Expectations and responsibilities

All lab members should:

• Be driven, focused, and passionate about their work.
• Be collegial and supportive of everyone else on the team, and continually strive to maintain a collaborative and welcoming environment.
• Exercise independent thinking and judgement.
• Take on responsibilities, and reliably fulfill commitments.
• Be competent in required laboratory skills, especially animal handling.
• Perform first-rate work with attention to detail.
• Actively communicate your progress and project directions so we're all on the same page (see General Policies: Communications section below)
• Openly communicate your struggles and mistakes.
• Maintain the highest standards of moral and ethical conduct and scientific integrity.
• Openly communicate with me when you have issues with others in the lab. If you're not comfortable communicating your issues with me directly, there are resources in the department (other faculty or staff) who can help.
• Strive to stay current on the latest literature in our field (Twitter is a surprisingly good resource for this - follow scientists whose work is relevant to you).

Principal Investigator

My most important job is my role as a mentor to the trainees in my lab, and I take that role seriously.

As a mentor, I aim to ensure that my trainees are working on projects that align with their long-term goals and interests. I will, to the best of my ability, strive to keep roadblocks out of their way so they can focus on producing the highest quality research possible. Of course, one of my key roles is to secure funding so we can keep doing amazing research. I try to stay closely involved in research projects, but as a project matures, it's often most effective for me to help with higher-level strategizing and decision-making, thinking through results and implications, and working on communication/writing/packaging stories. Above all, my goal is to create an openly collaborative research environment where the research team is happy and productive while doing high-quality science. And as people begin to move on, I'm available to help them navigate their subsequent career choices. Some specific things I will strive to do:

• Support you scientifically, financially, psychologically
• Give you regular and timely feedback on your project ideas and progress, conference posters and talks, manuscripts, and grants

• Be available on a regular basis through regular meetings (1:1s for grad students & postdocs), Slack, impromptu chats in lab, and email. (Availability will unfortunately fluctuate periodically with grants, travel, and teaching.)

• Look for opportunities to further your career development - find talk opportunities (both local and more broadly), write recommendation letters, try to send you to conferences and courses (funds permitting)
• Help you prepare for your next career step
• Help make sure you maintain work-life balance, and always be open to any concerns about stress levels and anxiety

Post-Doctoral Fellows

Postdocs in the lab have of course gone through their PhD training, so they know how to take a project from its initial stages all the way to completion. The postdoc period is your opportunity to start proving yourself as a successful independent researcher. Postdocs in the lab should:

• Serve as role models for the trainees around you in terms of drive, independence, high-level thinking, scholarship, collegiality, and collaboration.
• Help mentor grad students and undergrads when they need it. I expect postdocs to really make everyone in the lab better.
• Seek out opportunities to present - journal clubs, lab meetings, conferences. I will do my best to find local outlets (other institutions, other groups' lab meetings) so you can continue to develop your presentation skills.
• To establish a track record of being competitive for funding, you'll want to start applying for grants (foundation fellowships, NRSA, K99).
• You have a lot of training under your belt, but you're also still really close to all the technical aspects of projects. So I expect you to challenge me when you think I'm wrong, because you'll often see things that I don't. It's really critical to add your unique perspective to our research and help shape its direction.
• By about year 3 of the post-doc, you should have some idea of what the next stage looks like for you, whether it's an academic job search, an industry position, etc. You'll want to be doing serious thinking about your career trajectory, and I will of course do my best to help you navigate the search.

PhD Students

PhD students are typically getting their core research training, often transitioning from being focused on coursework/studying to learning how to drive a research project. Some key roles and responsibilities:

• Develop your dissertation research. Initially you'll work on a project that I or others in the lab have spent a lot of time thinking about. Eventually (by years 2 or 3), you'll become the expert and will be proposing your own directions. During that time you'll probably have to do your qualifying exams and thesis proposal (specifics vary by PhD program).
• Help mentor undergrads and more junior grad students when they need it.
• Constantly improve your presentation skills, by presenting at whatever venues we can find - journal clubs, departmental venues, other labs, and conferences.
• Keep track of your deadlines and requirements - course registration, qualifying exams, thesis proposals and defenses, conference abstracts, fellowships, summer courses, etc.
• Apply for grants. For US citizens/residents, it's a really good idea to apply for graduate fellowships (NSF GRFP, NIH NRSA, NDSEG). For international students, there are many applicable foundation fellowships. It builds a really strong resume and also frees up more funding for everything we do.
• Start thinking through your career path and actively discussing it with me, so that together we can make sure you're taking the right steps and getting the training you'll need.

