Beehive handbook

The BEEHIVE Handbook

Zoom

The BEEHIVE Zoom link: https://gladstone.zoom.us/my/beehive

Lab values and culture

We promote a culture of warmth, celebration, and creative rigor in our work and lives. We nurture each other, we do not tolerate internally competitive or antagonistic behavior, and we raise each other up, both in learning and research, and also in our lives and careers. We play the long game. We develop methods and have a clear research agenda. We are good collaborators both within the group and with outside collaborators: We communicate our needs and abilities, ask questions, set expectations, and respect our own or externally-created timelines. We do not work with collaborators who do not respect the independence of our work and our expertise. We set ourselves up for doing research that has a positive impact on health and disease, with a focus on understudied populations.

"And all for love, and nothing for reward." —Edmund Spencer

Getting Started in the Lab

Website

Let’s get your name and picture on the website! Slack me your photo and info, and I’ll add it.

Setting up meetings with Barbara using the group calendar

Please check the calendar for the group meeting schedule. Ask Barbara/Liz for access to the lab calendar. Add your time to an available slot (or step in during Undergraduate Office Hours) marked with “meetings.” I am generally at Gladstone T/W and Stanford M/Th, and I float around on Fridays.

If you don’t add a meeting to the calendar, and don’t see it is there, assume that I don’t know about it. In other words, feel free to add meetings that we schedule with collaborators!

Group Meetings

Day, time, locations, presenters, papers to read: Group meeting spreadsheet. Make sure you are accessing the correct year/season. Don't be afraid to ask questions! Others probably have the same ones.

Group messaging

Staying connected with the lab/ask questions: Download Slack on your computer/phone or simply use the web browser (less intrusive). Feel free to sign up for the messaging platform Slack with an @stanford.edu or @gladstone.ucsf.edu email. You probably want to change your notification settings so you don't get spammed with emails. Liz is in charge of slack so feel free to ask her questions!

Create a GitHub account

Much of our work culminates in a method and a set of vignettes. These should all be developed and released publicly in GitHub. If you don’t know how to use GitHub, please check out tutorials, ask around, or take a short course on version control.

Computing

Sherlock Cluster (Stanford University)

The Sherlock Cluster is a free cluster for low- or moderate-risk data at Stanford. The lab has a folder on there, so please feel free to sign up for it. If your data are high-risk, you must use the Nero Cluster. Talk with Barbara to get a folder set up there.

If you use the Sherlock cluster for your research, please add the following to the acknowledgements for your paper: ‘‘Some of the computing for this project was performed on the Sherlock cluster. We would like to thank Stanford University and the Stanford Research Computing Center for providing computational resources and support that contributed to these research results.’’

Wynton Cluster (UCSF)

Currently you will need to be affiliated with UCSF to have access to Wynton. More soon.

The BEEHIVE Cluster (Gladstone)

We have our own local cluster at Gladstone! We are putting together a page to describe how to access and use this cluster. More soon.

How we work together

Letters of Support

It is expected that I will write you letters of support for internships, grant applications, and job applications. Please give me at least four weeks notice before this letter is due. Please send me your application and current CV. If you are a student, please send some version of your transcript. Feel free to remind me (and Liz!) as the deadline approaches.

Writing papers

I generally write papers on Overleaf. I have a paid account, so there is version control and change tracking, and I’m happy to start projects so we can get those features for the projects. I wrote up my writing notes, and I’d suggest to read them over as you write a paper with me to avoid having me tutorialize things like “how to write a methods section” during our work time together. Do not submit a paper with my name on it without me explicitly signing off on that submission. I have pretty strong opinions on how to write papers (clearly, for first year grad students, and structured well), so please write collaboratively with me and not independently.

Deadlines for papers and abstracts

I expect complete paper drafts to me two weeks minimum before a deadline; it is possible I will not sign off on a paper even then if the paper is not ready. I expect a complete abstract draft to me one week minimum before a deadline.

Paper submissions

I often like to submit papers as I like to shield you from harsh reviews/rejections as much as possible. Happy to discuss this policy though!

Paper revisions

I believe that a revision is often more important to get perfect than the original submission. Let’s talk through how to approach revisions, and complete them in a timely way together.

Conferences and workshops

I am happy to support your attendance at three conferences or workshops a year, with the important caveat that you have submitted something to present on your work with me at that conference. Please keep your eyes open for appropriate workshops and conferences for your research and career goals, and get my explicit sign off in advance of submission.

Open Science

I am a strong believer in open science, and I believe my record of open science reflects this. Furthermore, there are rules from funding agencies, including the NIH, that require some level of open science. To this end, I request the following:

  • We enter into collaborations where, ultimately, we can share some aspect of the data without compromising the study participants.

