Lab Compact, Philosophy, and Resources

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 transparent 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.

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 in this 2016 blog post. 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”. Cryo-EM or X-ray 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?” 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.

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.

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.

There are no specific “set hours” for the lab, but generally I expect people to be around from 10-4:30. We benefit from a flexible schedule to accomodate caregiver responsibilities, personal fitness, etc. You are expected to attend 1:1, subgroup, and group meetings. The lab is very flexible with rescheduling, just send a message ahead of time and we can likely accomodate it. By default these meetings have resumed in person, but a zoom option can be made available for COVID-quarantine or other issues. It is ok to occasionally miss group meeting for events like travel, illness (don’t come in and don’t feel like you have to attend on zoom if you aren’t well!), major equipment usage (beamtimes), class (although we do our best to schedule around rotation student class schedules), or other rare lab-related events (e.g. time points for uncooperative experiments). If you miss a group meeting, it is expected that you will contact the presenter, get a copy of their slides, and engage them in a conversation about your questions/feedback. These guidelines help us maintain interactivity even when other circumstances get in the way of live attendance.

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. In addition, my door is always open, and my mentality is that I work for my students and staff. Read these guidelines from University of Wisconsin-Madison Institute for Clinical and Translational Research (UW ICTR) on 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.

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. The UCSF COVID-19 website provides financial, emotional health and wellbeing, telework, and more resources to support you during the COVID-19 pandemic.

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.

Lab Notebooks

Transparency starts with thorough documentation of your work and all members are expected to record all of their work in a lab notebook. Our lab uses the electronic notebook Benchling for recordkeeping, which allows us to share protocols and makes our work visible to all other lab members. Our lab’s guide to using Benchling can be found here, and our guide on how to craft good notebook entries is here. UCSF has also published a guide for record keeping. These guides should be read thoroughly before starting your lab notebook. 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 the registry and conventions for labelling locations are also in the Lab Notebook Guide. The primary guiding principle in keeping a lab notebook is that someone who doesn’t have familiarity with your research should be able to recreate your work solely using the information you record in your notebook. Remember: Your notebook isn’t just for you! Additionally, when we work together to troubleshoot your experiments, a good, detailed lab notebook is absolutely essential. I don’t like to micromanage, and a good notebook also allows me to avoid it. Great notebooks also make me confident in personalized career development. I want people to leave when they are ready, and a comprehensive lab notebook allows this to happen: you can move on to the next stage in your career, and the thorough documentation allows us to continue to build on your science within the lab. Although extensive notetaking may slow you down in the short term, it will definitely accelerate things in the long term. Main highlights:

1. Write your notebook so your work can be recreated solely from the information you record. Be very detailed.
   • Log plasmid maps, strains, oligos, storage locations, catalog numbers and batch numbers of kits, reagents, antibodies, peptides, enzymes, plates, etc.
   • Include calculations, times, temperatures, etc.
   • Screenshots or text of parameters used to run software
2. Use a naming convention to make finding your notes easier for yourself and others.
   • For projects: Initials_YearProjectStarted_ProjectName.
   • For subfolders and notes within, take advantage of alphabetical sorting with a numbering scheme. (see images below as an example)
     • Project Folder > Subfolder 1 > notebooks titled: 000, 001, 002, 003, etc. makes referencing old notes easy and makes linearity clear
     • Project Folder > A-01 > notebooks titled 01.0.0-A, 01.1.0-A, 01.2.0-A, etc. A nice thing about this is that you can see the title of the note in the ‘tabs’ and know exactly which folder to look for it in. For example, 02.3.0-B is a notebook entry found in folder B-02.
     • Use minimal nested folders within a project. Project > subfolder 1 > subfolder 2 is the furthest down it should go.
     • Currently, there’s no way to “peak” to see a folder’s contents without opening the folder.
3. Date everything. Date notebook entries and physical samples. This makes it much easier for you and others to retrace your steps. Plus, it makes using the calendar in Benchling easy to track items and work. (Must use “insert > new day” or “ctrl + \” for the Benchling calendar to work.) 4. Input all handwritten notes. Either type it out or attach a photo. 5. Record mistakes and things that don’t work. 6. Include data, both raw and analyzed. 7. Protocols should include: title, what the experiment sets out to achieve, materials needed with CAT numbers, procedure.
   • Copy a protocol to make changes and append a version number (v1, v2, etc.)
   • Add in the protocol’s intro what was changed and why
   • Lab protocols are in the top folder _Fraser Lab. If you create a new protocol that will be useful to anyone else in the lab, add a copy to the folder.

