Lab Compact and Philosophy


The Fraser Lab Mission is to do fantastic open science. We engage in a lot of collaborative projects and strive for transparency in all things (see also our potential conflicts of interest), but especially in our publishing practices. We believe great science is made possible by our lab values that heavily emphasize mentorship and the well-being of every member of the lab. Sustaining a positive working environment involves conscientious communication and bidirectional feedback, among other general lab expectations. These values also prompt us to acknowledge that our institution was built on unceded Ohlone land. We take career development seriously, which includes not only regular attendance at conferences but also making use of all the resources available to us both at UCSF and more broadly. In return, we take tracking and sharaing our data very seriously. We are very fortunate to have access to an incredible wealth of scientific literature, a strong track record of grant and fellowship funding, and our amazing colleagues and core facilities at UCSF. Finally, this is a living document informed by a growing collection of external resources — we aim to iteratively improve upon everything described here!

Fraser Lab Mission

We want to produce high quality research in an uncompromising and highly transparent manner. We strive to work on unique problems using rigorous methods and like to disseminate our work as it occurs and have a strong focus on publishing preprints in addition to the traditional peer review process. Our software and scripts are open access on github, and we continuously amend our policies to make our data and methods more accessible to the community. We strive to be anti-secrecy in all things, and try to forge new lines of work that don’t compete with other labs.

Proteins are not static structures, and our scientific mission is to bridge the interface between statistical mechanics and biology to characterize protein structures as sets of conformational ensembles. Further, we push the boundaries of how we think about this structural framework to understand how physical, chemical, and genetic perturbations can shift the relative balance of those conformations. Through this mapping of stimuli to sets of structures we gain valuable insight into a variety of biological processes that can be applied to mutational design or small molecule discovery.

Core Lab Values

Our motto is “Beer and Tacos”. While our lab culture is not alcohol focused, it represents our mentality. The phrase was first coined by Dayn Perry regarding baseball scouting. You can find the full origin story here, but in short “Beer and Tacos” is about finding synergy between 2 or more things especially in cases where they are presented in opposition. For example, we like to publish preprints AND recognize the value of review-coordination and visibility that traditional journals provide while there are labs out there that staunchly choose a side. Similarly, two groups can ponder over whether to go out for a beer or to go out for tacos, but they don’t have to be mutually exclusive. Why fight? Beer and tacos can be enjoyed together. Certainly in the current state of science both routes of publication have their place. We should all be empowered to talk about our work at all times. We work on unique problems and disseminate quickly using preprints as a strategy to avoid the dreaded “scoop” without compromising our research or our ideals. “Beer AND Tacos”. CryoEM or crystallography for protein structure? Both! “Beer AND Tacos”. We find ways to make things work so we get the best of multiple worlds. Or in the words of Dayn Perry, “Why construct an either-or scenario where none need exist?”

Beer and Tacos Acrostic

We’ve used our motto to frame what we value. The lab represents a diverse group of students and professionals with respect to race/ethnicity, gender identity, sexuality, nationality, religion, political affiliation, caregiver and family commitments, and beyond. We strive to create a welcoming environment for all people, including underrepresented groups. As an advisor, I have the bias of my background, and other people have the bias of their background. I try to understand where you’re coming from, along with where I’m coming from, and that shapes how we can work together.

These values are ideals and we’re all growing towards embodying them. I want people to call me out when I’m not living up to them, and I will call people out when I think they’re not living up to them. We are imperfect and trying to grow and be better together. This document also helps us be accountable to each other as we try to live up to these ideals.

Land Acknowledgment Statement

The Fraser lab recognizes that the University of California San Francisco sits on the unceded land of the Ramaytush Ohlone (pronounced Rah-mah-tush O-lone-ee) peoples, the original inhabitants of the San Francisco Peninsula. As settlers on this land, we want to recognize the historic, and ongoing, discrimination and violence inflicted upon Indigenous people in North America. Please read our full statement here.

Resources

A comprehensive collection of resources for all of the topics listed in this compact has been compiled to support our development and health. This list grows as we do and can be found here.

