Lab Manual

Introduction
Mentorship from Linden
1. Post-docs & graduate students
2. Linden’s expectations of you
  1. Post-docs
  2. Graduate students
Lab Policies
Fin

This page contains the lab manual. The lab manual describes the rights and responsibilities of all SNaP Lab members, and it introduces our general research approach and lab policies.

Introduction

Welcome to the SNaP Lab! We’re glad to have you with us and hope that you’ll have an awesome time. This manual was developed by Dr. Linden Parkes and serves as your first point of reference as a new lab member. Our goal is to create a fun and inclusive lab that strives for scientific excellence and supports the professional development of all its members. We want you to be happy and productive while you are here!

This lab manual draws from many others, including those written by Jeremy Manning, Mariam Aly, Bridget Callaghan, Jonathan Peele, Ted Satterthwaite, and Alex Fornito.

Who is this lab manual for?

Every new member is expected to read this manual and use it as a reference. We believe clear communication of expectations is important, and by reading this manual you will come away with a good understanding of ours. You will also be clear on what you can expect from Linden as your mentor and PI.

This lab manual is a live document and will be updated periodically. All lab members are welcome to submit feedback and/or edits that improve the content, clarity, and usefulness of this document. Feedback can be submitted directly to Linden (e.g., via Slack or during meetings). Edits can be submitted by following the instructions here.

What will you get out of reading this lab manual?

You will obtain the following:

An understanding of your rights and responsibilities as a lab member.
An understanding of Linden’s expectations of you while you are a lab member.
An understanding of our lab practices and policies.

Rights and Responsibilities

As a member of the lab, you are entitled to certain rights, and you agree to take on certain responsibilities.

Note, this content was taken from Jeremy Manning’s lab manual.

Your rights as a lab member

You are entitled to a safe work environment free from harassment, abuse, violence, and discrimination in any form.
You are entitled to be supported and respected by all lab members.
You are entitled to openly share your scientific ideas and constructive feedback with all lab members.
You are entitled to appropriate credit (e.g. authorship, acknowledgement, letter of recommendation) for your work and ideas.

Your responsibilities as a lab member

You agree to contribute to a safe work environment and to refrain from behaviors that harass, abuse, expose to violence, or discriminate.
You agree to support and respect all lab members, including yourself.
You agree to openly share your scientific ideas and constructive feedback with other lab members.
You agree to clearly communicate and document your contributions to each research project (e.g., through GitHub commits and issues, reports, updates on Slack, etc.).
You agree to carry out your work with integrity and diligence, adhering to the highest possible standards of scientific excellence.
You agree to utilize lab resources (including equipment, money, time, etc.) responsibly and sustainably.
You agree to maintain the cleanliness of shared areas (e.g., office space, kitchen).

General recommendations and expectations

Big picture

Science is hard, but it is also fun, and we want you to have fun doing it! As such, in addition to the above core rights and responsibilities, we recommend you consider the following:

Work on what you’re passionate about, work hard at it, and be proud of it!
Scientists have to be careful. Don’t rush your work. Think about it. Implement it. Double, triple, and quadruple check it. Incorporate sanity checks. Ask others to look at your code or data if you need help or something looks off. It’s ok to makes mistakes, but mistakes shouldn’t be because of carelessness or rushed work.
If you do make a mistake, tell your collaborators (especially if the paper is being written up, is already submitted, or already accepted). We admit our mistakes, and then we correct them and move on. You will not be punished for making a mistake and owning it.
If you’re struggling, tell Linden or someone you trust. Your health and happiness come first. The lab looks out for the well-being of all its members. We are here to help. It’s ok to go through hard patches (we all do), but please don’t feel shy about asking for help.

Small picture

There are also a few day-to-day things to keep in mind to keep the lab running smoothly.

If you’re sick, stay home and take care of yourself. Because you need it, and also because others don’t need to get sick. If you feel able to take your meetings virtually, do that. If not, reschedule your meetings as soon as you can.
You aren’t expected to come into the lab on weekends or holidays, and you aren’t expected to stay late at night. You are expected to dedicate your contracted hours (e.g., 40 hours for full-time members) primarily to your lab responsibilities and get your work done (whatever time of day you like to do it).
Dress code is casual, but you may dress up if you want! However, the dress code is not too casual. When interacting with participants or presenting your work, don’t wear pajamas and sweat pants; jeans are fine.