Data Deposition

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 cryo-EM 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
• Protein Diffraction - X-Ray diffraction images
• PDB - Protein structures
• GenBank - Raw sequencing data
• MaveDB - Deep mutational scanning (DMS) data
• Mave Registry - DMS experiments

As a scientist, it should be a pleasure to keep up with current literature. We believe should dedicate a few hours each week to scanning and reading new preprints and journal articles - and we recommend a strategy that leverages RSS feeds to follow the literature. This activity helps increase one’s breadth of knowledge. In working through these papers, we inevitably end up studying a small number more deeply, which includes scanning and reading the literature cited by that paper. This activity helps increase one’s depth of knowledge and supplements the project specific-reading we do in preparing for qualifying exams, writing fellowships/grants, and planning projects. Both breadth and depth of understanding are essential and staying on top of the literature using RSS is a gateway to accomplishing both. Every other week at group meetings, we have a mini journal club where each lab member shares 1 slide and a 60 second summary of an interesting paper they have read. Occasionally, we do journal clubs jointly with other labs to have an in-depth conversation about papers and methods of particular interest. When the journal club focuses on a preprint, we will summarize the discussion and post a public review.

I like to take an active role in the preparation of all our manuscripts and love to help people clarify their writing for fellowships and job applications. Many learners are often afraid to show PIs anything other than finished work. This is a mistake! I expect a draft to be very rough and a starting point to grow from. If you think it’s time to start a paper, let’s get in a room (or a zoom) and start hammering out an outline! I prefer to write in Google Docs. I like to use the Document outline features, Cross Reference for figures and tables, and Paperpile (importing by PMID so that metadata is consistent) for references. Let me know if you want me to track changes so you can see my edits, but note that I never want to see your changes tracked! If you are stuck writing, schedule a meeting and we can sit down with the document on the big screen and write together. This is one of my favourite things to do. We start by outlining section headings, then by writing topic sentences for each paragraph, then by filling in paragraphs with text. I find that adding references to sentences in the introduction early can be quite clarifying (always using an Author-Date reference style until the late stages). I generally do my best work with other people in the room. We will iterate a lot before we finalize a product. Sometimes my advice will focus on a specific piece of “bigger picture” feedback and sometimes we will wordsmith sentences.

Figures

Panels for figures should be as scripted as possible. I like to do layouts in Keynote, which is a good middle ground between no features (embedding in Word/Google Docs) and too many features (Illustrator). But there are lots of different workflows in the lab. Generally, as we write, I prefer that you embed the figures in the document and share a folder with the raw files (images, Keynote files, illustrator files, etc). For simplicity, when writing grants and papers, I prefer to embed figures in the top row of a 2 row/1 column table that extends the entire width of the page. The figure legend should be written in the second row. Other workflows are possible, but less efficient for me. However, it is also a way to expose me to potential new tricks/programs, so while I may lose patience, I’m willing to entertain it from time to time.

Authorship

I believe that conversations about positions in author order should occur early in a project. Communicate with me and I will help navigate these conversations with collaborator labs. I err on having more authors on a paper: everyone with a meaningful contribution must be included.

Resources on writing

• David Mobley Writing Tips
• David Mobley Style Guide
• Arjun Raj Style/Figure Guide

Sharing results openly and swiftly are keys to 21st century science communication. The real end goal of any research is to get the work out there for others to build on, not to publish in journals. We share openly at conferences, but recognize the role of publication as a more permanent and accessible form of communication. In publishing our work, we welcome peer review, but most importantly, we also maintain our own high scientific standards by posting preprints when we judge them to be ready for sharing. Posting preprints has important consequences for accelerating science. The traditional “behind closed doors” journal organized peer review process can delay the disclosure of important results by months. Moreover, it is often plagued with politics and biases that are harmful to the scientific process as a whole. Increasingly, I find myself most invested in the final push to posting preprints than in the subsequent parts of the process that lead to journal publication. Posting a preprint is under our control and a great time to celebrate as a group! However, the reality is traditional journal-based publishing still provides the highest visibility for work and coordinates review that can add value. Our current approach involves:

1. Disseminating our results via preprints
2. Celebrating and posting a tweetorial that explicitly welcomes reviews/feedback posted as comments on BioRxiv
3. Submitting for publication in traditional journals (selected by the first author, with preference for Open Access)
4. Responding to peer review from both the journal and comments
5. Ensuring that the final work is placed in repositories like PubMedCentral for open-access and that other materials and data end up repositories

This strategy embraces our “Beer AND Tacos” motto. We currently do both (post preprints and publish in journals). 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. JF is ready to skip step #3 (submitting to journals, above) whenever lab members decide they are ready to opt-out of the journal system. A current perceived roadblock is that preprints are not indexed in PubMed (although on ORCID Google Scholar etc). A secondary roadblock is that the term “preprint” rather than just “BioRxiv manuscript” implies that it is on the way to being complete rather than the manuscript of record.

