Lab Handbook


I’m so glad you’re intersted in the lab. Whether you’re a prospective student or postdoc, a current lab member, or just someone who’d like to see more about our inner workings, here you’ll find an overview of how we do our thing.

Mission, expectations, and values

Our mission

Our mission is to conduct rigorous, impactful science for the public good. Our approach to that includes:

  1. Building up our society’s intellectual and physical capacity to anticipate, manage, and heal from crises, especially as they relate to infectious diseases;
  2. Conducting our research in an open, honest, and responsive manner;
  3. Fostering a healthy scientific community both within and beyond our lab.

Academic integrity

Scientific integrity is of the utmost importance, especially when dealing with research questions that by definition can have far-reaching impacts on many peoples’ lives. It’s OK to be wrong; I’m wrong all the time. The important thing is to learn from our mistakes, to humbly accept criticism, and to defend our ideas based on their own merit rather than by our personal stake in their success. At a baseline, this means to never “fudge” data or images, to post the maximum amount of code and data that doesn’t compromise privacy or safety, and to respond to reasonable requests for information from other scientists.

People can sometimes be unnecessarily and unhelpfully critical, especially in the age of social media. Twitter is an amazing communication tool and yet it can be a frightening place. Online confrontations are often a major test of integrity. Academic integrity requires personal integrity in all of our scientific dealings, both online and offline. If someone has said something annoying, write out your unfiltered thoughts in a private text document and then wait to write your actual reply until you’ve cooled off. If someone has said something offensive, hateful, or threatening, tell me or someone else who you trust, and we’ll deal with it together, immediately.

Equity and Justice

For our purposes, equity involves providing to each according to the needs of each, and justice is essentially long-term equity, achieved through systems-level change. Both are key pillars of our lab, guiding both the work we do and the way we do it. We work towards these aims in the following ways:

  1. Outreach: There remain huge disparities between the overall demographic composition of the U.S. and the demographic composition of the people who pursue higher education and academic careers. This ultimately puts a limit on our ability, as researchers, to be as scientifically creative and socially aware as we might otherwise be. One of the most fundamental ways we can help to address this issue is by sharing what we do with students who might not otherwise see scientific research as a viable career option. We’ll schedule periodic outreach activities at schools in the Denver/Boulder area as well as in rural districts to do our part to close this gap.
  2. Recruitment: I aim to maintain a diverse lab with trainees from a wide variety of backgrounds. Lab openings will be posted publicly to try to draw from a wide pool of applicants. This is an area where I’m actively trying to learn, since I don’t yet know how best to advertise to prospective trainees from underrepresented backgrounds. If you know of any schemes or have any suggestions, please do let me know!
  3. Lab community: As a lab, our greatest resource is each other. I will provide various opportunities for lab members to share about their life experiences, from what they’re currently experiencing to what got them to where they are. Each new lab member will have the opportunity to use their first lab meeting to share a bit about who they are, where they came from, and what they’re aiming towards. The aim of this is to get us thinking about how other people experience the world and to bring that experience into our own daily workings.

    Also, it’s one of my highest priorities to make sure that each lab member has the resources they need to feel fulfilled and at the top of their game. I’ll do my best to anticipate what those things are, but if there’s anything I’ve missed, please don’t hesitate to let me know and we’ll work to address it. I encourage you to think broadly about this – whether its some piece of technology, a change in our meeting times, a change in the vocabulary I or other lab members are using, suggestions for how to navigate healthcare resources, or just some time off, we can figure something out. I recognize that not all lab members will need the same things – this is one of the principles of equity – so I want to make sure that, whatever it is you need, you’re getting it.

  4. Research: We are public health scientists, and as such, issues of justice and equity lie at the heart of our research. I encourage trainees to think deeply about how their research will impact various communities and to bring that thinking into both their analysis and their write-ups of their work. Many of our research problems will involve optimizing something, and I encourage trainees to think about what “optimal” actually means – is it a reduction in overall morbidity and mortality? For whom? At what costs? Could it backfire? Will it help reduce existing inequities, or could it exacerbate them? Whenever possible, I encourage trainees to incorporate these sorts of questions formally into their analyses.

My expectations of lab members

The rest of this document contains more detail on my expectations of lab members and my expectations of myself, but in brief, I expect that lab members will:

  1. Speak and act respectfully towards their colleagues, collaborators, and the public;
  2. Put their best effort into their work;
  3. Communicate responsively;
  4. Conduct their research in an open, honest, and rigorous manner;
  5. Let me or another trusted mentor know if they are facing any challenges that they are unable to resolve on their own, and especially if they feel they are being treated in a way that makes them uncomfortable;
  6. Think creatively and deeply about how they can best support the public good, through their research and other academic work.

