News from the Fraser Lab


The Minute for Diversity Slide

Leah T. Roe
26 June 2020

…is a slide during every person’s group meeting presentation about what makes you a diverse individual or a diversity topic you are passionate about. It is a quick moment at the start or end of every group meeting devoted to bringing awareness to our varied life experiences. The slide is meant to help us get to know colleagues beyond science, understand cultural differences, and develop respect for one another.

The idea was introduced to me as an undergraduate researcher at the Molecular Foundry, a national user facility at Lawrence Berkeley National Lab. Adapted from the Segalman lab, Ron Zuckermann and Rita Garcia introduced the Minute for Diversity slide to foster a welcoming community for a facility with constant flux of international scientists. In practice, it helps people feel more connected to one another by sharing something that would not normally come up in work conversation. Unintentionally, the slide also serves to get to know normally shy people and makes careers in science more accessible to younger lab members. I often find it to be the most memorable part of a person’s group meeting. It is up to the individual on how much they would like to share about themselves and whether they would like to keep it lighthearted or bring awareness to more serious issues.

A few I’ve seen over the years include:

Personal

  • Stories, pictures, traditions, foods, and cultural touchstones from how one grew up by proud community members
  • How to capture stunning photos by a photographer
  • Restaurant recommendations by a foodie
  • Travel advice on their home country by international scholars
  • Beautiful ceramics by an artist
  • How to check for tick bites by an outdoor enthusiast
  • Videos of salsa performances by a dancer
  • What to do if you are victim to a canine bite by a recently injured postdoc
  • Quarantine fashion by a bored graduate student

Awareness

  • Discrimination against marginalized people in STEM (Race, LGBTQIA+, gender identity, and more)
  • Mental health in STEM and on-campus resources
  • Open access initiatives in STEM
  • Personal data privacy
  • Voting
  • Team building, effectiveness, and efficiency

After leaving the Foundry, I have shared the practice with the labs I have affiliated with since and plan to continue this trend as I move through my training. I highly encourage PIs and learners to introduce the Minute for Diversity slide during your next group meeting, and make it a habit for everyone in subsequent meetings. I would love to see the day that this is the norm in academia.

Examples provided below with brief context from myself and several lab mates across the various labs I’ve worked in at UC Berkeley and UCSF.

Zuckermann Lab

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Created for a labmate who was having a bad day and “just wanted to see some puppies.” A lighthearted way to say I classify myself as a “mutt.” (NOT meant to promote eugenics!) - Leah Roe, Undergraduate Research Assistant

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I can’t thank my mom enough for having me take art classes since I was 7. Although I seldom practice art now (I’m working on improving this), I identify greatly with it. Art has brought me joy, therapy, sadness, a break from the sciences, but also a connection to the sciences (many chemical reactions are surely driven when your pot is in a kiln). Art has helped me identify my own uniqueness and to acknowledge the grand beauty in diversity— for that, I am eternally grateful. - Joselvin Galeas, Undergraduate Research Assistant

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I grew up in Guatemala, which is located in Central America. I enjoyed the Minute for Diversity section in lab meeting because it gave me the chance to talk about the country I’m from. - Virginia Garda, Undergraduate Research Assistant

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For my diversity slide, it was important for me to honor my family, in particular my parents and my grandmother who helped raise me. They taught me resilience, and supported me in taking on this research opportunity. While my dad was never allowed to go to college in China, he was always reading and learning, and I’m grateful he passed on that growth mindset to me. - Nancy Luo, Undergraduate Research Assistant

Fraser Lab

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For my own biracial identity - Chinese and Ashkenazi Jewish. The article describes how diverse knowledge and teams work together to problem solve more effectively. - Leah Roe, Junior Specialist

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While we should appreciate human progress by broad metrics, we need to scrutinize the world more deeply to root out the inequalities that are nevertheless widespread. - Hersh Bhargava, Biophysics Rotation Student

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For diversity I thought it best to understand where I come from. I grew up moving every couple of years with a hippie dippie mother bouncing about from festivals, Hawaii off the grid yurts, VW buses, Italy, and Northern California woods. The slides depict the somewhat hectic bopping about. - Willow Coyote-Maestas, Visiting Graduate Student

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I wanted to spend my time during quarantine learning something new since I couldn’t go into lab to do experiments. So I decided to learn how to make different cocktails. - Roberto Efraín (Robbie) Díaz, Tetrad Graduate Student

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A colleague of mine died by suicide and it caused me to start thinking about how students in academia feel, especially marginalized students. It prompted me to look at the literature about how we can overcome feelings of burnout and depression. - Roberto Efraín (Robbie) Díaz, Tetrad Graduate Student

If you are in need of mental health services or are in crisis, please reach out to Student Health and Counseling Services, Faculty and Staff Assistance Program, or Mental Health Board of San Francisco for immediate assistance.

