NMFS Open Science visioning document

Prepared by Eli Holmes (NMFS Open Science lead) with help and review from Christine Stawitz (FIMS), Kathryn Doering (FIT), Josh London (AFSC, NMFS R UG), Molly Stevens (SEFSC), Amanda Bradford (PIFSC), Eric Ward (NWFSC) and Diana Dishman (WCRO)

The overarching vision of NMFS Open Science is to support scientists, developers, resource managers and policy analysts within NOAA Fisheries (NMFS) in fulfilling NOAA’s Open Science mandates: NOAA Data Strategy, NOAA Fisheries Data Vision, DOC Open Source Code Policy, Federal Data Strategy, and the Federal Open Access Memo.

Delivering on this ambitious vision requires actively supporting staff in transforming to reproducible workflows and work products that will empower timely, transparent, and accessible data-driven science and decision-making. Such transformation calls for both increased collaboration across offices and regions towards shared scientific data science tasks and expanded support of open science, open data, and open source communities and initiatives within NOAA Fisheries.

Focus areas:

• Support Open Science and Open Data literacy across NOAA Fisheries
• Identify staff training needs and facilitate access to this training via our partners (below), advertising events, and organizing trainings and workshops
• Support and amplify NMFS Open Science user groups and communities
• Facilitate collaboration and exchange of open science tools and products tailored to NMFS staff needs and tasks
• Identify technical and administrative barriers that staff face in transitioning to open science and advocate for solutions

• Coordinate with and grow devops support and infrastructure teams to transition to cloud-based production workflows tailored to the needs of NMFS staff engaged in data-driven science and decision making. These needs are often very different than NMFS IT cloud-resources needs and weather or ocean modeling needs.

• “Open science is the principle and practice of making research products and processes available to all, while respecting diverse cultures, maintaining security and privacy, and fostering collaborations, reproducibility and equity.” NASA Transform to Open Science *

Executing

NMFS Open Science is largely strategic: the leaders of different NMFS open science initiatives work together to identify common needs and areas of synergy to execute the NMFS Open Science vision of supporting staff in fulfilling NOAA’s Open Science mandates. The leaders meet to discuss the most pressing needs for scientists, developers, resource managers and policy analysts within NOAA Fisheries, triage these needs and promote solutions, and identify areas where collaboration can improve data-driven workflows and build capacity. NMFS Open Science also organizes discussions and outreach efforts to support and communicate the importance and value of open science approaches, e.g. giving presentations NOAA-wide, keeping local leadership updated, and sharing outreach materials.

NMFS Open Science successes to date (2020-2022)

• Supported staff in transitioning to open science workflows via NMFS Openscapes program (fall 2022 cohorts, 160 staff)
• Developed a GitHub SOP to help staff use GitHub in support of open science while adhering to NOAA policies
• Supported expansion of GitHub Enterprise Cloud as a development platform for staff
• Developed documentation for development of common NMFS reports in reproducible formats such as Quarto, R Markdown, and R Shiny.
• Supported publishing of web applications and automated reports on Posit Connect
• Run the NMFS R User Group which connects 230 R users from all the science centers and regional offices in an active Google Spaces which members use to get peer help on technical questions.
• Supported staff training via 8-week 1 hr trainings on R/GitHub; open to all and, attended by 50 to 250 staff each week. Coordinated 11 1-hr trainings from Posit and Microsoft open to all NMFS staff. Curated a calendar with links to 1 to 4 hours a week of free training on R, GitHub or Continuous Integraion: beginner to advanced topics

NMFS Open Science 2023 focus areas

• Complete establishment of the NMFS GitHub Enterprise account as a secure controlled-access development environment
• Expand NMFS Openscapes team training broadly across NOAA Fisheries and include delivery of a Data Science course (similar to the Bureau of Labor Statistics DS academy)
• Pilot test NASA’s Open Science Certification program as a way to support Open Science and Open Data literacy
• Complete a scoping document on barriers staff face in accessing or using NOAA, NOAA Fisheries and co-manager data and climate data (cloud and on-premise)
• Catalyze establishment of more user groups similar to the NMFS R User Group (RUG), such as a NMFS Python User Group (PUG) and a NMFS Stan User Group (SUG).
• Expand use of GitHub Codespaces to more teams via GitHub Enterprise; developing more expertise in setting up virtual environments and more devcontainer templates.
• Work with Microsoft Azure to pilot a JupyterHub/RStudio environment provisioned to work with earth science data in the cloud for NMFS staff similar to that being tested by NASA
• Pilot participation in the University of Washington eScience OceanHack week to both help NMFS staff learn to use diverse oceanographic and fisheries data sets and to support skill-building for underrepresented groups in ocean sciences.
• Continue supporting products created as part of 2022 focus areas

