Policies and Advising Manual

Date: April 2, 2025 7:57 PM — Table of Contents

Policies and Advising Manual

General Lab Work Expectations

Science is hard, but it’s also fun. In the Holmes Lab, we want to make sure that everyone experiences a positive, engaging, hostility-free, challenging, and rewarding lab environment. To maintain that environment, we all have to do a few things.

Expectation of Lab Members – Big Picture

Support and respect your fellow lab-mates. Science is collaborative, not competitive.
Help others, and you can expect others to help you when you need it.
Scientists have to be careful. Don’t rush your work. Think about it. Implement it. Double and triple check it. Incorporate sanity checks. Ask others to look at your code or data if you need help or something looks off. It’s okay to make mistakes, but mistakes should not arise because of carelessness or rushed work.
If you do make a mistake, you should definitely tell your collaborators (if they have already seen the results, and 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.
We all want to get papers published and do great things, but we do this honestly. It is never okay to plagiarize, tamper with data, make up data, omit data, or fudge results in any way. Science is about finding out the truth, and null results and unexpected results are still important. This can’t be emphasized enough: no academic misconduct!
Prepare to share your code. It is our goal to make all code, and if possible, all collected datasets, available to the broader scientific community. Make sure your code is well documented and, upon publication, we will strive to share it with the world (Lab GitHub).
If you’re struggling, tell someone. 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 okay to go through hard patches (we all do), but you shouldn’t feel shy about asking for help or just venting. Feel free to reach out to Avram at any time with questions or concerns.
If there is any tension or hostility in the lab that arises, something must be done about it. Lab members should feel comfortable in the lab. If you don’t feel comfortable expressing your concerns to other lab members, tell Avram.
Stay up to date on the latest research by using RSS feeds, following scientists on google scholar, and/or getting email updates from your favorite journals. Also consider following scientists on Bluesky.
Have a life outside of the lab, take care of your mental and physical health, and don’t ever feel bad for taking time off work.

Expectation of Lab Members – Small Picture

There are 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’re sick, reschedule your meetings and participants for the day (or the next couple of days) as soon as you can.
You aren’t expected to come into the lab on weekends and holidays, and you aren’t expected to stay late at night. You are expected to get your work done (whatever time of day you like to do it).
Show up to your meetings, show up to run your participants, show up to your classes, and show up to lab meetings.
Be on time. Especially when you are running participants – in fact, our lab policy is to show up 15-20 minutes early to set everything up. And be on time for your meetings: respect that others have packed days and everyone’s time is valuable.
Make sure to also keep the study materials locked away and the key stored away in its proper space.
Keep the lab tidy. Eating in lab is fine, but clean up food waste, crumbs, spills. Put lab equipment back where you found it. Keep common areas uncluttered.

Principal Investigator

I promise to abide by all of the above, and to also…

Support you (scientifically, emotionally, financially)
Give you feedback on a timely basis, including feedback on project ideas, conference posters, talks, manuscripts, figures, grants
Be available in person and via e-mail on a regular basis, including regular meetings to discuss your research (and anything else you’d like to discuss)
Give my perspective on where the lab is going, where the field is going, and tips about surviving and thriving in academia
Support your career development by introducing you to other researchers in the field, promoting your work at talks, writing recommendation letters for you, and funding your conference travel as often as finances permit
Help you prepare for the next step of your career, whether it’s a post-doc, a faculty job, or a job outside of academia
Care for your emotional and physical well-being, and prioritize that above all else

Post-Docs

All of the above, and you will also be expected to…

Develop your own independent line of research
Help train and mentor students in the lab (both undergraduate and graduate) when they need it – either because they ask, or because I ask you to
Present your work at departmental events, at other labs (if invited), and at conferences
Apply for grants when appropriate (e.g., NRSA, K99). Though I will only hire you if I can support you for at least one year, it’s in your best interest to get experience writing grants and if you get them, you’ll be helping out the entire lab as well as yourself (because you’ll free up funds previously allocated to you)
Apply for jobs (academic or otherwise) when you’re ready, but no later than the beginning of your 4th year of post-doc. If you think you’d like to leave academia, that’s completely okay – but you should still treat your post-doc seriously, and talk to me about how to best train for a job outside academia
Challenge me when I’m wrong or when your opinion is different, and treat the rest of the lab to your scientific expertise and perspectives.

