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Open Science: Bay Area Open Science Group Meetings

A guide for Open Science at UC Berkeley.

Bay Area Open Science Group

Bay Area Open Science Group

Bay Area Open Science Group Logo with mapAre you interested in making your research more openly available? Want to learn about open science tools and platforms that can make your research more effective and reproducible? The Bay Area Open Science Group is intended to bring together students, faculty, and staff from the Stanford, Berkeley, and UCSF communities to learn about open science, discuss the application of open science practices in a research context, and meet other members of the community who are interested in (or already are) incorporating open science practices into their work.

 

Spring 2025 Meetings:

We meet on the 4th Tuesday of the month from 2-3pm via Zoom. All are welcome to attend and join the conversation!

  • January 28 - Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps - 
    Dr. Fabio Ciulla is a postdoctoral research fellow in the Climate and Ecosystem Division at Lawrence Berkeley National Laboratory. He earned his M.S. degrees in Physics from the University of Rome La Sapienza and completed his Ph.D. at Northeastern University in Boston, focusing on nonlinear dynamics of diffusive phenomena on geographical networks. At Berkeley Lab, his research includes developing data-driven models to predict water quality and leveraging state-of-the-art machine learning algorithms to detect undocumented legacy oil and gas wells across the United States.
    • Brief description of the study:
      Undocumented Orphaned Wells (UOWs) in the U.S. pose environmental risks, including methane leaks and groundwater contamination. This study used historical topographic maps, available as open-source data from USGS, and a U-Net computer vision model to detect well symbols in the maps and flag UOWs when there is no match among known wells. Applied to areas in California and Oklahoma, it revealed 1,301 potential UOWs with high spatial accuracy.
    • Related article: Ciulla, F., Santos, A., Jordan, P., Kneafsey, T., Biraud, S. C., & Varadharajan, C. (2024). A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: A Case Study for California and Oklahoma. Environmental Science & Technology. DOI: 10.1021/acs.est.4c04413
    • Zoom registration
  • February 25 - Open Science for Preterm Birth Research: Advancing Discovery Through a Public Data Repository and a DREAM Crowdsourcing Challenge - Tomiko Oskotsky is a physician-scientist in the Sirota Lab at the Bakar Computational Health Sciences Institute, UCSF. She earned her B.S. in Biochemistry from UCLA and her M.D. from the Medical College of Wisconsin, where she was elected to the Alpha Omega Alpha (AOA) National Medical Honor Society. Her research involves interrogating diverse datasets, including electronic health records, to better understand human health and disease. Her leadership roles include co-leading the March of Dimes preterm birth research data repository and directing the UCSF AI4ALL program, which teaches AI to underrepresented youth.

    • This talk will be centered around the development and administration of a March of Dimes-funded public data-sharing repository for preterm birth research, emphasizing its role in promoting open science and collaboration. She will discuss the organization of a DREAM crowdsourcing challenge that leveraging data from this repository and other publicly available datasets with the goal of predicting preterm risk among expectant individuals. The session will demonstrate how open data initiatives can accelerate discovery in preterm birth.

    • Zoom registration

  • March 25 - Case studies in transparency: OSF (Open Science Framework) at UC Berkeley
    • Join the BAOSG in March to learn about successful use cases for the OSF (Open Science Framework) platform. Professor Mariam Aly and Professor Don Moore, both from UC Berkeley, will join us to share their experiences using the platform to support and extend their open, transparent research practices.
      • Mariam Aly is an Acting Associate Professor in the Department of Psychology at UC Berkeley. Her lab studies how memory systems contribute to attention, perception, and prediction. Mariam is passionate about making academia more equitable and inclusive by increasing transparency, accountability, and fairness.
      • Don Moore holds the Lorraine Tyson Mitchell Chair in Leadership at the Haas School of Business at the University of California at Berkeley. His research interests include overconfidence, including when people think they are better than they actually are, when people think they are better than others, and when they are too sure they know the truth. He is only occasionally overconfident.
    • Zoom registration
  • April 22 - Open Science and Health Policy: Forward Progress or Complete Chaos?
    • This month, the Bay Area Open Science Group will feature Kathryn Phillips, PhD, Professor of Health Economics and Health Services Research at UCSF, in a conversation on open science and health policy. Although the move towards open science – including data sharing and open access publication – continues, these efforts must now consider the changing policy environment. Kathryn will lead a discussion on open science and health policy with topics to include evolving trends in open science, particularly open access publication, and how these trends might be impacted by the changing policy environment. Kathryn will bring her perspectives as both a researcher and Editor-in-Chief of an open access journal. Her thoughts will be informed by her 2024 publication on open access, her upcoming participation in the National Academy of Sciences Journal Summit, and an upcoming one-month residency at the Brocher Foundation (Geneva) to focus on open access publication globally.
    • Zoom registration
  • May 27 - TBD