Mentorship from Linden

In addition to the above rights and responsibilities, depending on your role, you can expect certain standards of mentorship from Linden during your time in the lab.

Note, This content was modified from Mariam Aly’s lab manual.

Post-docs & graduate students

In addition to your rights and responsibilities, you may expect;

Regular meetings with Linden. Typically, these meetings will occur weekly and run for 60 minutes. Note, some flexibility is expected here to account for periods of the year where Linden may be traveling, sick, or otherwise unavailable. You will have the option to meet in-person or via zoom.
Timely feedback on manuscripts, grant submissions, and fellowship applications. Typically, Linden will aim to return your work to you within 2-4 weeks (see lab policy on deadlines). Note, this timeframe may vary depending on the length of the document, level of feedback needed, and Linden’s current workload.
Career development support. This may include, but is not limited to, introducing you to relevant researchers in the field, promoting your work at relevant talks, writing recommendation letters for you, as well as supporting your publication costs and conference attendance as finances permit.
Help preparing for the next step of your career, whether that is an academic or non-academic post.

Important
Regarding letters of recommendation, Linden can only write about his experience working with you. For example, if you want something in your letter about your teaching skills, then you need to find opportunities to teach within the lab! If you want something in your letter about mentoring undergraduate students, then you need to get that experience in the lab. Make sure to talk to Linden about your goals and what you need to be doing to reach them.

Linden’s expectations of you

In return for mentorship, Linden will expect certain standards from you as a lab member. These expectations are designed to keep everyone in the lab moving forward productively and happily. Help Linden to help you!

Post-docs

Linden expects that you will;

Commit ~40 hours a week, on average, to your research and lab responsibilities.
Come prepared to meetings to provide updates on your research.
Develop your own line of research that is consistent with/complementary to the lab’s goals, and publish your work in peer-reviewed journals.
Help mentor other trainees in the lab (e.g., undergraduate and graduate students), either because they seek it, or because Linden asks you to.
Present your work at lab meetings, to the broader university community, at other research labs, and at national and international conferences. Linden will help you coordinate this.
Apply for eligible grants/fellowships (e.g., from NIH, NSF).
Apply for jobs (academic or otherwise) when you’re ready, but no later than the beginning of your 3rd year as a postdoc. Note, this may need to be sooner depending on your funding situation.
Submit work for feedback in a timely manner such that Linden has adequate time to provide it (see lab policy on deadlines).

Important
Regarding work hours. As a postdoc, you’re expected to work your contracted hours each week (~40 in the case of a full-time postdoc), but Linden won’t micromanage your time. Academic research is highly flexible. Linden does not expect you to be at your desk 9am-5pm, 5 days a week. Linden does expect you to put in the work, though, and to (on average) work the equivalent of a full-time week. This could be 9-5, or it could be 12-8, it’s up to you. It could also mean taking every Wednesday off and working a day on the weekend to make up. Whatever your work schedule is, please communicate it with Linden so that he is aware of it. Finally, research ebbs and flows. Sometimes things will be busy, and you might find yourself putting in >40 hours a week to get everything done (e.g., when a paper or grant submission is coming up). Other times things will be quieter, and you can take that time back.
Regarding funding. Though we will only hire you if we can support you for at least two years, it is beneficial to your professional development to get experience writing, and to be awarded, your own grants. If you plan to stay in academia long term, becoming a practiced grant writer is essential. Additionally, if awarded, grants will provide you a great deal of independence during your time in the lab (e.g., you won’t have to depend on lab finances to support conference travel etc.).

Graduate students

Linden expects that you will;

Commit ~25 hours a week, on average, to your research and lab responsibilities.
Come prepared to meetings to provide updates on your research.
Develop your dissertation research; this should ideally include at least 3 substantial pieces of work that come together to address a central research question. If this sounds daunting, don’t panic! Linden will help you.
Strive to publish your dissertation work.
Help mentor undergraduate students, either because they seek it, or because Linden asks you to.
Present your work at lab meetings, to the broader university community, at other research labs, and at national and international conferences. Linden will help you coordinate this.
Apply for eligible grants/fellowships (e.g., from NIH, NSF). Getting grant writing experience early is important and will better set you up for success during your postdoc (if you choose to do one).
Engage in Teaching Assistantships (TAs) if and when it becomes required.
Manage your program-related deadlines, and communicate them with Linden so that he can assist you with meeting them.
Submit work for feedback in a timely manner such that Linden has adequate time to provide it (see lab policy on deadlines).