Leadership for NMFS Open Science’s efforts come from these groups

NMFS Openscapes (leads: Eli Holmes NMFS/NWFSC and Julie Lowdnes Openscapes) A mentorship program to help teams and individuals make real and durable progress on transforming to open science workflows. NMFS Openscapes focuses on staff involved in data-driven science and regulatory work. It is run by Openscapes.org, an organization that facilitates organizational change to open science with a focus on government and academic organizations in resource management. In addition to NOAA Fisheries, they have worked extensively with NASA, EPA, California Waterboards, and many universities. The NMFS Openscapes mentors is a group of 1-2 staff from each science center and the West Coast Regional Office who act as the local representatives for training programs at each center and office. 160 scientific staff from SEFSC, NEFSC, SWFSC, PIFSC, NWFSC, AFSC and WCRO participated in the fall 2022 Openscapes cohort program.

NOAA Fisheries Integrated Toolbox (lead: Kathryn Doering NMFS/OST) The NOAA Fisheries Integrated Toolbox (NOAA FIT) aims to promote sharing of software solutions within the agency. The NOAA FIT is a curated, web-based portal of software tools used within NOAA Fisheries. These tools support open science workflows for NOAA Fisheries research and operations. The NOAA FIT also includes resources to empower NOAA Fisheries scientists and developers to create reliable and shareable software.

NOAA Fisheries Integrated Modeling System (lead: Christine Stawitz NMFS/OST) The NOAA Fisheries Integrated Modeling System (FIMS) is a software system designed and architected to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. The FIMS is created by a large team assembled across FMCs that practices highly collaborative Agile Software Development. The FIMS developers support the NMFS Open Science community by sharing their expertise at talks, trainings and co-work sessions. Once the FIMS is put into use, the FIMS team will work with the NMFS Open Science community to run trainings, workshops, and hackathons to encourage co-development of the system by stakeholders following open science principles and practices.

NMFS R User Group (admins: Kathryn Doering NMFS/OST, Emily Markowitz NMFS/AFSC, Josh London NMFS/AFSC, Eli Holmes NMFS/NWFSC) The NMFS R User Group (NMFS RUG) supports an active Google Space with over 230 members from NMFS science centers and regional offices. The NMFS RUG provides a way for R users and developers spread across NMFS to network and help each other. The NMFS RUG admins organize monthly sessions on topics of interest to members, with a focus on topics specific to NOAA Fisheries applications. In addition, NMFS RUG maintains a calendar of events of interest from R organizations across the world. The calendar and advertising of events on the Google Space have increased awareness of and participation in community-supported educational events by NMFS staff to support their learning journeys. Local FMC NMFS RUG representatives help advertise NMFS RUG and its events locally.

NOAA Fisheries Posit Connect Governance Group (co-leads: Christine Stawitz NMFS/OST, Kathryn Doering NMFS/OST) Posit Connect is a product allowing for seamless web publishing and cloud-based execution of small production tasks, such as automated report and documentation generation. This product has large benefits for the community of R developers within NOAA Fisheries since it simplifies cloud publishing in a familiar interface. The centralized OST Posit Connect server was one of the early collaborations across FMCs for open science goals. Without a shared server, many FMCs would have to stand up their own open source Shiny Servers on Google Cloud Platforms locally, requiring individual costs to FMCs as well as decentralized and duplicative administrative costs. The governance group has representatives from each science center, GARFO, and OST.

