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.
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!
Fall meetings will take place on 9/24, 10/22, 11/19
Check back for the speaker schedule!
Looking for info from past meetups?
Read our recent reflectionon the themes that emerged from our 2023-24 meetings:https://doi.org/10.5281/zenodo.12702026
Check out ourcollaborative 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 - 11AM - 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.
- Zoom Registration
- NOTE: March meeting will take place on MARCH 19 at 9 AM Pacific.
- 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
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 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 viaOverleaforGoogle 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.
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!
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 languagethat help expand traditional notions of defining and assessing quality researchers.
Tuesday, March 28, 2023, 2-3 PM - Joshua Buckholtz,Center forOpenand ReproducibleScience 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).
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.
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.
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
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 aboutCurating 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.
- Join us in October to learn aboutCurating 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.
- November 30: (note, 5th Tuesday instead)
- Mario Malicki (https://metrics.stanford.edu/people/mario-malicki)
Open peer review is the least practiced aspect of open science. Yet itmay teach us a lot about how manuscripts can change from their submittedversion to their (peer-revied) published version of record. Mario Malicki will givean overview of 21 studies that analysed manuscript changes and hisownstudy in which I analysed changes between 121 epidemiology preprints and
their subsequent published versions. Finally, he will present a call fordeclaring changes to manuscripts with each published paper.
- December (no meeting)
- January 25, 2022
- Adrienne Mueller (Stanford)- Project Based Training in Reproducible Methods for Undergraduates
- REGISTRATION:https://berkeley.libcal.com/event/8583241
- Adrienne Mueller (Stanford)- Project Based Training in Reproducible Methods for Undergraduates
- February 22, 2022
- (Rescheduled from September)We are excited to have Dr. Biftu Mengesha from UCSF join usto discuss “Innovating Education in Reproductive Health” - a project to create open curricula on sexual and reproductive health. We look forward to learning about this fascinating open educational resource project.
- REGISTRATION:https://berkeley.libcal.com/event/8583259
- (Rescheduled from September)We are excited to have Dr. Biftu Mengesha from UCSF join usto discuss “Innovating Education in Reproductive Health” - a project to create open curricula on sexual and reproductive health. We look forward to learning about this fascinating open educational resource project.
- 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!