Publishing

Publishing preprints and sharing results openly is the key to 21st century science communication. The real end goal of any research is to get the work out there, and I find myself most invested in the final push to posting and preprint than any other subsequent part of the process. We maintain our high scientific standards by publishing preprints of high quality research when it’s ready. The peer-review process of traditional journals can delay important results by months and is often plagued with politics that are harmful to the scientific process as a whole. However, the reality is traditional publishing still provides the highest visibility for work and coordinates qualified reviewers. Our current approach involves disseminating our results via preprints and is followed by publishing in traditional journals. See “Beer AND Tacos” above. We currently do both because it gets us where we need to be, but we are full proponents of a modern world of publishing that encompasses transparency, speed, fairness, peer-review, and visibility. This is evolving, and as a group we want to lead by example and be on the vanguard of that change.

I like to take an active role in the preparation of all our manuscripts, and I have protocols to facilitate this. A Twitter feed I follow, @drugmonkeyblog, voiced the issue of how students are often afraid to show PIs anything other than finished work. I expect a draft to be very rough and a starting point to grow from. Regarding authorship, I believe that conversations about positions in author order should occur early in a project, and I err on having more authors on a paper than less. Everyone with a meaningful contribution should be included.

Peer Review

We believe that transparency in peer review is critical to improving the quality and professionalism of reviews. We only review manuscripts that have been posted on BioRxiv and we post our peer review comments publicly on Biorxiv as well. Peer review is also viewed as a training opportunity and all lab members who co-review with JF are credited for their contribution to the review. JF recognizes that he holds certain privileges that allow him to post peer review comments non-anonymously without fear of repercussion. Unfortunately, this is not the case for all researchers. JF is willing to post reviews on behalf of anyone, both in and outside of the Fraser lab, who wishes to remain anonymous.

Guidelines for how to engage in respectful and constructive peer review can be found on the Peer Review in the Life Sciences course page.



Conflicts of Interest

As an advisor, there are often conflicts of interest between what’s best for me and the lab and what’s best for my lab members and their careers. There is opposition between wanting to keep the talent you’ve fostered and helping people to move on with their careers. I am constantly trying to prioritize the aspirations of people. In the end, if I am aligned with people’s long-term goals, most things fall into place.

We occasionally also do sponsored research in the lab and I consult for companies to the extent my primary responsibilities allow. These activities can create potential financial conflicts of interest. I’m as transparent as possible about this work and relationships while honoring confidentiality agreements. If these financial conflicts cause an issue with the work or working relationship between me and a lab member, I want people to feel like they can have those conversations with me early, and I am happy to talk about it. My department chair would be a good person to talk to if you don’t feel comfortable talking to me about it directly.

Mentorship

The most important things I can do are to give people the resources to accomplish what they want to accomplish in the lab, and to make sure what they’re doing is setting them up to grow for the position they want next. I believe that a mentorship relationship is a two way relationship. This means I expect lab members to mentor up, defined as ‘the mentee’s proactive engagement in the mentor-mentee relationship, so that both parties mutually benefit from the relationship and move forward towards an agreed-upon purpose or vision’.

The kinetics of career transitions are more determined by their personal desires for what they want to do in their career and less on my desires to keep them in the lab longer (see Conflicts of Interest). I recognize the itinerant nature of their time in the lab and so I try to push people to consistently revisit the question: what’s next? I expect lab members to critically think about their next step and what they need to get there on both a short term and long term basis. I try to work as hard as I can to give my lab the resources, including my time and my guidance, towards their goals.

In terms of project work, I believe in supporting lab members to become independent leaders in their specific subjects. This means I stay engaged in the project and provide critical feedback while guiding members to follow their ideas and directions. To get the best out of both of our time when meeting, I encourage members to follow this guide on one-on-one meetings and to read advice on how to get the most out of meeting together. I expect members to recognize and ask for additional feedback and support when needed. This means that members should demand my time and attention as much as they feel is necessary, for example asking for additional meetings for projects or careers, one-on-one journal clubs, or feedback on writing.

Specifically I aim to:


Career Development

As people’s career preferences evolve over time, I expect people to be engaged in a constant conversation with me. I think about “what’s next” as being such an important part of mentorship because how they think their work in the lab feeds into their longer term career goals allows me to tailor training, networking, conferences, and even aspects of their project around what I think would be most beneficial for their goals. In addition, when you begin in the lab we develop an Individual Development Plan (IDP), and we will review this plan yearly through surveys, activities, and a focused meeting. In addition, the Avasthi lab has put together a series of great activities that are very helpful in finding your path.