Undergraduate Students

• Undergraduates are initially admitted to the lab on a probationary basis for three months. By the end of the probationary period you must demonstrate competency on animal handling skills to continue working in the lab. There is a training checklist for these skills. A graduate student, postdoc, or lab manager will evaluate your performance on the checklist items. Be advised that training and certification to handle animals will take up the vast majority of your time during this period.
• Initially most undergraduate students will assist more senior lab members on projects. As you gain more experience and expertise, we hope you'll take on more responsibility towards driving projects and setting direction.
• Be in charge of setting your lab schedule, sticking to it, and communicating when any issues come up.
• Make sure you complete your required trainings/certifications (e.g., lab safety, animal handling as applicable, etc).
• Keep track of your deadlines - registration for course credit, applications for salary or travel funding, undergraduate conferences and symposium opportunities.
• Pay attention to details. If you're working on a task, provide quality control and ask questions if something doesn't seem right. We expect high-quality output from every single person in the lab, regardless of the scale of the work, or the pace it gets done at.
• Communicate. Provide regular updates, unprompted. Slack is great for this. As much as I'd like to be able to be on top of everything everyone is doing, without regular meetings, it's easy to overlook people's progress or roadblocks if they don't speak up.
• Ask questions. Voice your confusion. Get comfortable not knowing things, and don't be afraid to look stupid - nobody's going to judge you for not knowing something.
• Talk to everyone in the lab, not just your mentor. Get to know people and projects and expand your horizons! Everyone in our lab is willing to help if s/he has time.
• If something goes wrong or breaks, speak up immediately. (Communicate!)
• Attend lab meetings (schedule permitting). Start reading papers, even if they're over your head. Become an active participant. I expect the discussions in lab meeting to sometimes be hard to follow, but the people who get the most out of lab meetings are the people who speak up and ask questions.
• Maintain a clean lab environment. This is especially important as you'll be in and out of the lab in spurts, and it's easy to leave a few things laying around, etc. - this then adds up to a lot of clutter and can make the workspaces unusable!
• This is your opportunity to get to know what research is all about. We want to welcome you and have you develop into a colleague and valued member, and we want you to have fun.

Rotation Students

Our goal in the rotation is to determine if the lab is a great fit for you, and vice versa. Typically you will be paired with a grad student or postdoc, and your aim will be to advance a small piece of an existing project.

• Read literature and become familiar with current topics in our field
• Familiarize yourself with the experimental and computational techniques we use in our lab
• Get a sense of which topics interest you
• Get to know all the members of the lab and understand our culture
• Determine good fellowship application topics / projects to write about

Code of conduct

Essential policies

The lab and university are environments that must be free of harassment and discrimination. All lab members are expected to abide by the policies of the University of Rochester, which you must read. Your certification that you've read this lab manual is also affirmation that you will abide by these policies.

We are committed to maintaining an environment that is free of harassment. If you notice someone being harassed, or are harassed yourself, tell me immediately. Hopefully I am never the cause of your concern, but if so, please reach out to a trusted faculty or staff member in our department or look carefully at this page for more info on what to do.

Scientific Integrity and Research Conduct

Our lab is also committed to maintaining the highest standards of scientific integrity and research ethics. One portion of this mindset is that we do not tolerate research misconduct. To summarize that link, research misconduct can consist of:

• Fabrication - making up data or results, and recording or reporting them.
• Falsification - manipulating research materials, equipment, or processes, or changing or omitting data or results such that the research is not accurately represented in records or reports.
• Plagiarism - appropriating another person's ideas, processes, results, or words without giving appropriate credit.

While research misconduct occurs for various reasons, often a driving factor is the pressure to produce results. Unfortunately the need to produce results is always there (it's part of the job), and is never an excuse fabrication, falsification, or plagiarism. If you're feeling severe pressure, reach out to me to talk about it. And always remember that the goal of our work is to arrive at new truths, while research misconduct is the antithesis of that goal.

I take a very hard line on research misconduct. If for some reason you are concerned that our work is not maintaining the highest standards of research conduct, please report this to me immediately. And if you are not comfortable discussing with me directly, please reach out to a trusted faculty or staff member that could serve as an intermediary to help resolve these issues, or to the university's Research Integrity Officer.

Reproducible Research

This section is currently quoted verbatim from the Aly lab manual, because I agree with every word they said:

“If you gave someone else your raw data, they should be able to reproduce your results exactly. This is critical, because if they can’t reproduce your results, it suggests that one (or both) of you has made errors in the analysis, and the results can’t be trusted. Reproducible research is an essential part of science, and an expectation for all projects in the lab. For results to be reproducible, the analysis pipeline must be organized and well documented. To meet these goals, you should take extensive notes on each step of your analysis pipeline. This means writing down how you did things every step of the way (and the order that you did things), from any pre-processing of the data, to running models, to statistical tests. It’s also worth mentioning that you should take detailed notes on your experimental design as well. Additionally, your code should also be commented, and commented clearly. We all know what it’s like to sit down, quickly write a bunch of code to run an analysis without taking time to comment it, and then having no idea what we did a few months down the road. Comment your code so that every step is understandable by an outsider. Finally, it is highly encouraged that you use some form of version control (e.g., Git in combination with GitHub) to keep track of what code changes you made and when you made them, as well as sharing code with others."

I’ll add that in addition to commenting your code, you should use informative variable names (using camel case) and avoid the use of “magic numbers”. Make your code as “self-documenting” and flexible as possible. Your future self will thank you for it.