We benefit from feedback on our manuscripts, most often in the form of journal organized peer review, and we are enthusiastic about offering our feedback to others to help improve their manuscripts.

Why review papers?

For our lab, we are motivated by the ability to potentially improve:

• the clarity of how the scientific results are communicated

• the contrast between what is supported by results and what is speculative

• the speed and transparency of the publication process

These values represent a change of focus from some traditional ideas of peer review that center on gatekeeping (“does this paper belong in nature?”). We want to write reviews that are constructive, empathetic, and respectful - and we think that this can be done in a way that enhances the rigour of the manuscript. Our process for writing reviews focuses on advice on reading manuscripts, writing the review, and editing ourselves so that our final reviews obey FAST (Focused, Appropriate, Specific, Transparent) principles to foster a positive preprint feedback culture.

Transparency in peer review

Accordingly, we believe that transparency in peer review can improve the speed, quality, and collegiality of the publication process. As such, we only review manuscripts that have been posted on preprint servers and we post our peer review comments publicly. We support other initiatives to improve peer review (such as Review Commons and FeedbackASAP.

Peer review as training

Peer review is also an important training opportunity for lab members in scientific thinking and writing. All lab members who co-review with JF are credited for their contribution to the review. Following our guidelines for drafting reviews, we iteratively revise the review to make sure it is constructive. JF is always happy to look over reviews and if he hasn’t meaningfully contributed, lab members are encouraged to post as solo review authors. We have also run a course on Peer Review in the Life Sciences.

Anonymity in peer review

Additionally, 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.

Responding to reviews

On the other side of the coin, How do we react to our reviews? We try to put ourselves in the shoes of the review. We assume the best intentions and adopt a default state that this offers us an opportunity to clarify the communication of our science. A detailed guide of how to respond to reviews is also available.

My mentorship philosophy is centered around making sure what lab members are doing is setting them up to grow for the position they want next. I view my job as to make sure that the lab provides: the resources to accomplish what they want to accomplish in the lab, an environment conducive to developing new ideas, and tailored support for the next steps in a career (e.g. tapping into my network, prepping chalk talks for faculty positions, etc). It also is important to think of this relationship as 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’.

As articulated in the mentorship section, my primary goal is to make sure each person can grow during their time in the lab in a way that sets them up for the position they want next. That position can be in academia, industry, other ventures, or even growth to new responsibilities within the lab. I view helping people to grow in their careers as being key to doing exciting science in the lab. As people’s career goals may evolve over time, I expect people to be engaged in a constant conversation with me about what they are interested in exploring. I think about “what’s next” as being such an important part of mentorship because knowing about someone’s longer term career goals (or uncertainty therein) allows me to tailor training, networking, conferences, and even aspects of their project around what we think can be most beneficial. We do a few things in the lab that help provide enough structure to ensure that these conversations happen for everyone at a regular interval.

• Every summer, each lab member has a 1:1 meeting with me to review their Individual Development Plan (IDP). In that meeting, we focus on how to line up your timeline, papers, training goals, and networking opportunities. This helps us to structure a discussion about career goals and how we can work together to achieve them. In the past, as preparation, I ask people to prepare for these career focused meetings by completing:

  • the ScienceCareers IDP

  • a lab summer survey

  • a review of the series of great activities that The Avasthi lab collated

• In the future, we are going to improve upon the summer survey by making the Science Careers IDP optional after the first year in the lab and by adapting the more questions from Stanford’s IDP and the DePace lab Yearly Planning Meeting.

• We have opted for once a year and not gone for more “corporate” style goal setting exercises, but it is something we might experiment with (perhaps only with a small subset of lab members) going forward.

  • But, we have started to include timelines in group meetings and thesis committee presentations. This activity helps to let other lab members know what you are thinking about as far as experimental planning, publication strategy, and career structure.

In addition, I love it when lab members prompt me for additional meetings to check in and discuss career development. The cadence and topic of these additional meetings can also change over your time in the lab.

In summary, I think people’s primary aim while they’re here is to align the science they are doing with setting 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.

Some General Advice for Postdocs

I think it is good to have a decisive plan about industry, academia or other career goals very early in your postdoc. It is fine to change directions, but having an initial plan allows us to discuss the adjustments that need to be made as your career plans to.