NOAA Fisheries GitHub Team This is an ad-hoc team that is working on improving GitHub (including GitHub Enterprise Cloud) support for data-science staff. Modern data science is highly collaborative. GitHub is currently the most widely used platform for this type of data science collaboration and development. GitHub Enterprise Cloud (in the Microsoft suite) provides an industry-level secure (FedRAMP low-impact Software as a Service baseline authorized) controlled-access development environment where NOAA Fisheries teams can work securely on private, pre-public, and public projects. A significant advantage of GitHub Enterprise Cloud is that the server is managed and updated by GitHub. GitHub Enterprise Cloud licenses also provide on-boarding training. This is a collaborative effort between OCIO, OST, and NMFS science center IT and science staff. Rick Methot NMFS acts as executive sponsor.

Note these are not the only open science groups at NOAA Fisheries. They represent the groups whose leadership has been actively involved in NMFS Open Science efforts in 2022. Many other groups involved in synergistic open science efforts have been involved via NMFS RUG events and by participating in NMFS Openscapes cohorts. For example, the Integrated Ecosystem Assessment (IEA) teams have adopted open science workflows and participated in peer mentorship of other teams via the Openscapes cohorts and NMFS R UG organized events.

What sort of NOAA Fisheries teams have have benefited from NMFS Open Science efforts? The fall 2022 Openscapes teams gives good examples.

In fall 2022, 160 staff, in 4 cohorts of 40, across all the science centers plus WCRO participated in Openscapes. Teams come in with a goal for the 8 1.5 hour sessions (over 2 months). Goals are highly team-specific but they all focused in some way on making workflows more reproducible and efficient by embracing open science and open data. Many teams take part multiple years as they work to keep improving their workflows and expanding to more parts of the project. Some teams have successfully made major transformations of their workflows, e.g. the AFSC Marine Mammal Stock Assessment group at AFSC and the SEFSC internal stock assessment coordination group.

The peer cohort of 40 helps each other, giving feedback and showing how they solved similar challenges (perhaps the previous week!). Mentors also help teams. In this way, teams are able to make progress that would have been impossible on their own. Once a week there are also cross-cohort co-working when peers across all the centers can help each other (by sharing a current barrier and getting feedback).

Here are examples of teams. This is from the AFSC cohort.

• The Marine Mammal Lab/RSST Lab Manual team focused their efforts on developing lab manuals for their teams.
• The AFSC Genetics team worked on streamlined analysis pipeline.
• The PCod Tagging and MARVLS team set out on the dynamic task of streamlining multiple data sources to product workflow and diversified data management.
• The MML Field Report team focused on new methods for working together and developing a ready-for-publication field report.
• The Oyster Monitoring and MML team discussed how their universal work needs can be improved by learning GitHub project boards, Quarto, Mural boards (inspired by the PCod tagging team) and RMarkdown.
• The Groundfish Assessment Program Data Workflow team is working to codify the methods used to calculate survey design-based indices.
• The MACE team worked 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 REFM Spectroscopy Tools for Life History Measurements team worked to develop standardized scripts for processing and analyzing spectroscopy data that can be reviewed and shared easily among multiple individuals and centers.

NMFS Open Science leads and helpers

NMFS Open Science is a group effort. The following are the core participants with the top 4 heavily involved in all our planning and visioning plus our high-level (national) efforts

Lead Eli Holmes (NWFSC, NMFS Openscapes)

Christine Stawitz (FIMS, 2022 NMFS Openscapes mentor)

Kathryn Doering (FIT, 2022 NMFS Openscapes mentor)

Josh London (AFSC MML, 2021-22 NMFS Openscapes mentor)

Molly Stevens (SEFSC, 2022 NMFS Openscapes mentor)

Emily Markowitz (AFSC, 2021-22 NMFS Openscapes mentor)

Amanda Bradford (PIFSC, 2022 NMFS Openscapes mentor)

Adyan Rios (SEFSC, 2022 NMFS Openscapes mentor)

Diana Dishman (WCRO, 2022 NMFS Openscapes mentor)

Eric Ward (NWFSC)

Margaret Siple (AFSC, 2021-22 NMFS Openscapes mentor)

Kevin Steirhoff (SWFSC, 2022 NMFS Openscapes mentor)

Erin Steiner (NWFSC, 2022 NMFS Openscapes mentor)

Bai Li (FIMS, 2022 NMFS Openscapes mentor)

Juliette Verstaen (PIFSC, 2022 NMFS Openscapes mentor)

Rick Methot (NMFS, executive sponsor for GitHub Enterprise efforts)

Contact NMFS OpenSci admins.