Bondy-Denomy Lab

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A lifelong hobby - Tap dancing! It became an outlet for stress as I grew up. I also helped teach the PE tap dancing classes at UC Berkeley while I was an undergraduate. - Leah Roe, Junior Specialist

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I learned woodworking in high school and used it as an outlet before I started grad school. I learned how to make indoor and outdoor furniture and my family dinner table is one of my projects. - Matt Johnson, Bioinformatics Graduate Student

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The Spring Festival or Chinese New Year is approaching. According to the Chinese Zodiac cycle, 2020 is the mouse or rat year. Next is the Chinese Zodiac cycle that circles every12 years. Calculate what is your zodiac animal. Some traditions for Chinese New Year. Dumplings! It is more of a culture for northern Chinese, but not so much for southern Chinese actually. In some areas of China, people eat rice cakes or sticky rice balls with fillings (called Tang-Yuan) in Chinese New Year Eve. People set off firecrackers on CNY Eve and the morning of the new year. Traditionally, firecrackers were thought to scare away a monster that comes over during new year. “Chun-Lian” or Spring Festival Couplets are good wishes written on red papers and taped/glued around the doors. Some of the wishes are taken from ancient Chinese poetries. Even if not, they are often written in a poetic way. Lastly, lucky money!! Chinese culture (or east asian culture in general) values seniority. On CNY morning, we often visit our grandparents to “Bai-Nian” by saying good wishes and bowing to them, for instance wish them longevity and good health. In return, they give us lucky money in red envelopes to bless us a prosperous year. - Yuping Li, Postdoctoral Fellow

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Here, I show my California-based lab mates about how we prepare for hurricanes in Miami. Growing up, my parents and I would stock up on food and gas early to avoid price scalping and long lines. We would also install proper shutters, avoiding the unreliable “X” tape method. Though we never had an electric generator, this is a popular appliance for many during hurricane season, as the power will certainly be cut! - Senén Mendoza, Tetrad Graduate Student

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Here, I show off my quarantine hobby: fermentation. On the left side, I educated my labmates about the process for growing a sourdough starter from scratch and I show some of my mediocre results. On the right, I show my kombucha project, involving making a fresh SCOBY from scratch and preparing subsequent ferments for a tasty and refreshing treat. None of these experiments would have been possible without my assistants Salem and Lincoln (in the middle)! - Senén Mendoza, Tetrad Graduate Student


Black Lives Matter!

James Fraser
04 June 2020

We don’t have the language to describe the brutality of the murder of George Floyd, Breonna Taylor, Tony McDade, Ahmaud Arbery, and so many more. We believe Black Lives Matter. We are disgusted by the police brutality that we are observing and that has gone unchecked in this country for too long. We are shocked by the militaristic actions going on right now. It’s hard to focus on anything - and it’s even more horrible we can’t be together in person because of the global pandemic.

As a lab, we are committed to understanding the systemic racism that led to the world being as it is today - and how it contributes to the structures of science being as they are today. We are listing a few of the things we are doing to promote equity. The purpose of this list is to provide actions that other scientists - especially other labs at UCSF - can take:

  • We have taken DEI champions training and are committed to attending future trainings
  • We want to reduce Racial Profiling and Discrimination at UCSF by enforcing UCSF ID badge rules for all members of our lab. We want security to identify ALL building entrants, regardless of their race, ethnicity, gender, age, disability, or role at UCSF. We want UCSF and UCPD to directly partner with communities of color to make our campus a safe and inclusive environment for all UCSF members.
  • We participate in the SEP high school intern program
  • We have opened up lab meetings and other ‘regularly scheduled events’ to allow for the discussion of recent events, initiated by James Fraser.
  • We begin our lab meetings with a “minute for diversity”. We use this time, initiated by Leah Roe, to share something about our backgrounds or a reflection on diversity.
  • We recently established a lab compact, compiled by Jen Michaud, and a lab interview procedure with a rubric, compiled by Jen Michaud, Iris Young, Erin Thompson, Roberto Efraín Díaz, and Galen Correy.
  • Roberto Efraín Díaz initiated a Diversity Equity and Inclusion book club as part of his Gilliam Fellowship
  • We are listening and are committed to continual improvement and sustained action

We welcome feedback on any of the initiatives above and other actions we can take as a lab.