What you can expect from Avram

I am typically on campus every Monday and Wednesday during the academic year from roughly 9:00 AM through 4:00 PM. I keep an informal schedule and have an open-door policy for my advisees. That means that I am usually available for informal discussions or to take a quick look at data when I am not teaching or attending meetings. I enjoy looking at preliminary results and helping to puzzle though analyses code, and these informal meetings keep me in touch with what is happening in the lab.

Occasionally, I need focused time for writing and, if that is the case, I will let people know. I often disappear to the library for a few hours to avoid distractions when I need to write. I will meet individually with each graduate student and post-doc at least one hour per week during a regularly scheduled time that is mutually convenient. These meetings will involve a review of progress of the student’s ongoing project and/or a discussion of the scientific and methodological issues related to that project. I expect the advisee to come prepared to these meetings with their latest results and a list of issues to be discussed.

I also will hold a scheduled full lab meeting for all individuals working in the lab (students, post-docs, visiting students, research staff), for at least 60 minutes per week. The agenda for these meetings will vary but will often include a more structured presentation by a lab member on a research topic. This may mean a presentation of that student’s research study, or the discussion by the group on a journal article or method. Additionally, we hold a weekly multi-lab meeting for at least 75 minutes per week. Currently, we are sharing this meeting with the Parkes Lab. This meeting provides the opportunity for students to present their work and solicit feedback from a larger audience. Students and post-docs are expected to present in this meeting at least once per year.

As a rule, I don’t hold evening or weekend meetings. I can recall instances in the past where one-off weekend meetings were held prior to a conference presentation, grant deadline, international collaboration, or job talk, but this would be a rare occurrence. If you have limits on your ability to be in the lab due to a disability, a religious event, a medical emergency, or other reason, just let me know so an accommodation can be made.

I keep a more relaxed summer schedule and do not come to the lab every day. Nevertheless, I do hold lab and individual meetings during the summer. In addition to weekly meetings, and occasionally dropping by the lab, you can usually find me working in my office. My door is almost always open; if it is, feel free to ask for a chat. I will always say yes, though sometimes I can only spare a couple of minutes or might ask you to let me finish typing a sentence. If my door is closed, assume that I am either gone, in a meeting, or I do not want to be disturbed – so please send a message (Slack or e-mail) rather than knocking.

What I expect from you

I expect my primary graduate student advisees and post-docs to be in the lab for some part of every weekday. Working remotely can be very productive, but I believe that the intellectual environment of the lab benefits from the kind of informal interactions that occur when people are working side-by-side in one place.

I expect my primary graduate student advisees to consult with me before engaging in projects with other advisers and other labs. I do not oppose such arrangements, which can be very beneficial to a student’s intellectual growth. I do worry, however, about time management and overcommitment. We differ to the degree to which we can manage multiple projects and remain productive. Therefore, it may be that different guidelines may be used for different students, and that these guidelines may change when we meet to review our individual advising compact.

I similarly expect that my primary graduate student advisees consult with me before taking on additional work (such as teaching beyond the stipend) or volunteer activity (such as serving as a graduate representative to the IRB). In instances where my approval is required (such as approving a student to take on summer teaching), I have, on occasions, refused to provide that approval when I thought it would interfere significant with a student’s progress to degree. My concerns here are the same as above. I worry about time management and overcommitment.

I expect that my primary graduate advisees follow the departmental and university guidelines with respect to vacation time. That is, students can take two weeks of vacation at a time when classes are not in session. Advisees may also take off when the University is officially closed (e.g., the week between Christmas and New Year’s). However, note that the University is not closed during undergraduate recess periods - such as fall and spring breaks.

Hours

For graduate students, I understand having to be away for classes and TA-ing, but show up to the lab on a regular basis when you don’t have those obligations. To encourage lab interaction, try to be in most weekdays during ‘peak’ hours (assuming no other obligations) – e.g., between 11am and 4pm. This is not a hard rule, you can work at home occasionally, and I understand other obligations. But keep it in mind.