Fall 2024 Meetings:

We meet on the 4th Tuesday of the month from 2-3pm via Zoom. All are welcome to attend and join the conversation!

  • September 24 - Good practices better than none: Lowering the barrier to good research data management and sharing. We will be joined by Dr. Abel Torres Espin. Abel Torres Espin is an Assistant Professor at the School of Public Health Sciences at the University of Waterloo. He is also appointed as Adjunct Faculty at the Department of Physical Therapy at the University of Alberta and as an Assistant Adjunct Professor at the University of California, San Francisco. Abel is part of the data team for several multi-center big data observational studies aimed at capturing and analyzing as much data as possible from different populations. Additionally, Abel is an advocate for open science, data sharing, and reproducibility. He serves as the lead data scientist for health data-sharing initiatives like the Open Data Commons for Spinal Cord Injury and Traumatic Brain Injury. Abel also participates in initiatives on data-sharing standards. He will discuss his recent article, A practical guide to data management and sharing for biomedical laboratory researchers and lessons learned to lower the barrier to good data practices, perhaps at the expense of best practices. Related article.
  • October 22 - Sewers for surveillance: Harnessing wastewater monitoring data for public health action. Elana Chan (Stanford University) is a Civil and Environmental Engineering PhD candidate in the Boehm Research Group studying how wastewater monitoring data may be interpreted for public health action. Elana was recently awarded the 2024 Stanford University Libraries Data Sharing Prize for her transparent research practices including publishing her data and code alongside her research papers with detailed documentation in the Stanford Digital Repository. 
  • November 19 - A checklist to guide sensitivity analyses and replications of impact evaluations: This month the Bay Area Open Science Group will be joined by Sridevi Prasad. Sridevi is a Berkeley alum and a second-year PhD student in Global Health and Development at the Emory Rollins School of Public Health, specializing in water, sanitation and hygiene. Prior to Emory, she was a Senior Research Associate at the International Initiative for Impact Evaluation (3ie), where she was involved in their Transparency, Reproducibility and Ethical Evaluation Initiative. Sridevi will discuss a checklist she developed to guide researchers in planning and justifying replications studies. Attendees will learn how the checklist can be applied to impact evaluations and potentially other  transparent and ethical research practices. Related article.

Looking for info from past meetups?

Read our recent reflection on the themes that emerged from our 2023-24 meetings: https://doi.org/10.5281/zenodo.12702026

Check out our collaborative notes

Use the Open Science Team Agreements!

Want to talk about Open Science with your lab or team? We created a two-page template for teams to learn more about open science and select practices that work for them. Find it on Zenodo.

Fall 2023 Meetings:

  • September 26 [Note special time - 9-10 AM] - This month, the Bay Area Open Science Group will be facilitating a journal club discussion focused on the recent paper, “Teaching open and reproducible scholarship: a critical review of the evidence base for current pedagogical methods and their outcomes” (https://doi.org/10.1098/rsos.221255). Join us to discuss teaching open and transparent research practices. We will also be sharing a few exciting community updates during the meetup!
  • October 24 - Building your Open Science Career - Join the BAOSG and guests, Hao Ye (Curriculum Developer, Community for Rigor, U Pennsylvania) + Virginia Scarlett (Scientific Computing Associate, Open Data, HHMI Janelia), to discuss job searching and career pathways in open science.
  • November 28 - [Note special time - 11 AM - 12 PM] - This month Kate Tasker and Rebecca Tang will join us from the UCSF Industry Documents Library (IDL) - a free online archive of millions of previously-internal corporate documents from Tobacco, Opioid, Food and other industries that impact public health. Kate and Rebecca will give an overview of IDL, discuss how the documents are prepared for free open access, and share how researchers have used the documents for scientific and computational analysis, litigation, investigative journalism, and policymaking that protects and improves public health.