Many people think about how they perform in grad school as defining our career options, but it is also possible to envision working in grad school to explore or reinforce your long term career plans. I think people’s primary aim while they’re here should be trying to set themselves up for life beyond the lab. People who have been very focused on this have been well motivated, and it becomes really easy to recognize when to cut losses on a project or when to wrap things up and publish. It provides me with clarity of how to direct their work, and I really like having a very constant back and forth about it.

Feedback

We’re all growing, we’re all trying to live up to our core values, and essential to this is an emphasis on feedback. I am always open to feedback on how the lab and I can function better as long as it is respectful. I recognize that I can be defensive when facing criticism when I’m not watching myself, and I always try to fight against that. Because of this, when possible, I like to have a lot of structure with evaluation as it provides the time to digest it. We have surveys a couple times a year to give lab members an opportunity to voice how they think things are going. In the winter, we have an anonymous lab survey and have a group discussion. In the summer there is another personally-centered survey that is followed by a one-on-one meeting. Outside of these surveys, you can always come to me privately or otherwise.

I recognize that I don’t always give people the same opportunity of time on feedback I give them. I view it as part of my job to give people critical feedback, and I’ve learned to assess how people like to receive it. Some people need time to cool off after a presentation; some people want it written down; some people like to meet about it. I’m constantly learning how to give feedback to different people, and so my way of giving feedback to a person changes over time. Figuring out how to give people effective feedback is iterative and can be a long process, but I’m always trying to improve it.

Well-Being

I like to believe people are pretty good about self-regulating, but I recognize people are able to disguise that they are dealing with more than I can see. Bottom line, your primary concern should always be your physical and mental health. If you ever feel unwell, it’s best to stop what you’re doing (safely) and address the issue. Don’t put off or sacrifice your health and well-being to get in one last experiment.

Health and Personal Emergencies-

I trust people, and it’s expected that people will have emergencies. Take care of yourself and your loved ones. If somebody says, “I need some time” that’s all I need to hear, but I’m here to listen, to help, and to provide whatever resources and support I can both personally and professionally. I don’t need to hear any more details unless people are comfortable and they should not mistake my lack of asking with lack of caring or empathy, but rather just that I want to be respectful of people’s space. If you do have to leave the lab, if possible, please let me know what’s going on even if it’s as vague as “personal emergency” or “I need some time” so that we’re in communication about time away and that I know you are ok. In addition, try to pass off, reschedule, or communicate any time sensitive items like deadlines or microscope time. We are a community, and we are here for one another.

Work-Life Balance-

I’m not super prescriptive of how people work. I expect people to be really invested in their work and have a presence in the lab, but how they establish their rhythm of work-life balance is up to them. It’s easier to have balance when you’re working hard and enjoying it. I’m much more worried about when people aren’t working hard and are seemingly dissatisfied with the work that they’re doing; it seems to signal a misalignment of their work and life. As a parent, I am often not done with work when I have to leave the lab at the end of the day. I like what I do, and as a result I find myself catching up asynchronously. This means I often send messages and will very rarely (but not never) ask people to meet outside of working hours. While I try to minimize cutting into others personal time, this is how I achieve my work-life balance. I don’t expect people to respond to my late-night messages, and I expect people to arrange their time for their family, friends, health, relaxation, and recreation. People that don’t get enough recovery time aren’t as effective in the lab, and I want people to be happy.

Help-

Here are some resources for additional support, these and other resouces are listed in the Compact Resources.
For students - https://studenthealth.ucsf.edu/. For staff - https://hr.ucsf.edu/.

General Lab Expectations

As a researcher you are expected to develop your knowledge and skills, make incremental progress on your projects, and contribute to the running of the lab. This presupposes a lot of self-initiative and personal responsibility. The biggest driver of your academic career is you. Speak up when you need help or you find yourself going down an undesired path. Outside of this, you are also expected to document all of your work including methods, troubleshooting, and development. This information should be readily available to the rest of the lab. You are also expected to present your research both internally at group meetings a few times a year and to represent the lab at conferences and other national and international meetings. The lab values science communication, and we rely on feedback from group meetings and practice talks to hone our ability to make our science accessible to a variety of communities.

As a member of the lab community you are expected to be a team player. You are expected to follow lab policies, adapt as they evolve, and treat fellow members with respect. This includes respect for peoples’ lab areas and personal space and having consent for actions that will affect them. Lab members always ask permission before using or moving items belonging to a specific person including items in shared areas. Respect also means that when communicating to each other we empower rather than belittle people for their mistakes; we are all learning and growing. We are a collaborative, supportive lab so we ask for guidance from our fellow lab members with the understanding that academic careers get busier with time as people learn to take on more. As self-reliance is important to develop, we try to solve problems on our own first before seeking assistance. Also, you are also expected to contribute to the running of the lab by taking on repeating lab tasks that are rotated biannually.

