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Openscapes: Supporting kinder science for future us

We believe open science can accelerate data-driven solutions and increase diversity, equity, inclusion, and belonging in research and beyond.

We champion open data science: the tooling and people enabling reproducible, transparent, inclusive practices for data-intensive research.

Julia Stewart Lowndes PhD, Openscapes

Stefanie Butland, Gayle Hagler, Jeff Hollister, Farnaz Nojavan

Jim Hagy, Amara Holder

EPA Center for Environmental Management & Modeling (CEMM), May 9, 2023

Artwork by Allison Horst

Slides: openscapes.org/media | openscapes.org

https://www.utm.utoronto.ca/biology/biology-seminar-series

Thank you so much, so excited to be here today with Ileana Fenwick; thank you for this invitation!

We are so excited to share today about how Openscapes supports kinder science for future us

Openscapes is a movement and a community that I founded and have built together with my partner Erin Robinson and the growing Openscapes community.

We champion open data science: the tooling and people enabling reproducible, transparent, inclusive practices for data-intensive research. We believe We believe open science can accelerate data-driven solutions and increase diversity, equity, inclusion, and belonging in research and beyond.

Researcher focused

Title

Openscapes: Supporting kinder science for future us

Abstract

At Openscapes, we believe open science can accelerate interoperable, data-driven solutions and increase diversity, equity, inclusion, and belonging in research and beyond. Our main activity is mentoring environmental and Earth science teams in open science, and connecting and elevating them both through tech like R, Python, Quarto, and JupyterHubs and communities like RLadies, Black Women in Ecology Evolution, and Marine Science, Ladies of Landsat, and NASA. We’ll share stories and approaches about supporting open science as a daily practice – better science for future us – and welcome you to join the movement.

Bio

Julia Stewart Lowndes, PhD

Director, Openscapes

Julia Stewart Lowndes, PhD is a marine ecologist working at the intersection of actionable environmental science, data science, and open science. Julia’s main focus is mentoring teams to develop technical and leadership mindsets and skills for data-intensive research, grounded in climate solutions, inclusion, and kindness. She founded Openscapes in 2018 as a Mozilla Fellow and Senior Fellow at the National Center for Ecological Analysis and Synthesis (NCEAS), having earned her PhD from Stanford University in 2012 studying drivers and impacts of Humboldt squid in a changing climate.

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Hi, I’m a marine ecologist and Openscapes founding director

Actionable (Environmental) Science

Data Science

Open Source

teaching, mentoring,

community empowerment

Julia Stewart Lowndes, PhD

Founding Director, Openscapes

Senior Fellow, National Center for Ecological Analysis & Synthesis, University of California Santa Barbara

Mozilla Fellow • Better Scientific Software Fellow

Openscapes helps research teams transition to

inclusive open data science workflows

We mentor teams to better tackle their questions by

strengthening shared practices, underpinned by existing tools. Supercharge your research (Lowndes et al. 2019); Open software means kinder science (Lowndes 2019)

Motivation from our own data-intensive marine science

Our team found out the hard way that our default approaches

for data analysis were not reproducible by even ourselves.

Our path to better science in less time using open data science tools (Lowndes et al. 2017)

Open Science Community Member, entryway through R

Inclusive peer-learning role-modeled across disciplines & career stages

R for Excel Users (Lowndes & Horst 2020)

Julie presents

I’m Julie Lowndes, I’m a marine ecologist and Openscapes Founder.

I’m a Senior Fellow at UC Santa Barbara and a long time member of the open data science community which had led me to finding my place in this venn diagram: that teaching, mentoring, and empowering communities around environmental open data science is what I do best.

The motivation for Openscapes comes from my experience as a researcher, and specifically as part of the Ocean Health Index team where we found out the hard way that our default approaches for data analysis were not reproducible by even ourselves. I led a paper about our transition to doing better science in less time, and since then I’ve moved away from doing my own research so I can support other researchers full-time through Openscapes.