Spring 2024 Meetings:

  • January 23, 2024 - This month the Bay Area Open Science group is digging into Citizen Science for health research with Shamsi Soltani from Stanford. As big data proliferate, the importance of representing the lived experiences and diverse perspectives of individuals will only grow. Shamsi and her team used micro-scale citizen scientist-collected data from four Bay Area communities along with aggregate epidemiologic and population-level data sets to illustrate barriers to, and facilitators of, physical activity in low-income aging adults. These data integrations highlight the synergistic value added by combining data sources, and what might be missed by relying on either a micro- or macro-level data source alone.
  • February 27, 2024 - In February, we will be joined by members of the UCSF Decision lab. PI Winston Chiong and his team will join us in a conversation about how they incorporate reproducibility into their neuroethics and decision neuroscience research, showcasing practices and values from their lab handbook.
  • March 19, 2024 - This month the Bay Area Open Science Group will celebrate the 10th anniversary of SCOAP3, the Sponsoring Consortium for Open Access Publishing in Particle Physics, a groundbreaking partnership of libraries, funding agencies and research centers around the world to open the literature in the field of High-Energy Physics. Kamran Naim (Head of Open Science), Anne Gentil-Beccot (Open access coordinator and electronic resources manager, and Alexander Kohls (Scientific Information Service, Group Leader) of CERN will join us to discuss the SCOAP3 model, accomplishments and plans for the future, and will highlight data from participating US institutions.
  • April 23, 2024 - Supporting an Open Source Software Journal: Strategies for Effective Editing and Engagement. This month the Bay Area Open Science Group will be joined by Kelly L. Rowland. Kelly will discuss her experiences as editor for JOSS, a journal dedicated to publishing articles about open source research software across domains. JOSS’ scope includes software that solves complex modeling problems in a scientific context, supports the functioning of research instruments or the execution of research experiments, or extracts knowledge from large data sets. Kelly is a Computer Systems Engineer in the User Engagement Group at the National Energy Research Scientific Computing Center (NERSC), a division of Lawrence Berkeley National Laboratory (LBNL). Before joining NERSC, she obtained her Ph.D. from UC Berkeley in Nuclear Engineering with a Designated Emphasis on Computational Science and Engineering. Kelly has been an editor for the Journal of Open Source Software (JOSS) since 2021. 
  • May 28, 2024 - Will teamwork make the dream work? Promoting open science practices via big team science. This month the Bay Area Open Science Group will be joined by Nicholas Coles and Heidi Baumgartner. Nicholas and Heidi will discuss their experiences as co-directors of the Stanford Big Team Science Lab (BiTS). Nicholas is a Research Scientist at the Stanford Human-Centered AI center and founded the Emotion Physiology and Experience Collaboration, which is working to develop the largest publicly available dataset on emotion physiology and experience. Heidi is a Research Scholar at Stanford and is the Executive Director of ManyBabies, an international collaborative network focused on replication and best practices in developmental psychology research.

Bay Area Open Science Group

Bay Area Open Science Group Logo with mapAre you interested in making your research more openly available? Want to learn about open science tools and platforms that can make your research more effective and reproducible? The Bay Area Open Science Group is intended to bring together students, faculty, and staff from the Stanford, Berkeley, and UCSF communities to learn about open science, discuss the application of open science practices in a research context, and meet other members of the community who are interested in (or already are) incorporating open science practices into their work.

Meetings:

We meet on the 4th Tuesday of the month from 2-3pm via Zoom. All are welcome to attend and join the conversation!

Dates for 2022-2023:

Fall Semester 2022

Tuesday, August 23, 2022, 2-3 PM - Open Science Team Agreements

Click here to register for August Zoom Meeting

This month, the Bay Area Open Science Group introduces the “Open Science Team Agreement,” a template that research groups can use to discuss, adopt and implement open science practices. Ariel, John, and Sam (the co-hosts of Bay Area Open Science Group) have designed a prototype team agreement (available via Overleaf or Google Docs) and are looking for feedback. Join us to discuss what else should be included, and how team agreements can be used to kickstart conversations on open science. Potential adopters are especially welcome.

