Welcome! We are the Edge lab, a group of researchers studying evolutionary genetics at the University of Southern California (USC). We use mathematical, statistical, and computational tools to study the sources and consequences of genetic variation. Doc Edge (principal investigator) is part of USC’s Department of Biological Sciences (BISC), and part of the Quantitative and Computational Biology (QCB) section, which administers the Computational Biology and Bioinformatics (CBB) graduate program. We’re thrilled that you are interested in our work and considering joining the lab.
This short handbook starts with a statement of our purpose and general principles. The next section spells out what lab members can expect of me, what I expect from lab members, and general lab policies. Every situation is different, and I might make a decision that runs counter to stated policies (for example, regarding authorship) from time to time. (This handbook was influenced by the lab policies of my previous mentors, Noah Rosenberg and Graham Coop; by Mohamed Noor’s lab policies, as detailed in his book; and also by this essay by Florian Markewitz.)
Our group exists to train people to study genetics—especially evolutionary genetics, which is one of the most exciting areas of science—using quantitative approaches. Early evolutionary geneticists developed beautiful mathematical theory but had little data to work with. Genomic data have become widely available in the 21st century, and we now have a chance to use all that beautiful theory as a lens to understand it. In addition to providing insights into how evolution can unfold and has unfolded, evolutionary geneticists have important things to say about an incredibly wide range of application areas, including antibiotic resistance, cancer, infectious disease, climate change, biodiversity conservation, agriculture, forensics, and others. Evolutionary genetics can even inform the way we think about ourselves as humans—our history, unity, and diversity.
Training in the lab happens primarily via research projects. Trainees all carry out original research and present it in the form of publications, software/scripts, talks to scientific audiences, and outreach to diverse audiences and the general public wherever appropriate.
Our core principles are integrity, growth, joy, and community.
Integrity means that we conduct our scientific work honestly and transparently. Honesty means that lab members are expected to be clear and accurate about how they conducted their work, what limitations it carries, and what kinds of conclusions are warranted. Transparency means that we do our best to make our research products available to other scientists and the wider community, including not just papers but also data and code.
Growth means that we take our status as a training environment seriously. We choose projects and structure our work in a way that helps trainees get to where they want to go, whether that means academia, industry, nonprofit work, government work, or something else.
Adopting joy as a principle means that we aim for a state in which we are not just growing as researchers, but also enjoying ourselves. However, this doesn’t mean that everyone has to smile all the time. There are many things that can make it difficult to have fun doing research, including burnout, anxiety, workplace conflict, impostor syndrome, difficult situations in life outside the lab, and others. We do our best to support each other, removing or minimizing barriers to finding joy in our work.
The last principle is community. We gain by engaging with each other as labmates, with our immediate colleagues at USC, with other people working in our wider field, and with the public. We treat each other with dignity, and the environment in the lab is friendly and inclusive.
What all lab members can expect from each other
Lab members can expect each other to be collegial, kind, cooperative, respectful, considerate, and generous with their time and knowledge. Lab members can expect a safe lab environment that is free of harassment, bullying, and shaming.
We do not tolerate harassment on the basis of race, religion, gender identity/expression, sexual orientation, disability status, physical appearance, or other protected characteristics. For more information, see https://policy.usc.edu/discrimination. On campus, there are resources for dealing with harassment via the Center for Work and Family Life and USC Student health.
What lab members can expect of the PI (Doc)
Generally, lab members can expect me to be supportive of their work, career advancement, and general well-being. This includes advice in selecting, defining, and carrying out projects; a mutually agreeable scheme for meeting; and reasonably timely feedback on written work. As with other other labmates, you can expect me to treat you with respect and dignity.
1) Regular meetings. Graduate students and postdocs can expect to have one-on-one meetings with me to discuss progress, troubleshoot, and set goals. Meeting frequency is flexible according to the needs of each person and project, with the default being to meet either weekly or every other week. When my door is open, you can also find me for quick questions. We may also have “2+1” meetings where two people each discuss their work.
2) Strategy meetings. Once or twice a year, we will have “strategy” meetings in which we discuss big-picture progress and goals, including career goals, and your overall experience in the lab.
3) Feedback on written work. Lab members can expect me to provide relatively timely comments on drafts. If I am crunched, I may try to get back to you quickly with major suggested changes rather than trying to be thorough. Generally comments in the early stages of draft preparation will be in broad strokes, with more specific comments as drafts get closer to completion.
4) Resources. As funding allows, you can expect me to provide resources necessary to your work, including computational resources, software, and travel to conferences. All graduate students and postdocs will have primary use of a lab-owned computer, and I will purchase a new computer if a suitable one is not available. I will fund travel, lodging, and registration for one domestic conference/year for all graduate students and postdocs, with the possibility of an extra one or an international conference under special circumstances (e.g. in preparation for going on the postdoc market or academic job market). For various reasons, it is also a good idea for you to apply for your own funding when possible.
5) Networking. I will introduce you to people in our field at conferences, on social media, and when visitors come to campus.
6) Letters. Lab members can expect me to write recommendation letters for them. I will be open with you about the strength of letter I will be able to write at any time you ask. (The best time to ask is not necessarily immediately before you need a letter.) Please give me as much notice as you can about recommendation letters, ideally 30 days, particularly the first time you need a letter from me.
