and GitHub issue tracking. The lab manuals team saw this effort as an opportunity to unbury important lab and employee info from emails in one accessible page. Once complete, this MML lab manual will be moved to the Alaska Fisheries Science Center Marine Mammal Lab GitHub Organization.

The members of this team felt that their achievements and end products were more robust and inclusive because of how diversified their team was. The members of this team work across different programs and specialize in research on different species, and could share nuanced perspectives of what different documents and resources should include. 

The Alaska Fisheries Science Center Genetics team

The Genetics team, represented by Patrick Barry, Diana Baetscher, Sara Schaal, and Claire Tobin, sought to develop a streamlined analysis pipeline. The team created a new GitHub organization that allows them to oversee product development, assign issues, and direct overall project management in teams that include postdocs and collaborators.

GitHub provides tools for code versioning, documentation, and product testing that were critical for developing this pipeline. Together, they created different GitHub repositories for different projects and initiatives (e.g., sample collection, lab work, data storage) with links to resources and google docs.

Members of the team came from a wide range of open science experience levels and worked together to teach and learn from each other through this process. 

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The Pacific Cod Tagging and the Maturity Assessment, Reproductive Variability, Life Strategy (MARVLS) group

This team set out on the dynamic task of streamlining multiple data sources to product workflow and diversified data management.  This team is comprised of Susanne McDermott, Julie Nielsen, Kimberly Rand, Liz Dawson, Bianca Prohaska, Christina Conrath and Ajith Abraham and ranged across several Pacific cod tagging sub-projects across Resource Assessment and Conservation Engineering, the Maturity Assessment, Reproductive Variability, Life Strategy (MARVLS) group, and OFIS.

Data from the tagged fish are opportunistically collected when a tag pops off a fish and reaches the sea surface and satellite connection and need to be regularly integrated into reports, websites, and on data sharing platforms.

The team used mural boards to assist planning their database workflow and design. This visualization also helped motivate the team, outline what the next steps were, and create and assign tasks. When the team participants came together to work on this project, they were confronted with how similar their project themes and needs were.  

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The Marine Mammal Lab Field Report team

The Marine Mammal Lab Field Report team focused on new methods for working together and developing a ready-for-publication field report. This team included Kim Goetz, Megan Ferguson, Molly McCormley, Burlyn Birkmeier, and Amelia Brower.

For this project, the team leaned on Eli Holmes’s book chapter code and quarto discussion forums, especially since Quarto is new and quickly evolving. This allowed the team to delegate chapter assignments and other report tasks (e.g., create a new section, edit yaml file, build report) through GitHub issues for team members to work on.

The iterative and collaborative nature of the GitHub platform allowed the team to work through the idiosyncrasies of book and page formatting.

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The Oyster Monitoring and Marine Mammal Lab team

The Oyster Monitoring and Marine Mammal Lab team constitutes of Peter Mahoney, Skyla Walcott, Alex Zerbini, Gavin Brady, and Jordan Hollarsmith. The team is formed of a composite of people from across the center who assisted their peers on their Oyster Monitoring project.

For this effort, the team discussed how their universal work needs can be improved by universal lessons and learning GitHub project boards, Quarto, Mural boards (inspired by the PCod tagging team) and RMarkdown. In the Oyster Monitoring GitHub repository, the team worked together to develop the repository and documentation, and they worked with a SeaGrant Fellow to make an interactive quarto report website for the project.

The Groundfish Assessment Program Data Workflow team

The Groundfish Assessment Program Data Workflow team is working to codify the methods used to calculate survey design-based indices. This is a partnership of the Bering Sea and the Gulf of Alaska/Aleutian Islands groups, including Duane Stevenson, Lukas DeFilippo, and Sarah Friedman, and Zack Oyafuso. There are many bespoke scripts across the survey groups, for calculations of slightly different flavors of design-based indices, of which running each was often siloed to one person and underwent little to no code review. Expanding on the work already in the Groundfish Assessment Program Data Products GitHub organization, the team is developing an R package that will consolidate these analyses, interact directly with GAP Oracle databases, and include instructional documentation and vignettes. The package will undergo annual code review and validation, and promote greater collaboration and transparency with data users (e.g., stock assessors).

The team relied on GitHub for version control, to post, task, and address issues. In addition, the team led an effort to include the other members of Groundfish Assessment Program, by initiating working groups to focus on data processes, computations, and future technologies. The team hopes this effort will bring the two survey groups closer together, make these analyses repeatable and transferable, and help develop a future vision for Future Us.

The Midwater Assessment and Conservation Engineering team

The Midwater Assessment and Conservation Engineering team, represented by Denise McKelvey, Katherine Wilson, and David McGowan, provided the space and guidance for this team to further increase their skills in, and awareness of, the platforms that MACE already uses for collaborative development, maintenance, and sharing of code and standardized reports.

The tutorials offered by Eli Holmes and the examples of how others have adapted these lessons inspired the team members to envision new ways to collaborate as a team and leverage these tools. The course reinforced the team’s knowledge that Git can facilitate collaborations and increase efficiency by streamlining workflows, tracking issues, and supporting reproducibility.