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Ileana Fenwick

University of North Carolina PhD Candidate

Openscapes core team

Openscapes Pathways to Open Science Lead

openscapes.github.io/pathways-to-open-science

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A mentor community across organizations

NOAA Fisheries (NMFS) Research Scientist

University of Washington Affiliate Professor

NMFS-Openscapes Lead

nmfs-openscapes.github.io

Eli Holmes

PhD research:

Collaborative coding in R
GitHub for version control
Onboarding during COVID

We are learning together, improving our practices as researchers

We are a mentor community, supporting colleagues, leading programs, and role-modeling culture change within and across our institutions

Annual government reports:

Succession planning
GitHub for proj management
Quarto for collaborative reports

Ileana Fenwick and Eli Holmes are two amazing women who are marine scientists and data scientists. They are at different careers stages, Ileana is a 3rd year PhD candidate at UNC and Eli is a research scientist at NOAA for 20 years. Both participated in Openscapes as learners first.

Ileana learned how to code collaboratively in R, writing code that others would see, and also reusing other people’s code, and building relationships with them, asking questions. She learned to use GitHub and has talked about how important Openscapes was for onboarding to her PhD program during COVID, since it connected her to others and made her feel less alone.

Eli learned how to build spaces to have difficult conversations around succession planning; she’s a long time github user but for version control and she learned how to use Issues for project management with her team, and she learned Quarto, a new open source technical publishing system developed by Posit.

But they’re not only learners, they are mentors and leaders -

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What Openscapes brings

Focused on research teams, connecting to leadership
Centering climate
Kinder science, inclusion

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Openscapes helps shift culture by mentoring researchers to move from lonely science as they explore and navigate the open data science landscape safely with their teams.

Kinder science for future us

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Engage • Empower • Amplify

Openscapes helps research teams transition to inclusive open data science workflows

Part of the global Open Science movement

"We have to tackle a really hard problem: changing the cultural norms that are preventing us from embracing new ideas, truly working together and moving forward."

- NASA Transform to Open Science (TOPS) Initiative

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What if we connected our skills & values as a daily practice, for climate?

data science + open science

mentorship + teamwork + community

“To address our climate emergency, we must rapidly, radically reshape society. We need every solution and every solver”.

Ayana Elizabeth Johnson & Katharine Wilkinson, All We Can Save

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What if we connected our skills & values in our daily work, for climate solutions and justice? I’ve talked to many of you here who are looking for ways to contribute beyond efficient lightbulbs; you’re looking for daily practices.

In our work we’ve seen that when we combine Data science <> Open science <> Teamwork & community is a way for us all to help address our climate emergency. As Ayana Elizabeth Johnson and Katharine Wilkinson say in the book all we can save: “To address our climate emergency, we must rapidly, radically reshape society. We need every solution and every solver”.

I’m going to spend this talk telling two stories of what this looks like and invite you to join us

But first I wanted to tell a bit about me and what drives me to this work. I am often asked why a marine scientist would need data science, so I want to make sure you leave here knowing that marine scientists, as scientists more broadly, work with data every single day to do our science, and it is critical that we are supported to work with data responsibly and to code collaboratively.

So let me start off when a peek at my PhD work, which was here at Stanford University.

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Openscapes Initiatives

Champions Program - open data science mentorship for research teams (2 mo)

Designed to help teams of diverse backgrounds identify and address common needs so they can collaborate better

Mentor Framework - develop a mentor community across an organization that supports staff research teams in part through the Champions Program (3 yr)

Developing with NASA Earthdata and transitioning workflows to the Cloud

Reflections Program - open data science coaching for individuals (3 week)

Launching May 2023!

Pathways to Open Science Program - open data science community building for Black environmental & marine researchers (6 week)

Led by Ileana Fenwick of Openscapes in partnership with Black in Marine Science (BIMS) and Black Women in Ecology, Evolution, and Marine Science (BWEEMS).

Julie presents

We do this through two main activities

The Champions program is our flagship program; we mentor cohorts of 7-8 research teams over 2 months. This is the main way we’ve worked with NMFS so far, as Eli will tell you in a moment. The Champions program is designed to help teams of diverse skills & backgrounds identify and address common needs so they can collaborate better as teams.