Communication

Every week, each lab member has a one-on-one meeting with me to talk about current progress, issues, etc. To make the most of these meetings I request that you make an agenda and send it to me in advance of our meeting. [During COVID-19, meetings are taking place remotely and one-on-one meetings have been temporarily replaced by subgroup meetings, but the same principles apply.] In addition, my door is always open, and my mentality is that I work for my students and staff. Here are good guidelines from University of Wisconsin-Madison ICTR of how to make the most out of a mentor/mentee relationship.

In addition, the lab and myself are available through a very active Slack channel. Slack is a great tool that centralizes all of our communication. In our lab, we have a slack channel for almost everything. The @channel and @person prompts summon the channel or person at any time of the day so people have to be mindful of how people arrange their time especially during nights and weekends. It is a given that people can ignore slack messages outside of normal working hours to preserve their personal time and space. For urgent matters, you should contact people by phone/ text.

I try to be mindful of the fact that people have different preferred communication styles, and that I lie on one extreme end of that spectrum, namely that I communicate best in person and in real time. I am open to you communicating with me however works best for you, whether that means giving you time to think through your responses, making use of notes, or writing to me asynchronously on Slack. I also want to reinforce that my apparent terseness on Slack is a reflection of the fact that writing out my thoughts is comparatively inefficient for me, but not an indication of my mood or disinterest in a topic!

Conflict Resolution

As mentioned in Core Lab Values we embrace people from different backgrounds and with diverse perspectives. Part of embracing a group of diverse people is that sometimes people’s different opinions and perspectives will lead to conflict. While our opinions or beliefs may differ, we believe in respecting each other’s opinions.

However, we understand that conflicts and hurt feelings may still arise. We work to resolve conflicts between those with differing opinions in a timely manner. Our goal is to ensure that all lab members can feel welcome and part of the group. This allows for more awesome collaborative work and a more peaceful community. We acknowledge that it can take people different amounts of times or varying modes of communication to find resolution. We remain open to different styles and modes of communication and try to be non-reactionary or judgmental. If we have wronged someone else it is important that we acknowledge what we did wrong, apologize, and find a way to avoid it happening again in the future.

JF’s role in conflict resolution: Try to resolve conflicts among ourselves. JF is involved when any party feels it is necessary to do so. If a satisfactory resolution is not reached after involving JF, we can involve an external moderator, such as the Ombuds or a Restorative Justice circle facilitator.



COVID-19

The Fraser lab is aware of the imminent health risk posed by the pandemic and the need to take necessary workplace safety measures while being mindful of community members’ space and needs. Members are encouraged to take Zoom calls in auxiliary office spaces while on-site in order to maintain physical distancing and to not be unnecessarily subjected to laboratory hazards, as a courtesy to those working in the lab space. The Fraser lab also recognizes that wearing a facial covering while indoors and while proximal to others outdoors is a matter of safety as well as a demonstration to the public that scientists understand and take the COVID-19 pandemic seriously.

Due to limited occupancy of the on-site wet lab, all members are encouraged to do as much work from home as possible. When on-site work is required, an hourly scheduling system is to be utilized where members sign up in advance for flexible ‘shifts’ that adhere to UCSF on-site density guidelines. We expect that lab members will proactively communicate with each other regarding shift scheduling and be mindful of the scheduling needs and constraints of their fellow lab members. Moreover, these conversations should include volunteering to help each other out with lab tasks. While on-site, lab members should keep six feet or greater distance as much as possible. We are mindful of others’ comfort levels when a task requires people to be within six feet of each other and to keep these higher risk tasks as short as possible.

Resources for COVID-19 relief can be found on the UCSF COVID-19.



Lab Notebooks/Data deposition

As transparency and openness are key values to the lab, sharing our information both within the lab and externally to the scientific community is a top priority.