Tuesday, September 27, 2022, 2-3 PM - Free Open Access Medical education

Register for September Zoom Meeting

Dana Larsen - UCSF 

This month the Bay Area Open Science Group is learning about engaging with #FOAMed (Free Open Access Medical education): how medical trainees are utilizing online educational resources.

FOAMed, Free Open Access Medical education, describes online resources which are free and generally represent a crowdsourcing of content, such as blogs, microblogs (Twitter), podcasts, and online journal clubs. While FOAMed has been increasing within medical education, limited data exists on how to utilize this tool to supplement existing curriculum in order to fill gaps in trainees' knowledge and stimulate self-directed learning. In this session, Dr. Dana Larsen, principal investigator of a UCSF Innovations Funding in Education study, will discuss her design-based research project seeking to pragmatically build an adjunct curriculum for nephrology fellows using FOAMed resources.

Tuesday, October 25, 2022, 2-3 PM

Natasha Batalha (NASA Ames)

This month the Bay Area Open Science Group will hear from Natasha Batalha as she shares her experience as a Team Lead on NASA's TOPS (Transform to Open Science) Mission developing a curriculum on Open Results.

Register for October meeting

Tuesday, November 29, 2022, 2-3 PM

This month the Bay Area Open Science Group will discuss the slew of new federal open science policies coming our way including the 2023 NIH Data Management and Sharing policy and the recent OSTP memo "Ensuring Free, Immediate, and Equitable Access to Federally Funded Research". What does this mean for you and your research? Let's discuss!

Register for November meeting

Spring Semester 2023

Tuesday, February 28, 2023, 2-3 PM - Ruth Schmidt, Project TARA (Tools to Advance Research Assessment), Building Blocks for Impact

Ruth Schmidt is an associate professor at the Institute of Design (ID) at Illinois Tech, whose research sits at the intersection of behavioral science, humanity-centered design, and complex systems. She has been working with DORA for several years to tackle research assessment reform from a behavioral systems perspective, resulting in tools like "Building Blocks for Impact" to provide new structures and language that help expand traditional notions of defining and assessing quality researchers. 

Register for February meeting

Tuesday, March 28, 2023, 2-3 PM - Joshua Buckholtz, Center for Open and Reproducible Science at Stanford

This month the Bay Area Open Science group will be joined by Joshua Buckholtz, Director of Operations and Research Scholar at the Stanford Data Science Center for Open and REproducible Science (SDS-CORES).

Register for March meeting

Tuesday, April 25, 2023, 2-3 PM - Open Science in Bioengineering with the Fraser Lab, UCSF

This month, the Bay Area Open Science group will be joined by members of the Fraser lab at UCSF. James Fraser, Roberto Diaz, and Christian Macdonald will join us in a conversation about how they incorporate open science values into their bioengineering research, and how they think about getting credit for this work.

Register for April meeting

Tuesday, May 23, 2023, 2-3 PM - Open Data with Steve Diggs, Senior Product Manager for data publishing at the California Digital Library, UC

This month, the Bay Area Open Science group will be joined by Steve Diggs. Steve recently started at the California Digital Library (CDL) as the University of California Curation Center (UC3)’s new Senior Product Manager for our data publishing portfolio. Steve most recently worked at the Scripps Institute of Oceanography at UCSD where he has served as the Technical Director of the Hydrographic Data Office (CCHDO). Steve will discuss best practices in data publishing, adapting data repositories in response to researcher needs and preserving data to meet compliance requirements.

Register for May meeting

Tuesday, June 27, 2023, 2-3 PM - ChatGPT and SciHub, an informal chat

Join the Bay Area Open Science Group this month for an informal conversation about “open” information focusing on ChatGPT and SciHub. What do these tools have in common? What do they say about the future of scientific information access and open science?