  • Upon submission, we make code and pipelines publicly available on GitHub

  • Upon submission, we attempt to deposit the manuscript (suitably anonymized) into a preprint server

  • If people ask questions or have comments about our public work, we make a genuine attempt to respond to them.

Administrivia

Expense reporting

Because I hope to sponsor so many people for so many conferences, please choose wisely and try to find affordable travel/lodging options. Don’t assume I will reimburse other expenses unless it is approved in writing prior to purchase; I too have to get approval before making purchases.

Gladstone: email Liz and cc me. You must include receipts.

Stanford: email Jess and cc me. You must include receipts.

Requesting meeting room space

Gladstone: ask Liz.

Stanford: ask Jess.

Email lists

It's a good idea to sign up for a few mailing lists that announce talks related to the groups research.

Rotation students: Expectations

Rotation student funding If you require funding as a rotation student, please let me know at our first meeting.

When I work with a rotation student, I primarily look for the following things (more so than 1 care about a clear research win on your project), not in any order: 1. good communication; 2. good collaborator and mutual learning — let me ask questions too; 3. able to finish things and press submit; 4. openness to ideas and constructive criticism; 5. organization and proactively seeking out what they need to succeed, including funding; 6. someone who cares about professional and personal growth; 7. patience; 8. kindness; 9. good preparation and attitude about research and uncertainty; 10. knows how privileged they are to be at Stanford, and at the same time knows how deserving they are of this privilege.

PhD students: Expectations

I expect you to advocate for yourself when you want or need something

I expect you to be curious and ask questions when you are confused (or interested!)

I expect you to be a good collaborator with me and your labmates

I expect you to seek out biomedical collaborators, and cool data, and funding opportunities, and courses, and conferences – and to communicate these opportunities with me before committing

I expect you to know your program requirements (students) and be on top of them

I expect you to accept kind and well-intentioned feedback

I expect approximately a paper a year (preprints count)

PhD Funding

There are a lot of funding opportunities for PhD students; I expect you to apply in your first and second years. These include:

  • Knight-Hennessy (first year students)

  • PD Soros

  • NSF GSRF

  • GEM

  • NSRA (F31 NIH)

    In later years of your PhD, often opportunities arise (Apple, Facebook, Google, Microsoft fellowships) that you may have to compete internally for; please let me know if you’d like to be considered for one of these!

Postdocs: Expectations

I expect you to advocate for yourself when you want or need something

I expect you to be curious and ask questions when you are confused (or interested!)

I expect you to be a good collaborator with me and your labmates

I expect you to seek out biomedical collaborators, and cool data, and funding opportunities, and courses, and conferences – and to communicate these opportunities with me before committing

I expect you to communicate your career goals (as they arise) and your constraints

I expect you to accept kind and well-intentioned feedback

I expect that you may have residual work from your PhD, and I acknowledge you may spend a lot of time on that in your first year. I expect the same amount of grace will be shown to our work together when you move on from my lab with some dangling threads.

I expect approximately a paper a year (preprints count)

Postdoc Funding

I expect postdocs to write grants for funding when they show up and as appropriate funding opportunities arise. Funding for postdocs include both strictly postdoc funding and pathway to independence funding, the latter of which supports some amount of postdoc time and some amount of tenure-track faculty time.

  • NIH F32

  • L’Oreal Women in Science

  • HHMI Hanna Grey

  • Cancer Research Institute

  • Jane Coffin Childs Fellowship

  • Helen Hay Whitney

Pathway to independence funding

  • NIH K99

  • Burroughs-Wellcome

What you can expect from me

I am aligned with your career goals & ask you about them regularly

I will tailor decisions about your work to those career goals

I will give you advice for research/conferences/papers/jobs that I believe will help you accomplish your career goals and not mine

I do not believe I can make decisions for you. But I love discussing pros/cons of any decision that is hard for you.

I am hands off, but (generally) available. You can access my calendar – always make a meeting during my meeting blocks when you want advice or we need a whiteboard discussion about your work.

I will be a good collaborator to you (acknowledging I’m spread thin)

I will accept kind and well-intentioned feedback

In short, I have over a decade of experience working with students and postdocs, and I have a good track record of group members graduating on time and ending up in positions they want. You should feel you are able to rely on this expertise as you go through your program or time in my group.

Getting your cover article displayed at Gladstone

Email Meg McDevitt at Gladstone to ask if you could get it put up in the Gladstone Lobby at 1650 Owens! Nominate yourself!

Questions?

If you have any questions, please consult the FAQ. You can send technical or website questions to apiary2011@gmail.com (just a forwarding address to Barbara & Liz) and any group related questions to Barbara.