The team appreciated the coding tips that were shared and the cultural change movement that the course inspires: shifting away from work silos and moving towards collaborative and open approaches.

The Resource Ecology and Fisheries Management Spectroscopy Tools for Life History Measurements team

This team, comprised of Esther Goldstein, Sandi Neidetcher, Morgan Arrington, Irina Benson, and Beth Matta, is working to develop standardized scripts for processing and analyzing spectroscopy data that can be reviewed and shared easily among multiple individuals and centers.

This effort is part of a NOAA-wide strategic initiative to develop spectroscopy as a tool for life history measurements (e.g., age, maturity, fish condition). The team realized the need to shift away from siloed scripts used by individuals for specific projects to a generalized open-source format.

The team discussed how their work can be improved by using GitHub repositories to review and share scripts, GitHub projects to track issues to assign tasks, and RMarkdown/ Quarto for generating reports more efficiently. The team worked together to develop a GitHub organization, their first repository, practice reviewing scripts, and address issues as a team.

Continued Support of the 2022 Openscapes Cohort

Additional Alaska Fisheries Science Center Openscapes training

There is interest across Alaska Fisheries Science Center in further Openscapes training. There may be an opportunity for a third NMFS-wide Openscapes cohort in 2023. 

NMFS-wide 3-year Openscapes Cohort

An effort to fund a NMFS-wide 3-year Openscapes cohort has just been funded. This proposal has been submitted to the NOAA Broad Agency Announcement and is now being considered for funding. We ask that the center director and Alaska Fisheries Science Center leadership show their support for this opportunity by reaching out to NMFS leadership, allowing us to publish articles and blogs (e.g., SWFSC post on Openscapes) on our website about our cohorts’ successes, or by sharing this news with colleagues. This funding of this proposal would fold into the White House’s 2023 as the Year of Open Science (YOOS) initiative. Initiatives at other agencies have already been approved, including NASA’s “Transform to Open Science” effort, which may become a multi-agency effort. 

The NMFS Openscapes effort has received some notoriety. Josh London and others presented the cohorts’ successes with Openscapes at the Earth Science Information Partners Conference (ESIP) on January 26, 2023 (Slides). 

GitHub Enterprise

Additionally, science center representatives, HQ IT, OST IT, and all the center ITs have been working to transform how scientists and IT collaborate to manage, support and guide GitHub Enterprise Cloud use. There will be more updates on this in the coming months.

Opportunities for future training

At the conclusion of the training, cohort members were encouraged to share their hopes for how the Alaska Fisheries Science Center will continue to support and enhance open data science within our community. Their responses are summarized below.

• Alaska Fisheries Science Center, like other centers, is also starting to invest in GitHub Enterprise accounts with Office of Fisheries Information Systems support. GitHub enterprise provides greater support, security, privacy, and more tools to users. Users will need GitHub Enterprise training. 
• Advertising ways employees can add learning, teaching, or supporting and elevating peers to their work plans. For example: 
  • “Participate in _____ R Users Group meetings and aid in the development of R products that advance ____ modeling activities and automation of reports and data products.” 
  • “Plan and coordinate efforts within the ____ program to develop and promote R coding skills for research and in providing survey data products. A) Coordinate the development of R packages, R-developed resources, and other tools used and produced during the survey season.”
  • “Support and participate in and/or lead efforts that contribute to an organizational culture of equity, inclusivity, accessibility and a workplace where diversity and individual differences are valued and leveraged to achieve the vision and mission of the organization as defined by the NOAA Fisheries D&I Strategic Plan, mission, and goals.”

• HCMO guidance standard language for Leadership/Management, DEIA Committee Members or similar-type roles performing DEIA-related activities: “Lead, develop, resource, and/or oversee efforts that contribute to an organizational culture of equity, inclusivity, accessibility and a workplace where diversity and individual differences are valued and leveraged to achieve the vision and mission of the organization as defined by the NOAA Fisheries D&I Strategic Plan (Fiscal Year 2022-25), mission and goals.” The number of employees who include this language is being monitored as part of the F-SAT/I implementation plan, which is designed to get quantitative metrics and improve them on how we are doing as an agency. 

• Participants in the training also recognized the need for additional training in specific skills and technologies (e.g., R, Python, Jupyter notebooks, Julia, Git and GitHub, Quarto, Posit Connect, reproducible analysis, and collaborative writing). 
• Establishing best practices across science centers for sharing large, confidential datasets with collaborators without having collaborators interact directly with internal databases. These challenges are not unique to Alaska Fisheries Science Center and would benefit from cross-center collaboration.
• Allocating time for implementing open data science practices into performance plans by making the development of open science strategies and skills central to an employees’ priority activities and not an additional task relegated to ‘spare time’. 
• Continued development of user-driven connections, communication, and collaborative learning between centers and between divisions at Alaska Fisheries Science Center, including a focus on psychological safety. 
• Participants identified that they needed additional training in using confidential data with GitHub, and developing skills navigating GitHub project management, branching and merge conflicts, collaborative writing, GitHub desktop and GitKraken.