Here is what ChatGPt has to say on the topic:

Looking for reliable scientific information? Look no further than ChatGPT and SciHub! ChatGPT is an advanced language model that can answer your scientific questions quickly and accurately. Whether you're a researcher, student, or just curious about the world around you, ChatGPT has got you covered. On the other hand, SciHub is a platform that provides free access to scientific papers and articles that are otherwise hidden behind paywalls. With over 80 million papers available, SciHub is a treasure trove of information that can help you stay up-to-date on the latest scientific research. So whether you prefer asking questions or reading articles, ChatGPT and SciHub are the perfect combination for anyone seeking reliable scientific information. What do you think about ChatGPT’s enthusiastic boosterism? Do you consider ChatGPT and SciHub to be the “perfect combination for anyone seeking reliable scientific information?”

Join the conversation and let us know!

Recommended Pre-listen: https://radiolab.org/podcast/library-alexandra

Register for June meeting

Bay Area Open Science Group

Are you interested in making your research more openly available? Want to learn about open science tools and platforms that can make your research more effective and reproducible? The Bay Area Open Science Group is intended to bring together students, faculty, and staff from the Stanford, Berkeley, and UCSF communities to learn about open science, discuss the application of open science practices in a research context, and meet other members of the community who are interested in (or already are) incorporating open science practices into their work.

Meetings:

We meet on the 4th Tuesday of the month from 2-3pm via Zoom. All are welcome to attend and join the conversation!

Dates for 2021-2022:

  • September 28: 
    • Introductions and Open Science Group Discussion
  • October 26: 
    • Join us in October to learn about Curating a COVID-19 Data Repository, a public data repository built by the Yu Group at UC Berkeley to aid community-wide data science efforts in the fight against COVID-19.
      Tiffany Tang, a statistics PhD student in the Yu Group, will be discussing how the project came about, what it was like working in the time pressure situation, and some lessons learned in the process of creating an open-source data repository. We will also have plenty of time for questions and a more general discussion on creating an open-source data repository.
  • November 30: (note, 5th Tuesday instead)

Open peer review is the least practiced aspect of open science. Yet it may teach us a lot about how manuscripts can change from their submitted version to their (peer-revied) published version of record. Mario Malicki will give an overview of 21 studies that analysed manuscript changes and his own study in which I analysed changes between 121 epidemiology preprints and 
their subsequent published versions. Finally, he will present a call for declaring changes to manuscripts with each published paper.

  • December (no meeting)
  • January 25, 2022
  • February 22, 2022
  • March 22, 2022

    • Milo Johnson (https://miloswebsite.com/, starting a post-doc in the Koskella Lab at UC Berkeley this June)

      The linear format of scientific papers is an entrenched, constrained result of history that holds back efficient and effective transmission of information between scientists. Science requires depth, but the reality is that the majority of readers don’t care about the majority of things in a paper. And we know it! At conferences, scientists give 5-minute talks at poster sessions that effectively communicate their work to 95% of their audience, and the other 5% can ask follow-up questions about the details. Can we design a way to write scientific content in a similar way, such that the details are accessible behind a concise narrative? I'll present this idea along with some preliminary technical explorations, and I'll invite y'all to brainstorm with me about how we can make tools to improve communication between scientists!

  • April 26, 2022

    • Gather around virtually with colleagues at Stanford and Berkeley for a presentation on The COVID Tracking Project by Kevin Miller, a former team lead with the project who is archiving the project's data and collections for the UCSF Archives & Special Collections. The project was a volunteer-run, community-science program that became a critical source of national pandemic data accidentally and overnight. He will discuss how it was built, and the challenges of archiving such a massive, born-digital collection.

  • May 24, 2022

    • Join us in May as we get together virtually with colleagues at UCSF and Stanford to hear from the fledgling Open Source Science at Berkeley student organization. They will be introducing their group and seeking feedback for a planned 1-unit course on developing open-source scientific software. Rachel Clune, Orion Cohen, Tarini Hardikar, and Connie Robinson are chemistry graduate students at UC Berkeley. They share an interest in improving the scientific software ecosystem and teaching computational skills to the Berkeley community

  • Tuesday June 28, 2022

    • Examining the Openness of COVID-19-related Randomized Control Trials with John Borghi

Check out our website (https://bayareaopensciencegroup.github.io/) to get on our mailing list, or let us know if you want to present!

Open Science Librarian

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Sam Teplitzky
she/her
Contact:
Earth Sciences & Map Library
50 McCone Hall