At times I may work nights and during the weekends. This means that I will sometimes send emails or Slack messages outside of normal working hours. For the most part, I try not to, but sometimes I do. I do not expect you to respond until you are back at work (ignore me!). I do not expect there to be cases when I suddenly and urgently need something from you over the weekend (e.g., for a grant deadline), but should I anticipate that happening, I will bring it up in advance so we can plan accordingly. All this said, I realize that being told you can ignore my messages might not take away the stress of seeing my messages if you check your work email or Slack in the evenings or on weekends. If my off-hours messages are unwelcome and cause distress, please talk to me, and I will be better at not bothering you during your time off. Although I sometimes work weekends, I try to only do that when absolutely necessary. Please respect that by making sure to give me enough heads-up about impending deadlines so that I can get things done for you (e.g., write letters of recommendation, give feedback on manuscripts, etc) while maintaining my work/life balance.

Research

Choosing a research topic

Choosing good research topics is key to a successful graduate school career and beyond. There is no perfect formula for advising on research topics, which depends greatly upon the individual interests of the student. Presumably, a student has chosen to work in my lab because they have a general interest in our program of research. Consequently, in most instances, I have worked very closely with students on developing research topics that were very close to my core intellectual interests.

However, I have also worked closely with students whose research interests diverged into areas with which I had less familiarity. In several instances, this has involved applying techniques in which I have expertise (e.g., neuroimaging) to topics in which I am not expert (e.g., genetic, molecular, or cellular bases of brain function; machine learning prediction of behavior; etc). This often necessitated expanding the student’s advising team to make sure that the student could be appropriately advised and, in at least one instance, this led to a co-mentoring arrangement. In other instances, a student’s diverging interests led that student to switch to a different adviser whose research expertise was more directly relevant.

In general, research topics develop from conversations between my advisees and me about science that extend over many weeks and months. It is often the case that more direction from me is needed in a student’s initial years and less as the student’s research matures. Thus, re- search independence develops over time and at a different pace for different students. Funding issues in the lab play little or no role in the selection of research topics for graduate student advisees. This is not necessarily true for post-docs, whose research may be funded by grants to me on particular issues.

Publishing research

Like other labs, we will follow the APA guidelines with respect to authorship:

“Authorship credit should reflect the individual’s contribution to the study. An author is con- sidered anyone involved with initial research design, data collection and analysis, manu- script drafting, and final approval. However, the following do not necessarily qualify for authorship: providing funding or resources, mentorship, or contributing research but not helping with the publication itself. The primary author assumes responsibility for the publication, making sure that the data are accurate, that all deserving authors have been credited, that all authors have given their approval to the final draft; and handles responses to inquiries after the manuscript is published.”

As a general rule, the roles that different individuals take with respect to published research is decided early in the process - ideally before the research project begins. In a typical paper from my lab, the student is the first author and writes the first draft of the paper. I am usually the last author. I work closely on the design of the study, in evaluating the results, and in editing the drafts for final publication. If others are involved in supporting roles, they are usually included as middle authors. If an individual plays a purely technical supporting role, they may be acknowledged in a footnote rather than be included as a co-author. It is also the case that I might enlist a student - usually an undergraduate - to carry out a study that I designed in full and which I write up. In this instance, I might be the first author on the paper.

However, there have been exceptions to this policy. I have many times declined to be included as a co-author on work done in my lab for which I did not consider myself as having played a significant role. I do not approve of honorific authorships for myself or others. If I decline to be an author on a paper, it is almost always for that reason and it does not reflect on the quality of the work.

One problematic issue that arises frequently is the orphaned study. This is a study for which a student collected the data, perhaps wrote a draft of the results, but left the lab before the paper was accepted for publication. If the student continues to work on the paper at a reasonable pace after they leave the lab, they remain as first author. However, if the student abandons a project performed in my lab and under my supervision, then I reserve the right to assign another student to complete the analysis and publish the paper. In that instance, the amount of work that the departed student completed before leaving will determine whether they are included on the final paper, and in what authorship position. For example, if a student collected data that was never analyzed or written up, and that student stopped working on the project (e.g., perhaps the student was now employed outside of academia), that student might be acknowledged in a footnote. It is common for research to be presented as a conference as a poster or platform talk before it is published. In those instances, the authorship list for the conference may be different and perhaps more expanded than the final authorship list on the published paper. Typically, the student who conducted the research presents the paper/poster at the conference at the expense of the lab.