Important
Regarding research hours. Like postdocs, Linden won’t micromanage your time. Academic research is highly flexible. Linden does not expect you to be at your desk 9am-5pm, 5 days a week. Linden does expect you to put in the work, though, and to (on average) invest 25 hours a week in your research. As above, sometimes things will be busy, and you might find yourself putting in >25 hours a week to get everything done (e.g., when a paper or grant submission is coming up). Other times things will be quieter, and you can take that time back.
Regarding program requirements. Linden’s department home is in Psychiatry, which does not have a PhD program. As such, if you join the lab as a graduate student, you will likely come through another department that Linden has a secondary appointment in (e.g., Psychology, Neuroscience). Since Linden is not a core member of these PhD programs, it is important you actively manage your program-related goals and communicate them clearly with Linden. Linden can only help you manage your program-related goals if he knows about them, and he will only learn about them through you.

Lab Policies

Essential Policies

Code of conduct

The lab, and the university, is an environment that must be free of harassment and discrimination. All lab members are expected to abide by the Rutgers University policies on discrimination and harassment. All relevant policies can be found at the Rutgers Human Resources webpage.

The lab is committed to ensuring a safe, friendly, and accepting environment for everybody. We will not tolerate any verbal or physical harassment or discrimination on the basis of sex, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, or religion. We will not tolerate intimidation, stalking, following, unwanted photography or video recording, sustained disruption of talks or other events, inappropriate physical contact, or unwelcome sexual attention.

If you notice someone being harassed, or are being harassed yourself, tell Linden immediately. If Linden is the cause of your concern, then reach out to the department chair or another trusted faculty member in the department. Dr. David Zald is available for this purpose; Dr. Zald is the director of the Center for Advanced Human Brain Imaging Research, wherein the lab is based.

Research (mis)conduct

The lab, and the university, is committed to ensuring research integrity, and we take a hard line on research misconduct. We will not tolerate fabrication, falsification, or plagiarism. You should familiarize yourself with Rutgers’ policies, available from the website.

Research misconduct may be related, in part, to academic pressures regarding research output, and this is an important discussion. If you are feeling pressured to succeed, you should reach out to Linden and we can talk about it; but this pressure is something we all face and is never an excuse to fabricate, falsify, or plagiarize. Also, think about the goal of science and why you are here: we are all here to strive to get as close to the truth as possible regarding the brain and behavior. Not only is research misconduct doing you a disservice, it’s also a disservice to the field. And it risks your entire career. It is never right and never worth it. Don’t do it.

Authorship

At the start of a new project, the lab member taking on the lead role can expect to be first author (unless otherwise discussed with Linden) and Linden will be the last author. Other lab members who help over the course of the project may be added to the author list depending on their contribution, and their placement will be discussed with all parties involved in the paper. In some cases, where the other lab member provides extensive supervision, writing, and analysis support, they may be joint first author.

If a lab member takes on a project but subsequently hands it off to another lab member, they will most likely lose first-authorship to that lab member, unless co-first-authorship is appropriate. This most often occurs for short-term lab visitors (e.g., summer interns or students) who may begin a project but then decide not to finish it. However, if that short-term visitor wants to continue working on their project beyond their time in the lab, including taking it to completion, they are welcome to do so and will continue to receive support from Linden.

In cases where a lab member brings an incomplete project to the lab from their previous lab, Linden expects to be invited to participate as a coauthor if that lab member intends to spend significant lab time finishing that project. However, if the lab member intends to finish their carry over project entirely on their own time, then Linden does not need to be included. In either case, Linden expects you to communicate what you’re working on, and in what capacity, with him. This is important as Linden has reporting obligations to various funding bodies, and he needs to know which projects are being supported—in whole or in part—by certain grants.

All of these issues will be discussed openly, and you should feel free to bring them up if you are not sure of your authorship status or want to challenge it. As we often deal with large and complex datasets involving big collaborations, there are no hard and fast rules for authorship.