My pledge to lab members

In turn, I will:

  1. Speak and act respectfully toward all lab members, colleagues, and the public;
  2. Respond to good-faith requests for changes in how I act or speak;
  3. Communicate responsively;
  4. Provide feedback on work in a timely and gracious manner;
  5. Support your career development with guidance, letters, and introductions to colleagues;
  6. Maintain a physical and social lab environment that is conducive to enjoying the process of producing good work, and prioritizing your well-being above all else.

Lab life


  • One-on-ones: I meet with new graduate students (during their first year) and new postdocs (during their first three months) weekly. After that period, it’s up to the student/postdoc whether they’d like to continue meeting weekly or if they’d prefer to transition to every other week. Please send a brief agenda before each meeting (via Slack) to keep us on track. Meetings are 45 minutes, so that I can use the last 15 minutes to jot down notes about our conversation, send follow-up emails, and prep for the next meeting. The time is yours: I expect to spend most of our time talking about research, but feel free to bring up other career- and life-related things too!

  • Lab meetings: Once our lab reaches a critical mass, we’ll begin having weekly lab meetings. These meetings will be research-focused and oriented towards workshoping projects that are ongoing. Each week, a different lab member will present. The aim is for them to be maximally useful to the presenter. The meetings will last for an hour (we’ll do everything we can to not exceed that), and it’s up to the presenter to decide how best to balance between formal presentation and discussion/questions.

  • Research practice meetings: Once per rotation, we’ll replace one lab meeting with a “research practice” meeting. At each of these meetings, we’ll discuss a different topic related to various tasks of doing science, such as making presentations, writing manuscripts, using LaTeX, formulating compartmental epidemiological models, and so on. I’ll begin by giving a brief introduction to the topic and then we’ll open up to a discussion where lab members can share tips and tricks they’ve learned along the way.

  • Social justice meetings: Once per rotation, we’ll also replace one lab meeting with a “social justice” meeting, since health is about more than just disease, and more than just modeling. At these meetings, we’ll discuss a reading (to be chosen by lab members) that helps us to think more deeply about our citizenship in the lab, university, and our larger communities. Readings may focus on diversity, equity, inclusion, political advocacy, community service, and related topics. They should help us think imaginatively about concrete positive changes we can make to improve the lives of those around us.

Working hours

  • I expect lab members (including myself) to be semi-responsive electronically between 10am-4pm on work days (don’t worry, I won’t be timing your response time – just try not to be totally checked out).
  • I also expect lab members (again, myself included) to be physically in lab at least three days per week – the more the better!


  • Outside of meetings, most of our lab communication will happen on Slack. Please check Slack regularly, and let me know if you have any difficulties with using it!
  • Our lab directory, meeting calendar, and vacation logs will be housed on Google Drive.
  • I will periodically send emails, especially when forwarding information that I first received via email.
  • Virtual meetings will happen on Zoom.

I’ll do my best to limit our communication to these channels to avoid things getting overly complicated.

Social activities

Periodically, we’ll do fun things that aren’t related to modeling and diseases, like hikes, meals, and pub trips. We’ll do our best to make these accessible to everyone. These activities are not mandatory, and while I’d love for everyone to join, I recognize that people have other responsibilities, which may include simply taking some time at home to stare at a wall. That’s ok, I need that sometimes too. If for any reason you feel like you’re being excluded from social events, come talk to me and we’ll make a change.


Once per year, we’ll go on a lab retreat. Unlike social activities, this is something that everyone should make an effort to attend. These will be day-long, off-campus events during the work week where we have a bit of time for fun and a bit of time for science. The science portion will involve celebrating achievements over the past year, listing ongoing projects, and dreaming up new things for us to work on. We’ll also take some time to discuss lab culture and raise anything that needs to be changed.


In my experience, when trainees are told to take vacation on an as-needed basis “as long as they’re getting their work done”, it means that… they never take vacation, and when they do, they feel super stressed about how they should be working instead. I want you to take vacations (please!), and I want you to enjoy them. Toward that end, you’ve got 15 vacation days per year, in addition to weekends and school-sanctioned holidays, to use as you see fit, no questions asked. I’d appreciate if you let me and any other collaborators know when you’ll be away with some advance notice so that we can plan ahead, but no need to justify, and no need to tell me your plans (though I’d personally love to hear about whatever fun things you get up to!). Log your days on the Google Docs sheet, and do your best to use them all! If you end up needing more, let’s have a chat and I’m sure we’ll find a good way forward.

Sick days

We’re a lab that studies infectious diseases, so if you’ve got an infectious disease, or anything else for that matter, please stay home, and please rest. These don’t count toward your vacation days, and there’s no need to log them - it’s on an honor basis.