One last issue concerns the pace of research and publication. Science is a competitive enterprise with many labs often working on the same ideas, and publishing in a timely manner has important benefits. Yale is a high-level research university, and our graduate program is research-focused. Thus, my expectation is that conducting and publishing your research from the lab is your highest priority for your training. However, if a critical project (i.e., one central to the standing of the lab in the field or related to an important aim of the lab’s grant support) is languishing due to a perceived lack of effort, the leadership of that project may be changed.

Communication Guidelines

Electronic communication

Science requires a lot of ‘head down’ time and the constant use of electronic communication (email, Slack, text) can drive us all to the point of distraction. I do expect that we will use email or Slack to communicate and organize meetings, but I will be always looking for ways to reduce the lab’s dependence on a constant buzz of messages.

Journal publications

Submitting a paper for publication does not come with a prescribed deadline, but journal articles are more important to your career than departmental milestone documents. I generally work with students on papers in stages. With early drafts, I provide high-level organizational feedback. I frequently meet with students to ‘story-board’ the paper at the level of major points and major figures. In later drafts, I do word-level editing. In the early stages of a paper, where my feedback is organizational, I can usually provide it within one week. However, in later drafts, where I am word-level editing, a two-week period is more typical.

Oral presentations

In addition to writing papers, learning to give an oral presentation about your work and to defend the work to an audience is essential to a successful career. I encourage students to present their work at as many campus venues as possible (e.g., Current Works, internal lab meetings, lab meet ings of other groups) because practice in giving talks is important. Students will also be presenting their work regularly at my weekly lab meeting. Learning to structure, pace, and deliver a talk is important, and I will strive to help you develop these skills. A common approach used in many labs at Yale, including my lab, is to review a student’s oral presentation with them immediately afterwards, to give pointers and constructive feedback. Depending upon the importance of the talk, it is also common to have one or more practice talks beforehand, where the presentation is shaped and critiqued.

Learning how to answer questions from the audience is just as important as structure and pacing. For example, how a candidate handles questions is valuable information for a search committee to discuss following a job talk. You may find yourself presenting a talk to an advisory board for a granting institution, in which answering questions concisely and directly may be the difference between being funded or not. Throughout your academic career, you might find yourself presenting a talk to an audience in which individuals present are hostile to your research or skeptical of your results, and who express their opinions in the form of questions. Every faculty member has more than one story about giving a talk to a tough crowd.

My point here is not that I encourage hostile questions at lab meetings. Quite the contrary. I do not tolerate rude comments during talks in my lab or ad hominem remarks disguised as tough questions. However, I do encourage the asking and answering of questions. Students learn to ask questions in a constructive way, and students need to learn to defend their work. We are all personally invested in our research, and we differ in our sensitivity to questions that challenge our results. If anyone in the lab feels that the feedback they are receiving is not constructive, then they should bring this immediately to my attention.

Resolving Conflicts

If you have a conflict with another student, another faculty member, or a staff member that can’t be resolved with a conversation, you should bring this matter to my attention as soon as possible. It is my responsibility to you as your primary adviser to attempt to resolve disputes. If you have a conflict with me, you can talk to me directly. I have had such conversations in the past, so you needn’t worry about being the first. However, if you feel unable to talk to me directly, you can talk to a trusted faculty member, the DGS, or the Department Chair, who will then speak to me. You can ask them to maintain your anonymity if you so desire. If you have observed unethical behavior in the lab (e.g., anyone not following IRB procedures, or manipulating data, etc.), it is your duty to report this to me immediately and not attempt to resolve it on your own. The scientific and ethical integrity of the lab is my responsibility. I will not reveal your identity in investigating lapses in lab ethics.