Open science

Lab members are required to share their code online with the community. Generally, we will make our code publicly available simultaneously with the submission of a paper to a peer-reviewed journal. To keep code sharing centralized, we share our code on the lab’s GitHub page. This not does not preclude lab members from sharing code on their own repositories, but a complete release of the code associated with a paper must be archived on the lab’s GitHub.

We also share our work with the world via preprints. The lab policy is to upload a preprint of a manuscript simultaneously with initial submission to a journal (unless that is not allowable by the journal). The preferred preprint servers are bioRxiv and medRxiv. We also put PDFs of all our preprints on this website (see Completed Projects), and lab members should share these with whoever asks.

General Things

Lab structure

We are a hybrid lab. Rutgers is centrally located in the Northeast Corridor of the USA. As such, many lab members live spread out across the region, and some have relatively long commutes. We have chosen to support this by embracing a hybrid lab structure. However, this structure is not without its challenges; working from home is great, but it can create barriers to connecting with your colleagues, building and maintaing an intellectual environment, as well as being social. To combat some of these challenges, we expect all lab members to embrace the hybrid lab structure purposefully and help it be successful for everyone. To that end, we have implemented the following polices:

All-hands day. Everyone is expected to be in the lab at least one day a week on the same day. At the moment, that day is Monday.
Slack. We use slack for lab communication (see communication below). Everyone is expected to have Slack installed on their computers and engage actively with the lab there.

Communication

Slack will be used as the primary means of lab communication. Email is a notoriously oversubscribed communication medium for PIs, which can result in many missed emails. To combat this, all direct communication with Linden should take place on Slack, including exchanging attachments. We will also create dedicated Slack channels for each lab project. Upon arrival, you will be invited to join the lab’s Slack workspace and you will be expected to install Slack on your computer. On slack, we also have a handful of lab-wide channels:

snaplab_general. Gor general lab discussion.
snaplab_papers. For sharing papers.
snaplab_scrum. For coordinating our weekly scrum. The scrum is a place to discuss any coding/analysis challenges related to projects. It is accompanied by a weekly 60-minute zoom call that is available on short notice to anyone who wants to sign up and workshop a problem. If you want to sign up for a scrum, find the next open slot on the Meetings calendar (it will be marked by a calendar event called Scrum [OPEN]). Edit that event by replacing the [OPEN] with your name (e.g. [Linden]) and add a zoom link to the event. Finally, announce on the slack channel that you’ve taken a slot and check that people can attend! Lab members should be keeping the weekly scrum slot available by default, so they should be able to attend, but it’s always worth checking! If you want to move your scrum slot around to accomodate peoples’ schedules, feel free to do so.

Calendars

We use Google Calendar to track meetings, lab-wide events, and known absences. Upon arrival, you will be invited to the lab’s calendar, where you fill find:

Meetings. This calendar is where we record meetings that involve Linden. Note, you are not obliged to use this to record your own meetings that don’t involve Linden if you don’t want to.
Events. This calendar is where we record upcoming conferences, talks, activities, and other bits ‘n’ pieces.
Where am I? This calendar is where lab members note whether they plan to be on campus or in the lab on a given day. It also notes known absences (e.g., illness, travel, holidays, vacation, out-of-office). We have found this useful in helping the lab to maximize the value of our hybrid structure (e.g., it minimizes the risk of you coming in only to find that no one else is around). As such, please do your best to use it diligently for everyone’s benefit. For example, if you’re going to be on campus for the day but plan to spend all your time at UBHC and none at SRB, create an all-day event that reads “YourName @ UBHC.” This calendar is also useful for helping Linden to respect your off time; for example, putting your travel dates down ensures that Linden won’t bother you during your time away!

Deadlines

We are big believers in work-life balance. Linden will support you to maintain your work-life balance, and he asks that you support his by managing your deadlines diligently and factoring in ample time to provide feedback.

Give Linden at least 10 business days (i.e., excluding weekends and holidays) to do something with a hard deadline that requires a small time commitment (e.g., commenting on conference abstracts, completing paperwork, etc.)
Give Linden at least 15 business days to do something with a hard deadline that requires a significant time commitment (e.g., commenting on manuscripts/grants/fellowships, writing letter of recommendation, etc.)

