Expectations of group members
Core expectations of respect
I expect you to provide a respectful environment for everyone here, irrespective of race, color, religion, sex (including pregnancy, childbirth, and related medical conditions), gender, sexual orientation, gender identity or expression, national origin, ancestry, ethnicity, age, physical or mental disability, citizenship, marital status, genetic information, genetic status or characteristics, military or veteran status, or on any basis protected by an applicable law (a “protected characteristic”).
Please contact me as soon as possible if any issues come up, irrespective of if they happen in the context of our lab or not. I promise to listen and respond. If for any reason you feel uncomfortable contacting me about a problem, or if I have done something wrong, please contact the head Comp Bio admin Melissa Alvendia and/or one of the reporting options described in the Fred Hutch Open Door Policy. Note that Fred Hutch has explicit policies protecting people reporting issues from retaliation.
We are humans, not science robots.
- We love vigorous scientific discussions, but let’s be careful to do so in a respectful way that helps people grow.
- People come from different backgrounds with different training. Lack of expertise in a given area is no excuse for treating someone disrespectfully. Let’s work to advance everyone’s understanding.
- Your mental health is important! Learning how to keep equilibrium in a challenging environment is one of the core life skills, and I hope your time in the group helps you learn that skill.
Rigor and reproducibility
We must uphold the highest principles of scientific rigor.
- your conclusions to be an honest assessment of what you have found
- complete transparency with me if you find out a problem with something you have done, even if it’s after publication
- analyses to be performed using code that gets committed to a repository (if you are developing a software package this can be a second repository just for that paper)
- code for publications is made available upon submission of the manuscript, and made open upon publication of the manuscript
- computational experiments are made reproducible using a system that makes sense according to your project
- all files needed to reproduce your work, possibly including intermediate files, are compressed and uploaded to economy file storage.
How the group works
My overall goals are
- for you to become an independent researcher, and to help you make your next career step be the best it can be
- for the group to do top-notch science, with strong research productivity
- to foster an environment that enables you to be happy and productive
- to protect you from BS and to give you as much freedom as possible.
What I will and will not do
I aim to be a resource for your growth and for your work.
- I will respond to messages and turn paper drafts around promptly
- I love consulting on code
- I am always happy to meet with you
- I will do everything I can to assist your career development
- I will be a sympathetic ear with any personal problems you may have
- if there is something I can do to help, please ask!
Early on I will want to meet with you frequently to kick-start your projects. After that, we will discuss the best frequency for meetings.
- I am not omniscient: I only know what you tell me about how things are going
- I have no training on counseling for personal issues, but will be more than happy to help you find counseling should you need it
- I do not aim to be a role model for you about how you balance your work and the rest of your life. Personally, I love being with my family, I love working, I stay fit, and I work to advocate for environmental causes. I structure my life to maximize the time I spend on these things. This means that I will probably work more hours than you. I will send you messages in the early morning and on weekends. I do not expect you to read or respond to these messages outside of your work time, nor do I expect for you to start especially early or work on weekends.
Choosing your project
Project choice is the biggest determinant of success. A poorly scoped project takes much more time, especially in the peer review phase, than a well-scoped one.
Therefore we must ask
- Will this project provide real value either to end users (typically biological researchers) or provide a substantial addition to theory?
- Is it complementary to existing work in the field?
I encourage you to write the introduction to your proposed paper first, addressing these questions, before writing any code.
Expectations concerning work
If I am employing you full-time, I expect you to work the equivalent of standard full-time job. If you wish to work more, that is up to you. I also want you to have rich experiences in your life, so I encourage you to pack a bunch of work in and then take a block of time to go do something interesting. I don’t need to know the details of your vacation days, but if you want to take off a block of time, please let me know in advance.
I encourage internships when you pause your work in the group and try out another position, but when I am supporting you I expect that your position in the group is your sole source of employment. Similarly, I understand that you may have some things to finish off from your PhD or previous postdoc, but I expect that while you are in the group your focus will be on group-relevant projects. If you have questions about this expectation, let’s chat.
I wish for you to feel the joy of focused work. There are many distractions available at our computers, and I truly believe that you will be happier if you can keep those at bay. I have found the Pomodoro Technique, with 30 minute intervals interspersed by 5 minutes of something in the real world (away from phones and computers) to be very effective for enhancing flow. I encourage you to turn off Slack (and Twitter, etc) notifications, or at least modulate them: I’d rather allow you to focus and get a slow response rather than the other way around.
You will undoubtedly hit roadblocks or confusion on your project. I expect that you will think about how to get around them, and get in touch with me when you are having difficulty. If these roadblocks are external (e.g. waiting for data, or a computer problem) think long-term: could you be using your time to write or do something else to advance your projects?
Let’s make the group better
I love feedback of any kind, at any time. Please let me know how things are going, or email Melissa (see link above) if you don’t feel comfortable telling me directly. I will do periodic surveys to see how we can improve the group, and how I can improve as a PI, but don’t wait for the next survey if something is bugging you.
We are extremely lucky to have a talented and productive network of collaborators. Many of these collaborators are lab-based, setting up a symbiotic relationship: we depend on them for data and problems, while they depend on us for analyses.
I expect you to:
- Treat all collaborators with respect, no matter their level of computing or math expertise.
- Be responsive, and not drop the ball. Please respond to any emails within 48 hours, even if only to give a time estimate of when you can finish an analysis.
- Move analyses along promptly. This doesn’t mean that you have to drop everything you are doing every time they show up with data, but please do plan ahead and try to get things done quickly. Planning ahead may mean working with them to develop an analysis pipeline on alternate data before the real data shows up.
- Think about how we can make a win for them. Can we go beyond the original question they want to answer? Can we have a two-way conversation between experiment and analysis to write a joint paper?
- Respect their data. Data sets can take a lot of work to obtain, and we need to respect their wishes regarding how it gets used. Please be careful putting data in git repositories that may eventually become public: this can be OK, but we need sign-off from both the person generating the data and the PI before doing it.
The broader scientific community
Our goal is to advance science. Science benefits if our interactions with other research groups are constructive and rigorous. Keep these goals in mind when communicating in any medium: papers, paper reviews, email, or social media.
An offer of co-authorship should be extended to everyone who made a meaningful contribution to a manuscript. This is necessarily vague, as every project is different, however we in general work to be generous with co-authorship. Certainly if you contribute analysis or code to a project you will be a co-author. If our lab-based collaborators help design and scope a project, they should be co-authors.
In projects with many authors, we will set up author order as soon as it’s clear what needs to be done. If this is not being done, please mention it.
In cases where there are several contributors of approximately equal contribution, we will prioritize people based on career advancement: how much does this paper mean to this person’s career?
Keeping track of progress towards your career goals
Please post a summary of your work in #general every two weeks. If there is something that you don’t feel comfortable posting in a public forum, please send me a direct message.
You are required to do a yearly individual development plan (IDP). Eli has posted a template here which you can customize to your liking.
I also suggest taking some time every quarter to do a “mini-IDP” by answering these questions:
- What are the big steps required to advance to the next stage of your career
- What will you do in the next 3 months to advance those steps
I expect that you will budget enough time before you leave to archive your working files and upload them to economy storage.
I cannot accept gifts from trainees, no matter how sweet they are. Your research effort is the greatest gift.
I invite any comments on this document. Please let me know your thoughts!