Clone this website!

Ben Barad and James Fraser
03 May 2020

If you are starting a new lab or want an easy (democratized) way to run your lab website - please: Clone this website!

The Fraser lab website was built by Ben Barad 6 years ago using Github Pages. Since then, it has been improved upon by many members of the lab, and has been updated over 1000 times by James.

We love our lab website because it is so easy to use and update. Updates are done in markdown, which is very easy to learn. As part of on-boarding, new members add their own bio and picture. This also serves to teach people git and to get comfortable with the idea of modifying, breaking, and fixing the website! The publications page is particularly powerful with easy formatting based on IDs for Pubmed, the Protein Data Bank, BioRxiv etc. Similarly the members page makes it easy to add accounts for Twitter, github, and other services. We keep adding more features. For example, Jen will be adding alumni links for lab websites or LinkedIn pages in the near future!

In keeping with our lab principles on sharing, we decided from the beginning to share it with a permissive open source license, so that others in the community are able to copy and modify it to make their own lab websites. We’re glad they have!

Quite a few people have made websites based on the original Fraser Lab template, with varying degrees of customization:

Sites Ben Made:

Sites other people made (in no particular order):

Have you made a website using the Fraser lab or one of these sites as a template? We’d love to add yours to our list!

So what do I do to make my own?

Recently, our lab website has gone through some significant ugprades. These include moving to collections for most things instead of using the _data folder, moving to a CDN to load large files, and support for structure loading with UglyMol. This guide predates these, and while it is relatively easy to copy the website still, for this guide we recommend taking a copy of one of the releases we made before incorporating these edits: https://github.com/fraser-lab/fraser-lab.github.io/releases

  1. Fork this Github repository (or one of the ones others have made - just make sure it has a license to do so!) to your own organization, and rename it to organization_name.github.io - right away, you’ll start seeing a website appear at that URL! Optionally, download the site, and try building it using the instructions in the readme so you can edit locally. Either way, delete the current CNAME file, which points to https://fraserlab.com. Once you’ve done this, the website will start showing up automatically at https://organization_name.github.io - no further hosting or configuration required.
  2. Update the license - you can choose not to relicense your site if you don’t want others to use it as a template, but you need to include a copy of the Fraser Lab license somewhere (can be in an external folder)
  3. Change the readme, config.yml and news.xml files to be your lab’s name!
  4. Update _includes/header.html and _includes/footer.html for your website! In particular, change the university brand image and link in the header, and the link in the footer.
  5. Remove all the Fraser lab’s images and PDFs from the static folder, and put in member photos, key images/PDFs for papers, and any extra images that you want to use on your site.
  6. Remove all the posts from the _posts folder and write one or two of your own!
  7. Remove any extra pages that you don’t intend to use (in particular, Fraser lab has many pages related to different UCSF classes) by deleting the folder with the respective name. The minimum folders you probably need are _data, _includes, _layouts, _drafts,_posts, publications, research, members, static, and maybe news and join.
  8. Update index.md to change the homepage! You can change the image in _layouts/home.html. Change the sidebar on the homepage at _includes/sidebar.html
  9. Go into _data and do the following:
    • Replace entries in members.yml and alumni.yml with your own members and alumni!
    • Replace or delete sep.yml and visitors.yml based on your needs - do you have visiting scientists or undergrads/high school students to list?
    • Update navlinks.yml based on your needs - this controls what is in the navbar at the top of each page.
    • Replace entries in publications.yml with your own publications.
  10. Update the members page photos by changing _layouts/members.html. Update the members page sidebar by editing _includes/alumni_sidebar.html.
  11. Update the research page at research/index.md. Similarly update any other specific pages by editing the index.md or index.html file in each folder.
  12. Either update disqus to your own account at _includes/disqus.html, or remove it at _layouts/post.html if you don’t like comments on your posts.
  13. Remove sitemap.xml and optionally make another one of your own.
  14. Replace favicon.ico with one of your own!
  15. Add a custom domain using Github’s instructions
  16. Edit styles in static.css and _layouts and _includes to customize the site to your heart’s content!