Animal Research

Much of our work to understand the brain and to develop new treatments for disorders of the nervous system will involve research with animals. We do this out of necessity, and we hold the welfare of our animal subjects in the highest regard. Accessing and working with laboratory animals requires comprehensive training with our UCAR and registration and orientation with DLAM. Further, it requires a commitment to treat all of our animals with the utmost respect, and a responsibility to carefully monitor their health and safety. You must be on the animal protocol prior to working with animals. Detailed steps are on the lab wiki.

Authorship and Acknowledgement

In academic research, our primary currency is generally publications in journals and presentations at conferences. A critical aspect of these publications and presentations is appropriately allocating credit in the form of authorship and acknowledgement. Emory's guidelines on authorship largely follow the International Committee of Medical Journal Editors (ICMJE) recommendations. As a serious researcher, it is important that you familiarize yourself with these guidelines.

While there are multiple ways of interpreting such guidelines, our lab in general favors inclusivity. We aim to ensure that anyone who has made a substantial intellectual contribution to a piece of work is allowed to participate in its dissemination via papers and presentations. Note that while authorship is a privilege, it also comes with responsibilities, such as helping to draft and revise any communication of the work (including providing critical, intellectual feedback). Anyone listed as an author on a manuscript is certifying that they agree with its content, can discuss the implications in depth, and are agreeing to be held accountable for their contribution to the content. Contributors who do not meet the criteria for authorship may instead be recognized via acknowledgements.

Because authorship is one of the cornerstones of the entire research endeavor, we take it extremely seriously. Here are some helpful guidelines: Generally at the start of a project, the student or post-doc taking on a lead role can expect to be first author of the resulting publication. You can usually expect me to be last author. If the project is collaborative and another lab is the primary driver of the project, this may not be the case. Once it starts to become clear that a publication or presentation is likely to result from the work, it is important to lay out the scope of the publication and proposed authorship. It is rarely too early to begin talking about authorship - this is critical to ensure all authors are on the same page. This plan (scope, authorship) will evolve over time, but documenting this and maintaining it is critical for setting expectations appropriately. As a project evolves, and new researchers contribute, they may be added to the author list as appropriate (this is discussed with all involved parties). Sometimes projects take longer than a person's time in the lab. In this case, projects may be transferred to others, and if so the new researcher may become the main driver (and first author) on the project. This is a conversation between all involved parties. It is the responsibility of the person(s) driving the project (first author(s), and me) to make sure people's contributions are appropriately recognized. Whenever there is any question as to whether someone should be an author, we always err on the side of having a conversation with that person. It is never appropriate to assume someone will simply speak up to "claim" their authorship. It is also the first author's (or authors') responsibility to ensure all co-authors have the opportunity to read drafts and provide critical feedback before dissemination/submission. For any sort of submission, all co-authors should have seen a draft and had a chance to contribute/comment a minimum of 2 weeks prior to the submission. As an example, if you're planning on submitting an abstract to a conference, everyone that could be considered an author must have seen a complete draft at least 2 weeks prior to the deadline (and any lingering authorship questions must be discussed in detail by that point). In rare cases, it is possible to put together a submission in a shorter time-frame, but only if every co-author is comfortable with the process. If we do not have permission from a co-author prior to submitting something, we simply cannot submit it.

Collaboration

We often collaborate closely with partners external to the lab (within or outside of U of R). Being able to collaborate with world leaders in various fields, who have substantial expertise that is often complimentary to our own, is a tremendous privilege. Two keys to successful collaboration are that we always show respect for our collaborators, and maintain communication so there are no misunderstandings. These are intellectual partnerships, and generally, even if a collaborator's role is mainly limited to experimental design and data collection, their expertise on the project is invaluable.

Shared datasets

Building on the above, we have many projects with great researchers who share data collected in their labs. We do not share data beyond our lab without explicit permission from our collaborator. Datasets are also generally shared for a specific purpose, and any time we plan on using it in a manner that wasn't originally discussed (e.g., to test a different hypothesis), we communicate that with our partners and secure their permission.

Photos & videos

We want to create an environment where everyone is comfortable and we respect their privacy. Therefore photos and videos of other lab members can only be taken with their explicit knowledge and consent. Everyone has different degrees of comfort with pictures and videos, and we respect them equally.

Sometimes it is helpful to take pictures that include animals in the lab, e.g. to document procedures, experimental configurations, surgical techniques, etc. However, pictures of animals in experimental settings can make people uncomfortable, and in general there are a lot of sensitivities around animal research. Any existing pictures of animals in the lab are assumed to be kept 100% internal unless you have explicit permission from me for other uses, and do not make any new photos of animals without permission.

Occasionally you might want use pictures of other lab members in your presentations - check with them to make sure it's appropriate. Photos of animals in presentations are forbidden; make an illustration instead. You might want to share pictures of lab members for fun, e.g. on social media. Check with everyone involved to be sure that's OK.

(Social) Media

The messaging from the laboratory should be well-managed. In general, do not post information about laboratory business on social media or other sources. Do not comment to the media without express prior consent from Adam. If you have news, please let me know and we will coordinate University Public Relations. Feel free to share news that has already been posted through these channels.