If you want multiple back-and-forth rounds of feedback prior to submission, please plan accordingly. This is particularly important for grants/fellowships, as these submissions often comprise multiple lengthy components—that may each require their own rounds of feedback—and compiling strong submissions is nearly always an iterative process. This is why it is so important to start early!

Note that the above feedback deadlines may need to be adjusted to account for periods of the year where Linden may be traveling, sick, or otherwise unavailable. Linden will communicate these disruptions and provide updates on when you can expect your work to be returned.

Lab meetings

We will have a lab meeting every week, which everyone should aim to attend. The meeting will be a hybrid of in-person and Zoom. You can find it on the Meetings calendar. Note, owing to the relatively small size of the SNaP Lab, we are currently holding a joint lab meeting with the Holmes Lab.

Office hours

If he is in the lab, you can find Linden in his office. His door is almost always open; if it is, feel free to ask for a chat. He will typically say yes, though sometimes he can only spare a couple of minutes. You can find Linden’s lab attendance in the Where am i? calendar.

Computers

All lab members need a computer to get their work done. Depending on your role and the specifics of your project, the lab may provide a computer dedicated to you (e.g., laptop or desktop). Any computers purchased by the lab will remain the property of the lab and should be treated as such. In turn, all computers (including all peripheral equipment) must be returned to the lab when your tenure is complete.

Important
Postdocs and graduate students are expected to use their discretionary fund to cover the cost of their computer and peripherals (see below).

Finances

Discretionary fund

Full-time postdocs and graduate students, primarily supervised by Linden, will be given a $4,000 discretionary fund when they start at the lab. This amount is non-expiring and can be used anytime. The purpose of this fund is (1) to support trainees to get setup with their local computing needs and (2) provide opportunites to engage in professional development activities beyond things like conference travel (e.g., summer courses).

For (1), this might include the purchase of a new laptop and peripherals. If you’re a Mac user, all purchases must go via Kite & Key. Otherwise, we have access to a wide range of vendors, including Dell & Amazon. Regarding the latter, Rutgers places some restrictions on the Amazon catalogue, but we’re able to purchase most things. If you’re unsure, just send a link to Linden and he can check.

Publication costs

All costs related to lab publications will be fully covered by the lab. Linden will help facilitate these payments. Publication goals will be discussed over the course of a project to determine which outlet is the best fit. If you obtain your own independent funding that includes a budget for publication costs (e.g., through a fellowship or grant), then you will be expected to use that budget and the lab will cover the difference.

Travel

Presenting at conferences is critical to the dissemination of science and a major component of your development as a scientist.

As of 2024, SNaP Lab graduate students and post-docs who are primarily supervised by Linden, and who are in good standing, are entitled to $4,000 of funding for allowable academic travel per academic year (7/1 to 6/30). Expenses are counted against the year in which they are incurred, even if the conference occurs in a subsequent year. These funds will not rollover year to year.

We no longer require that this travel be linked to a poster presentation or talk; we are all adult learners and Linden trusts team members to evaluate what travel is most valuable for their development. To assist Linden with managing travel budgets, please log your expenses on the SNaP Lab Travel Spreadsheet as they are accrued. Also see the Booking travel at Rutgers tutorial for more information on practical details.

Lab travel funds are in addition to any funds supplied by Rutgers University more broadly, training grants (e.g., T32, K99), or otherwise. However, non-lab funds should be preferentially spent before using limited lab funds. Also, you are expected to make reasonable efforts to seek out alternative sources of travel funding on a per-conference basis (e.g., travel awards). This condition is meant to encourage all lab members to seek their own funding so that Linden can make prudent use of finite lab resources.

If you are presenting your work at a conference, it is our preference that results are in near-final form by the time of your presentation— i.e., the reported results in your poster/talk should be close to what will appear in the paper. We very much try to avoid a “rush for results” ahead of a conference deadline. Results should be solid and sent to co-authors a minimum of 7 days ahead of the conference deadline; this allows for a minimum of 5 days for co-authors to review results, as well as 2 days to integrate feedback and receive final sign-off from Linden.

Important
Conference travel is a privilege, and is dependent upon both available lab funding and being a positive force for the community. This includes supporting colleagues in collaborative projects, testing software, writing documentation, and regular attendance at lab meetings.

General reimbursements

For reimbursement of non-travel expenses, see the General Reimbursement.

Fin

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