• For those pursuing industry after the lab, note that you can leave at any time! Aligning your publication strategy with a job search is not always required and often building specific skills or demonstrating capabilities is more important. I will help by exposing you to my network of industrial collaborators and friends to help you get a sense of the options and differences in company size, field, etc.

• For those pursuing academia, we will focus on two things: 1) how to align your pre-printing/publication strategy with your job search cadence. 2) how your independent research “brand” will be distinct from the directions my lab will continue to pursue. In pursuing both of these goals, we want to finalize research products that open up new territory. This often involves embracing intrinsically a higher-risk/higher-reward strategy. I will work with you to edit your applications, practice your talk/chalk talk, and be a resource for grant editing your entire career.

• For those pursuing other careers, I will often ask how I can help provide exposure (e.g. writing or presenting) and think about what aspects of my network can be most helpful. The UCSF Office of Career and Professional Development can also be helpful.

Some General Advice for Graduate Students

I find that 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. One important thing to note: the end game timing is extremely different for applying for jobs in industry (weeks to a few months before you want to start) vs. academic postdocs (generally at least 6 months before you want to start).

Graduate school is generally a time of career exploration and career direction changes. It is ok to not know exactly what you want to do post grad school! But, eventually you will have to/want to leave. Putting aside time every 6 months or so to evaluate your career likes/dislikes help you narrow down your choices and that occurs at the very least at our Summer meetings and during thesis committee meetings. One great way to narrow down what you want to do postgraduate school is to know what you DON’T want to do. This helps prevent the trap of only thinking about your career post grad school during your last year.

It is also important to think about activities outside of the lab that will help in your career development or career decision making process. These may include participation in a club, such as the Science Policy Group or a podcast group, becoming a teaching assistant at USF or SF State, or a leadership position within your graduate school program or club. UCSF also has some great course/exposure avenues such as industry internships, the MIND program, and start-up classes/clubs.

Some General Advice for Postbaccs/Technicians

The calendar for graduate and professional school puts strong constraints on your career development. Engage me in a conversation early about what you want to highlight in your applications. I and others in the lab will also take an active role in to direct their work, and I really like having a very constant back and forth about it.

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 grant writing resources on the internal lab website.

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.

We strive to give clear presentations that explain our scientific results to new audiences. We know that delivering a good presentation is hard work. Below we outline advice for structuring and delivering presentations, focused primarily on external audiences, noting modifications for internal audiences below. When planning a new presentation consider first:

1) Who is your audience?
(Fraser lab group members, other graduate students from your program, specialists in your field at a conference, people evaluating you for a job/fellowship, etc)

2) What question does your presentation answer?
(is the answer a key data take away, a clear next step you want to take, a shift in how we approach a problem, etc)

The key to delivering a good presentation is to develop it with EMPATHY FOR THE AUDIENCE. We want to make sure that we are delivering our main question (occasionally questions) in a way that the audience can understand and appreciate.

A good presentation, especially a good external presentation, is not about showing off or overwhelming folks with data. Holding back data and having extra data backup slides is a great thing to be able to use during Q+A. Rather, a presentation is about getting the audience to understand:

• WHY you are asking the question (Background),
• WHAT the barrier is to solving it (Yet more Background and early results),
• HOW you solved it and you relate it to the barrier/the broader question (your results),
• WHERE you would like to go next (future directions).

If you are struggling with how your work fits this framework, ask for help and we will talk about ways to structure your presentation.

It is important to note that sometimes in science, especially if we are being ambitious, the HOW section can be about to how you are not able to answer the question, yet! That is ok! You should still relate your results to the barrier you identified and provide context to the broader question you are asking. This is an opportunity to point the way forward with a strong WHERE section.

In general, the biggest problems I encounter are too much time spent on the details of HOW and not enough on WHY/WHAT. Defining the scope of the question and the key barriers to answering it takes a lot of practice to get right. Another problem I observe frequently is that the scope of the WHY/background section is often not right for the actual question the presentation seeks to answer: people tend to give generic background that is not actually relevant to the question they are addressing.

In building a presentation around WHY/WHAT/HOW/WHERE, your presentation should develop a coherent narrative arc. This should naturally orient the audience as to what the stakes are for the field or what contrast you are trying to draw to previous work. Not all advice from books on this is applicable, but there are some great texts on how to create more of this narrative contrast of what is blocking progress and how you overcome it in presentations.

This structure basic structure is expanded for longer talks as well. In a longer talk, there is usually a single broad narrative arc with sections of the talk that connect to each other. Ideally the talk flows so that each segment connects to the next with a WHY/WHAT/HOW/WHERE->WHY… structure.