Personal development plans

Every six months, I’ll devote a one-on-one meeting to discuss progress, short-term goals, and long-term aspirations with lab members. I ask each lab member to fill out a short reflection prior to these meetings to make sure we get the most out of our time. Like our regular one-on-ones, this is your time, so let me know how I can be of most use to you!

Research best practice

Open science

I am a firm believer in making scientific discovery accessible to all. Our code is posted on public repositories on Github and our manuscripts are posted on preprint servers to ensure the widest possible access. If at any time you feel like I’m not living up to this ideal, let me know and I’ll make a change.

Writing code

Open code is one key part of conducting open science. Github is our lab’s tool of choice for achieving this. It’s ok to keep your code repositories private while they’re under construction, but I encourage everyone to make their full version histories public once a project is submitted for publication. It’s helpful to keep this in mind from the start! See Guidance for developing code for more detailed information.

Documenting research

We need our science to be reproducible, which means ensuring that lab work is sufficiently documented for members of the group to hand off projects to one another when necessary. Toward this end, each member of the lab will have a personal repository on Github where they’ll keep a running lab notebook. You can include as much in this notebook as you like, but at a minimum it should include enough information to re-create your thought process as you worked through various research problems. See the Guidance for developing code for pointers on how to set up an online lab notebook on Github using Markdown.

Writing manuscripts

Good scientific writing is as important as the science itself. I strongly encourage lab members to start writing as early as possible, since writing often helps to clarify thoughts and highlight key gaps in a project. I expect trainees to supply a fleshed-out first draft on their own, after which we can iterate back and forth with edits and revisions. I am competent with LaTeX (Overleaf is especially good), Microsoft Word, and Google Docs; feel free to pick whichever one is most suitable to your project and your skills. I’m a big fan of the IMRAD format (Introduction, Methods, Results, and Discussion) – please, no results immediately following the introduction. I’ve collected some pointers on writing good scientific prose on the Guidance for writing manuscripts page.

Giving presentations

Presentations are a key part of scientific communication. I aim to give lab members ample opportunities to present their work to a variety of audiences. Internal talks need not be especially polished, but external ones should be. See the page on Guidance for giving presentations for more info.

Public engagement

I strongly support taking opportunities to share research with the broader community. This might include giving presentations to high school groups, hosting science fairs for elementary kids, or writing popular science articles. Beyond research, I also strongly support lab members taking time to serve the community in ways that complement our research aims, like volunteering to help distribute information about vaccination clinics and advocating for public health reform. Our primary aim as a lab is to conduct good research, but feel free to devote some of your “work hours” to these aims too.

Physical resources

High-performance computing

See the OIT’s page on research computing for guidance on using the heavy-duty machinery.

Lab space

Lab members will have a dedicated desk on the first floor of the Engineering Center. Due to the odd configuration of the engineering center, my office is across the common area in a separate wing of the Engineering Center, but I’ll aim to stop by the lab space twice a day. Feel free to come knock on my door anytime and I’ll brew you a fresh cup of coffee or tea.


  • Epidemics: Held every two years, this is the central infectious disease modeling conference.
  • Ecology and Evolution of Infectious Diseases (EEID): Annual conference that brings together a wide range of quantitative ecologists; always funky, always fun.


Below is an incomplete list of recent collaborators with whom I can put you in contact, if it would be helpful:

  • Dan Larremore (CU Boulder): Infectious disease dynamics, science of science
  • Aaron Clauset (CU Boulder): Network science, science of science
  • David Bortz (CU Boulder): Mathematical biology, applied mathematics
  • Yonatan Grad (Harvard Chan SPH): Infectious disease dynamics, pathogen evolution
  • Marc Lipsitch (Haravard Chan SPH): Infectious disease dynamics, public health policy
  • Julia Gog (Cambridge): Infectious disease dynamics, applied mathematics
  • Sarah Cobey (U. Chicago): Infectious disease dynamics, pathogen evolution
  • Petra Klepac (LSHTM): Infectious disease dynamics, structured populations
  • Bryan Grenfell (Princeton): Ecology and evolution of infectious diseaes

Funding opportunities

Graduate students

  • F31: NIH training grant for research in the health sciences.


  • F32: NIH training grant for research in the health sciences
  • Life Sciences Research Fellowship: Training fellowship for basic life sciences research.
  • Burroughs Wellcome Career Award at the Scientific Interface: Training fellowship for research at the intersection of the life and computational sciences, bridging the late postdoctoral and early faculty period.

Where to go for help

If you have any questions or concerns about anything at all, you can reach out to Stephen ( anytime. If you need to talk to someone who’s not Stephen, you can reach out to Dan Larremore ( or Ken Anderson ( Also check out the resources available at CAPS, FSAP, the BOLD Center, and Wardenburg.