Once I have my own, how do I edit it?

For a new publication, just upload a photo and PDF, then update the _data/publications.yml file. Similarly, for a new member, just update _data/members.yml. New blog posts can be made by adding a new markdown file in _posts


Posting Peer Reviews

James Fraser
09 July 2019

A few years ago I started signing my manuscript reviews. My major motivation was to give the authors an opportunity to contact me to clarify what I meant or to ask how strongly I felt about statements without the delays of multiple rounds of review mediated by an editor. I figured that the positives for increasing the clarity, transparency, and speed of scientific communication would outweigh any potential negative side effects, such as “retribution”. Another positive was that I had to write each review thoroughly and fairly.

Despite some weird dynamics with editors, authors, and other reviewers throughout the years, I’ve found this to be a positive experience overall. But still had two nagging issues with peer review. First, I’ve had experiences where my reviews have been ignored after rejection at Journal #1 and papers have ultimately appeared in Journal #2 (or #3….) without ever responding to the substantive issues that I or other reviewers raised. Second, I was still bothered that we lose a tremendous amount of the written scientific record because reviews are only ever seen by the editors, authors, and reviewers themselves. This second issue is somewhat mitigated at journals like EMBO, Nature Communications, and eLife, which have more transparent review processes for accepted papers. And as part of ASAPbio, we are working on spreading this idea further in our initiatives on peer review

But, in the background of these larger initiatives and reflecting back on my own reasons for preprinting our lab’s work, I think there is more that we can do as individual scientists. Earlier this year, I decided to only review papers that have preprints associated with them so that I could post the reviews as comments on the preprints. I’ve openly reviewed 6 papers in the last year:

By far the best interaction has been with Sagar Khare’s lab, where they responded to our review on BioRxiv (and through Nature Chemistry, which eventually invited us to write a News and Views on their accepted article). It’s also been instructive to see that sometimes the authors interpret a remark very differently than the way I intended it and we can clarify the point directly. I also like the idea that the authors can start thinking about our comments immediately, instead of waiting for all the reviewers and the editor to collate things together. Another side benefit is that I can work more efficiently: the proliferation of Elsevier Editorial System accounts overwhelms my ability to use a password manager and now I can just email the editors a link to my comment.

The weirdest interactions I’ve had has been with some journals who worry that I’m breaking the confidentiality of the review process (for example). The authors have already posted a preprint - so I’m not sure about my responsibility to keep their manuscript confidential as it is already public. Similarly, I’m confused as to whether posting a public comment on a public manuscript is the same as corresponding directly with the author (presumably the editors are worried about backroom deals, not public comments)?

Since adopting this stance, my reviewing load has been substantially lower. I’m considering just picking some preprints to review with lab members (even when not asked by a journal to review them) and posting our reviews. Hopefully the authors can incorporate the feedback and add it to their portfolio when they are seeking journal sanctioned peer review.

The etiquette of commenting on preprints is still developing. By posting manuscripts on a preprint server, are authors inviting the same type of scholarly feedback that now occurs behind closed doors? I’m operating under the assumption that authors would welcome this type of feedback. As a reviewer, posting our reviews gives us the same benefits that drew us to posting preprints in the first place: transparency, speed, and scientist-control of disclosure!

Finally, I recognize that I can do this because of my secure position at UCSF. We need mechanisms to help folks who aren’t in as secure a position to be able to contribute in an anonymous, but somehow credited way, as well. My hope is that by moving the scientific communication culture towards something that is more open and transparent, potential for retribution will be reduced and the need for anonymity will be decreased.


So Long Brandi and Rahel

James Fraser
15 February 2018

Goodbye Rahel and Brandi!

Last Friday saw Rahel’s thesis talk and a goodbye party at Spark for Brandi. Rahel moves down to Stanford as a postdoc, where she will be exploring the exciting developments in cryo electron tomography in Wah Chiu’s lab. Brandi will move to Boston to take a Scientist position at Relay Therapeutics, a company focused on exploiting protein dynamics for drug discovery. Brandi was already pretty familiar with Relay as she had been collaborating with them since joining the lab in 2016!

So long!