Practicing

Once again, we know that delivering a good presentation is hard work. Therefore, practice, feedback, iteration are key to deliverying good presentations. In practicing, you will receive advice from many people - be grateful. It is wonderful to get feedback. But, don’t listen to all of it (even the advice on this page!). Pay special attention to those who say they didn’t understand parts of your talk - this is the most valuable feedback: use it to refine and clarify your message.

You will develop your own style in time. For example, different people have different rhythms of presenting. JF uses about a slide every 20 seconds. Others can spend 2-3 minutes on even very simple slides and are captivating speakers. There are lots of opinions out there on what makes a great scientific talk and how to design effective slides. You do you!

During practices, I find it is often helpful to have a copy of the slides (at least 4 slides per page) printed out for me to take notes on. This enables me to write notes that associate feedback with specific slides. If you can send them along, great - if not, no worries (either the raw file or a PDF with is fine).

When I practice a new talk for the first time, I WRITE EXACTLY WHAT I WISH I COULD SAY FOR ALL SLIDES. When I give the talk, I don’t stick to a script, but by writing out the talk once, I know the ideal version of what I would have covered. This exercise also helps to refine the content and flow of talks.

Feedback Teams

After each group meeting a rotating team consisting of 2-3 lab members will briefly give feedback on the presentation. This feedback should critically evaluate the construction and delivery of the presentation e.g. arrangements on slides, background, pace of speaking, the clarity of the points they are making, and the flow from one slide to another. The team should point out the presenter’s strengths as well as a few points to improve. As a member of the feedback team, you should also absorb the critique so that all our presentations benefit from participation.

Slide design

An overarching philosophy of mine is “Minimize text on slides”. Avoid walls of text bullet points and especially reading walls of text. The main text on a slide should be a single Title sentence at the top of the slide. This should be different for every slide and be a single sentence using simple and active language. You should be able to read the titles of the slides only and have a pretty good understanding of the talk. Do not rely or count on being able to use a laser pointer ever. Better to just avoid using laser pointers all together. If you design your slides so that there is only one thing to concentrate on at a time and that thing is obvious, then you don’t need a pointer. Making good, visually simple slides is hard and will take a lot of iteration. It is related but distinct from making good figures for your paper. Note: You can consider a slightly different balance of text on slides if you are distributing the slide deck without presenting it (e.g. to a company). But in this case, it is good to have 2 versions of your slide deck, one text light (for presenting) and one text heavy (for distribution).

Handling Q+A

Be nice and don’t get stressed if someone misinterprets the talk (that is an opportunity to clarify for next time). Try not to be defensive in answers. It’s hard work! Start by rephrasing the question. This is a good practice in the zoom age and also makes sure you are answering the question they intended to ask. Get used to using the slide navigator in presentation mode so that you can quickly broadcast a relevant (and often backup!) slide in response to a qustion. Be honest, but have fun! If you don’t know or can’t yet address a question with data, it is ok to speculate a little. Just be sure to clearly distinguish speculation and answers grounded in data or prior literature.

Special considerations for non-external talks

• Group meetings:
  • Start with the Minute for Diversity slide
  • Resist the urge to have too much background. If you are worried about new lab members not having enough context, invite them to coffee before and talk to them about the project or show your last intro. Accordingly, we expect internal presentations to spend a bit less time on WHY than for an external talk.
  • Internal talks are an opportunity to “data dump” a lot more than in an external talk. Show the warts! Tell a story of not only what you learned, but also of what didn’t work along the way.
  • You can spend a lot more time on WHERE you are going next with your research. This is your best opportunity to get feedback on next directions.
  • We like the overall title of the presentation to be in the form of a question.
• Thesis committee Meetings:
  • Have a plan for what you would like to discuss for the “advisor outside the room portion” - even if that plan is to say “everything is going fine”
  • The background should not be too general and you shouldn’t spend too much time on what has worked. This meeting is to get advice about what isn’t working and what’s next!
  • Include a Timeline! Where are you on the Path to PhD? What papers do you anticipate trying to write and when? When are you going to look apply for what’s next? (this might also be good to include in Group meetings!)

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.

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.

Resources

If you are in need of support, there are mental health resources provided by UCSF for students and staff. Additional resources, including those listed above, can be found in Resources.

Within the Fraser lab

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.

Beyond the Fraser lab

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 commitment 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.

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.

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.

This development of this compact was guided by similar compacts and philosophies of several labs, see links.

• Avasthi Lab, Dartmouth College
• Heemstra Lab, Emory University
• Matreyek Lab, Case Western Reserve University
• Moghe Lab, Cornell University
• Syed Lab, University of Minnesota
• Mentoring resources, University of Wisconsin-Madison ICTR