Internal-

Lab members are expected to document all of their work in a lab notebook, and this information should be accessible to other members of the lab. Currently, the lab uses the online electronic lab notebook, Benchling. Guides for using Benchling and for keeping lab notebooks are located on the [internal website] (https://sites.google.com/fraserlab.com/fraserlab-private/lab-administration/lab-notebook-guide?authuser=0). Read these guides thoroughly as it details how to format your notebook and how we keep our lab data organized. Additionally, members are expected to keep the shared lab protocols up-to-date and to contribute new protocols as they become relevant to the lab. Lab notebooks are backed up biannually.

Benchling also allows us to keep track of our samples and data through a registry/collection. While it is highly recommended you take advantage of the registry to organize your samples, especially for samples that should be made accessible to the rest of the lab, it is your choice how to organize your samples while a member of the lab. However, when you leave the lab it is required that you clean out all superfluous samples and log the samples you keep in the lab’s collection so other lab members are able to locate them. Directions for using registry and conventions for labelling the location are also in the Lab Notebook Guide.

External-

Lab members always make their data, materials, processing details available to the public through deposition to various public repositories. Lab code is made accessible through github. Data and information are regularly deposited to the repositories listed below as well as others. We happily share our plasmids and other materials freely by request.

As data deposition to some repositories can be involved, current lab efforts include making guides that will assist people through the process. A guide for depositing cryoEM structures by Jenna Pellegrino is posted on our blog, and more will be added as they become available. Internally, these guides are located on our shared protocols in Benchling.

List of repositories:

Addgene - Plasmids
Zenodo - datasets
Diffraction Pattern - XRD data
PDB - Protein structures
GenBank - Raw sequencing data
MaveDB - Deep mutational scanning (DMS) data
Mave Registry - DMS experiments


Literature

As a scientist, it should be a pleasure to keep up with current literature. You should dedicate a few hours each week to scanning and reading new papers. A blog post on our website describes a good method of how to keep on top of literature. As a part of weekly group meetings we have a mini journal club where we share interesting papers we’ve read. We also post these papers to twitter with #fljcnlt and to a slack channel with the same name. Additionally, we have journal clubs jointly with other labs several times a year to encourage in depth conversations about current papers and methods.

Collaboration

Internal-

In addition to myself, all of your lab members are a resource. It is expected that you will develop collegial relationships within the lab and occasionally work on shared projects. The spirit between lab members should be of cooperation and not adversarial competition. To that end, we try not to reinvent the wheel and make efficient use of everyone’s time by sharing our knowledge. Protocols are updated and shared in Benchling for everyone in the lab to use and several guides exist on the internal lab site for nearly every task, administrative or scientific, that anyone may need. We are all here to help each other, but also be mindful and respectful of your fellow lab members’ time. If someone in the lab has helped you a lot on a project they probably should be included as an author on your publications.

External-

The diverse nature of work in the lab encourages a lot of collaboration with partner labs both within UCSF, at other universities, and in industry. We seek to collaborate with labs who share a positive environment and a committment to open science. Lab members are expected to foster relationships with our collaborators inline with our values of transparency and cooperativity. In other environments collaborations have been tricky for some people. However, our collaborations have been very positive, and I try to do my part to ensure that continues to be the case. Lab members can expect me to be actively involved in both the details of the project as well as communication with the partner labs. I will have my lab members’ backs and manage difficult conversations such as authorship. I also feel an important factor to fruitful partnership is to all actually be in the same place from time to time and so I encourage travel for scientific collaborations. I’m happy to provide funding to facilitate these visits and meetings.

Grant Writing/Funding

For all science career paths, being able to explain yourself and the value of your work is an invaluable skill. Funding our research is vital to keeping the lab running and grant/proposal writing is the responsibility of the entire lab. My lab members and I collaborate together to write grants and proposals to fund themselves, to fund lab research and equipment, and to request use of scientific facilities outside of UCSF. There are resources on the internal website to assist with this.

Conferences and Travel

Talk about your work openly. Share early. A key component to information transparency is getting it out there. People should present their work at conferences as they are great ways to communicate our results and get other people excited about our work. Conferences are important to build your network as well as your science communication skills. I think everyone should attend 1-2 conferences a year. I encourage people to charge lab-related travel expenses to the lab. Your time is valuable; consider this when booking flights and ground transportation.


This development of this compact was guided by similar compacts and philosophies of several labs, see links.
Matreyek Lab, Case Western Reserve University
Syed Lab, University of Minnesota
Heemstra Lab, Emory University
Mentoring resources, University of Wisconsin-Madison ICTR
Moghe Lab, Cornell
Avasthi Lab, Dartmouth