The Mentor Framework is where we develop a mentor community within an organization that amplifies existing efforts and scales the Champions Program (3 yr). This is what we’re developing with NASA Earthdata, specifically around transitioning workflows to the Cloud, and It is the framework we aim to repeat and iterate with other orgs too.

This is a quote from one of the 2021 Champions from AFSC describing how Openscapes helped transition how they work, and is a good transition to Eli

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Champions Cohorts Details

Openscapes Champions lesson series

Available for use and reuse: openscapes.org/series

Example: AFSC Champions Cohort

Five times over two months, on mostly alternating Fridays.

Dates: January 28, February 4, 11, 25 and March 11, 2022
Times: 12:00-1:30pm PT
Where: remotely, via Zoom
Who: Cohort of 7 AFSC teams. openscapes.org/faq
Cost: Free; this opportunity is sponsored by AFSC
Expected time commitment: The minimum expected time commitment is 6hrs/month for 2 months: The Cohort meets together 3 hours/month, and teams also meet independently to further discuss topics (“Seaside Chats”)

Sign up by Jan 7: AFSC Openscapes 2022 Interest Sheet

Ask Us Anything: Dec 10, 11-12pm, or contact Jeremy, Josh, Em, Megsie

18 Cohorts so far

Cohorts of 7 research teams meet virtually 5x over 2 months to explore open data science & apply to their own shared workflows (Pathway)

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Amara Holder, Air Methods and Characterization Division (CEMM-AMCD)

Jim Hagy, Atlantic Coastal Environmental Sciences Division (CEMM-ACESD)

CEMM Champions Stories

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Jim’s slides, 3-5 mins

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Amara’s slides, 3-5 mins

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How we work:

Openscapes’ Flywheel

for movement building

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The Openscapes Flywheel:

A framework for managers to

facilitate and scale inclusive Open science practices

Robinson & Lowndes 2022 (preprint)

Leverage common workflows, skills, tools

Work Openly

Invest in learning and trust

Inspire

Flywheel

Create space and place

Welcome

Empower

Learning culture

Engage

A Future Us mindset

Amplify

Open leaders

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Collaborative software to build habits and community

Reflect and share ideas early

Meetings to learn together, invite others

Role-model open

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Identifying the common parts of data analysis

Wickham & Grolemund 2016

Science!

Towards less reinventing:

Julie

The first was stepping back and thinking about the common parts of our data analysis.

This is HW’s conceptual diagram for data science where he illustrates the importance of tidying data first before beginning to ask your research question. this was criticatl for us to separate out the common parts we were all reinventing so we could collab on those common parts and then give more creative energy and time for the science.

Less reinventing

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This is probably the most impactful figure in my science-life. The idea that no matter your question, your study system, etc, you will need to go through these deliberate steps if you’re working with data. And it’s really in this grey box of Understanding where the Science starts. So this is separating your science questions from this first part, which is import and tidying.

The idea of tidying your data first and then being streamlined with the tools you can use for science is amazing. So not starting the science too soon. I’ve been burned by this, and it means forever building bespoke approaches to accommodate weird data formatting. And knowing that tidying data takes a huge percentage of analysis time

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RMarkdown & Quarto: reimagine the way we work, share, think

Analyses and narrative together, rendered to reporting output of your choice.

Iteration & reproducibility

Communication: open, earlier

Our RMarkdown file renders to:

HTML!

Text

Code – R, Python,

SQL, bash...

Imagine never copy-pasting a graph into your doc again!!

Outputs as Word, PDF, but also HTML: Share a URL rather than attaching a file!