7) Career support. Lab members can expect me to support their career goals and help them find their next job. I am fully supportive of careers in industry, nonprofits, government, and other sectors. At the same time, I am most competent to advise about academic careers. In the event that I cannot advise you about next steps, I will do what I can to connect you with other mentors who can help you. I cannot guarantee anybody an academic job in the current market, but if you want to pursue an academic job, I will work with you to enhance your chances as best I know how.
8) Respect. You can expect me to respect your time and your life outside the lab.
What the PI expects of other lab members
My general expectations are that you are honest in your work, that you communicate with me (especially about obstacles you’re facing that I can help with), that you take part in the lab community, and that you treat your labmates and broader community with respect and dignity.
1) Act with integrity. I expect you to carry out your work with integrity. This means being honest about methods, data, and limitations in all communications about the work (including with me, but not just with me).
2) Take care of yourself. Your well-being is more important than your research. Please take care of yourself, whatever that means to you—have fun, read, exercise, play sports, watch sports, pray, cook, eat, make art, play music, binge-watch all five seasons of Friday Night Lights, connect with friends and family, go to shows, go to therapy, be involved in your community, volunteer—whatever makes life meaningful and joyous for you. Take time off when you need it. Take some vacation! (Please let me know when you are going on vacation, and remind me when you are leaving.) There is no exact upper bound on vacation time as long as we agree you are making sufficient progress toward your goals, but there is a soft lower bound: I strongly encourage you to take at least 3 weeks a year off.
3) Tell me what you need. Please keep me informed (and remind me whenever necessary) of major deadlines and obligations that will affect your work or for which you need something from me. For example, make sure I am informed about recommendation letters you will need from me, abstract submission deadlines for conferences, and major coursework or teaching obligations.
4) Be responsive. Please respond to emails from me (or from other lab members) within 2 business days (if the email requires a response). If I ask you a question that’s hard to answer quickly, a simple, “Got it, will think about this and get back to you,” is fine. You are not expected to respond to any communications from me on weekends, while you’re on vacation, or outside your normal working hours. Please copy me on communications about our joint work with other researchers or with the press.
5) Tell me how things are going. Generally, if something is going wrong in your work, I will want to help, but I can only help if I know what is going on. Please be forthright with me about how things are going and about any obstacles to your work, whether those arise from the project itself, limited resources, or your work environment. Just as importantly, I also want you to tell me when things are going well and when you have success!
6) Try to make progress. I expect you to work to make progress toward shared research goals at a mutually agreeable rate. There are many ways of defining a targeted rate of progress, and there are many ways to achieve that rate—we will aim to find a groove that works for you.
7) Keep track of what’s going on in your subfield. I expect you to engage with research related to your work, including some combination of reading original research papers, reading abstracts and reviews, and going to talks. Different people have different ways of doing this, and one of your responsibilities is to find a way that works for you.
8) Be a kind labmate. I expect you to be welcoming of all new lab members and lab visitors, and I expect you to be cooperative, considerate, and respectful with everyone in your professional community.
9) Be present as part of the lab community. Please attend and participate in group meetings whenever possible, understanding that unavoidable conflicts will sometimes arise. Lab members will lead group meeting on a rotating basis, either providing a research update or leading a journal club. Beyond attending group meetings, please work out an attendance schedule that allows you to participate in the lab community to the extent possible. One of the benefits of computational work is that it’s often possible to work from home or from anywhere, and you’re welcome to take advantage of that. At the same time, working on one’s own too much can be isolating, and there are a lot of benefits to being around other people who are working on similar projects. Circumstances will differ due to things like family obligations and commutes, and different people work better on different schedules and in different environments. With that said, a good default for full-time lab members is to try to be around the lab most weekdays for several hours, with at least a few hours in the middle of the day. This is only a rough guideline—some people may need to come in less because of personal circumstances, and if we ever need to increase progress toward your goals, coming in more often is one of the tools we’ll consider.
10) Meet your professional obligations. I expect all lab members to abide with the USC policies that pertain to them and complete any mandatory training. I expect CBB graduate students to stay on top of program requirements (coursework, qualifying exams, committee meetings, etc.) I expect all lab members to hold themselves to high standards of professional conduct, both in the lab and when they are representing the lab at conferences, etc.
1) Interpersonal conflict. In case of interpersonal conflict in the lab, the first course is to work things out directly with the other person if possible. In cases where direct communication does not work, please schedule a joint meeting with me so that we can work on the conflict together. If we cannot resolve a conflict together, then we will go to another resource, such as USC’s Office of the Ombuds. (In some cases you may not feel safe addressing the conflict with a labmate directly, such as undergraduates who have a conflict with a postdoctoral or grad-student mentor, and in that case you may involve me initially.)
2) Transparency and reproducibility. We post preprints of original research to preprint servers (such as bioRxiv or arXiv) and post code that allows other researchers to reproduce simulations and data analyses using services like GitHub and Zenodo. A corollary is that lab members need to manage and back up their code over the course of a project to allow for reproducibility.
3) Lab space. Please be considerate about your use of the lab space, keeping things sanitary and reasonably tidy. Please keep the lab space physically secure by locking doors when you are the last to leave, etc.
4) Authorship. We follow the ICJME policy on authorship. First or co-first authors are generally expected to have made the largest contribution(s) to the project overall and to lead the drafting of the manuscript. We err toward sharing credit and involving more people in writing.