And that same URL will update rather than re-attaching a new version of the file 😍

rmarkdown.rstudio.com

Data science as an entryway to open publishing (Lowndes & Tierney 2020)

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Communicating impact

of movement building:

Champions Cohorts

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Inspire 💫

“I’m staying in the job because of Openscapes”
Morale, workforce dev, succession planning, organizational resilience
Policy change, NOAA GitHub

Leverage common workflows, skills, tools

Open educational resources & software
Connecting open communities: rOpenSci, RLadies, Carpentries, Pangeo, Turing Way, Black in Marine Science, BWEEMS, NASA, NOAA, Cal EPA, ESIP cross-gov sessions

Work Openly

Share imperfect work early
Team building where people have felt alone

Invest in learning and trust

“I never thought I could learn GitHub, now I’m teaching my boss”
Technical skill building “I’ve saved 400 would-be emails in 4 months”
Teaching, mentoring, coaching skill building; don’t have to be an expert to share what you know

Welcome

Art, storytelling
Community events, talks, & blogs (ESIP cross-gov takeaways 2022, 2023)

Empower

Learning culture

Engage

A Future Us mindset

Amplify

Open leaders

Create space and place

Rethinking meetings - Seaside chats, coworking
Shared folders & docs
Inclusion as a daily practice

Flywheel

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“As fisheries scientists, we know that when we’re in rough seas, it’s important to keep the ship afloat AND get out of the storm.

Openscapes helps teams steer out of the storm of email chains with 37 versions of the same spreadsheet and to the calmer waters of open science and meaningful collaboration, using tools like R.”

Adyan Rios

NOAA Southeast Fisheries Science Center

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NASA Openscapes: Supporting Open NASA Earth Science in the Cloud

https://nasa-openscapes.github.io

earthaccess Python library

Learning events, tutorials, lessons learned

Cheatsheets & guides

2i2c JupyterHub: Python, R, Matlab

“Openscapes has created a collaborative environment for DAAC staff to collectively support open science initiatives for NASA Earthdata users. We’ve developed awesome material to help Earthdata users. Perhaps just as important as what we’ve done however, are mindsets we’ve grown into along the way. It’s okay to share imperfect works in progress. We are better at dreaming and implementing the future together.”

– Cassandra Nickles NASA Physical Oceanography DAAC

Julie

The mentors are learning how to work in the Cloud together using a 2i2c JupyterHub, where they are supporting researchers to work there in Python, R, and Matlab. They are leading learning events using tutorials they created and reuse and iterate for different audiences and events for researchers and other NASA staff, They are also identifying user needs and developing where they see needs including the earthaccess python library; cheatsheets and guides. They describe how they are now working openly with each other across their silos, feel braver speaking up in other places, and that they are comfortable sharing imperfect work with each other and getting and receiving feedback.

2i2c

Work of the Mentor Community

How to grow it - working on real researchers in the science teams

Luis showing this real example of work the Mentor community has done

We are really grateful for our NASA Mentors, and to NASA who is supporting their time so that open science can be a paid part of their jobs.

We’re supporting Support Mentors towards establishing a common set of NASA Earthdata tutorials that they can then build off their DAAC-specific and science examples

Again, these recurring themes. Wanted to reuse existing so needed to identify what is unique to NASA earthdata and what’s not, tease that apart to reuse existing. Only contribute to combine and fill gaps rather than reinventing

We center researchers, and we focus on this feedback loop between tooling and people

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Because of Openscapes, I have renewed hope in how we can bring about a kinder future in science.

I see a commitment in the open science community to bridging the gaps where we’ve left members of our community behind, and it inspires me.

Ileana Fenwick

Univ North Carolina,

Openscapes

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Movement building

What’s possible because all this

More time on science & solutions

It’s not just about time saved - it’s better products, less lost day-to-day & during succession

Improved morale

Help get unstuck, less lonely, staying in jobs. Real relationships. Institutional culture change.

Climate and social change

Connecting our biggest challenges with our daily work. Collective agency, voice, action

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Join us:

Twitter, Mastodon: @openscapes

openscapes.org�nasa-openscapes.github.io

nmfs-openscapes.github.io

Openscapes at the Water Boards

Learn, reuse, remix, support others, grow the movement

https://openscapes.org/series

openscapes.github.io/approach-guide

Thank you!

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Julia Stewart Lowndes, PhD

@juliesquid

Thanks to the people who made this possible!

Not pictured: more people!

Diverse, inclusive teams and communities are key

Slides: openscapes.org/media