If you feel that you have been the target of harassment of any kind and in any context, you can bring this to my attention. I am familiar with the resources available on campus and I will strive to get you the support you need. You can also report the harassment to a Dean’s Designee, the Title IX office, the University-wide committee on sexual misconduct, or the Office of Institutional Equity and Access. If you choose to discuss matters with me, I can maintain confidentiality in most cases if you wish. However, like all faculty, I am bound by the law to be a mandatory reporter for Title IX complaints.

Expectations for Ethical Behavior

Personal ethics

I expect that everyone in my lab will treat everyone else honestly and with respect. I expect this of myself also.

Lab ethics

All lab members must read the IRB approved research protocols that govern the research con- ducted in the lab and abide by those protocols. If informed consent is required by the protocol governing your research, then it must be obtained and documented appropriately prior to running subjects.

All students are responsible for documenting each step of their data acquisition and analysis procedures. The method of documentation (e.g., a traditional data notebook, an electronic notebook) should be discussed with me beforehand. Regardless of the documentation method, it needs to be accessible by me and must remain with the lab. All code and associated files used for analysis must also be documented and preserved in a manner approved by me (e.g., in the Holmes Lab GitHub repository). The documentation and associated code must be sufficient to allow me or a designee to replicate your analysis results and reproduce your figures. As PI of the lab, I am responsible for the accuracy of lab results.

You also bear responsibility for your results. I am familiar with cases of suspected research fraud by graduate students. In those unfortunate cases, having step-by-step documentation is a strong defense. Whenever possible, students must test code they have written or statistical approaches that they are pioneering, with calibration or simulation data to make sure that the analysis is producing legitimate results. Additionally, students are expected to identify another lab member to check and review their code and analysis pipeline. It typically the case that this “code buddy” will receive authorship credit in any resulting manuscript.

Students must keep dated drafts of major revisions to manuscripts, and that those drafts are preserved in a manner approved by me.

Ethical lapses

Making a programming or analysis error is not an ethical lapse. However, realizing that you made an error and then hiding that fact is an ethical lapse. We should always be on the lookout for mistakes. If we find one, even in a paper that was already accepted for publication, we must admit the error and investigate its effect upon our results. If this means a paper is retracted or withdrawn, that is a better outcome than publishing a result that we know is incorrect.

Repeatedly analyzing data using different preprocessing approaches or covariates with the goal of achieving a significant p value, a process known as p-hacking, is not permissible in the lab. It is also not permissible to stop the acquisition of data before the agreed-upon number of subjects were acquired because you achieved a significant result in an intermediate analysis. All procedures for analysis and all subject groups tested must be reported in the published work.

Open Science

In recent years, there has been a strong support for more transparent lab procedures and reporting to remedy what has been called the replication crisis. Moving forward, I am interested in implementing more of the tenets of the open science movement in my laboratory such as preregistering studies, making all code public, and contributing data to open data repositories.

Reproducible Research

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. As noted above, the lab’s GitHub is https://github.com/HolmesLab.

The lab’s GitHub should be used to share code, stimuli, and data with the world. Only share data after you’ve spoken to Avram (we don’t want to share the data too soon, before you’ve had a chance to look at it thoroughly yourself). When you share code, make sure it’s flawless, because we don’t want to distribute buggy code to the world! Have your “code buddy” and other lab members check it if possible. Ask Avram to get access to the lab’s GitHub.

Reproducibility is related to replicability, which refers to whether your results can be obtained again with a different data set. That is, if someone ran your study again (with a different group of participants), do they get the same results? If someone ran a conceptually similar study, do they get the same results? Science grows and builds on replicable results – one-off findings don’t mean anything. Our goal is to produce research that is both reproducible and replicable.

Diversity, Equity, Inclusion

The RWJMS Psychiatry Department and the Holmes Lab is committed to Diversity, Equity and Inclusion. At the time of this writing, the Psychology Department and the University are each developing guidelines to ensure Rutgers provides an equitable and inclusive environment where all members feel safe, supported, and valued.

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 gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, ethnicity, or religion. We will not tolerate intimidation, stalking, following, unwanted photography or video recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention. Finally, it should go without saying that lewd language and behavior have no place in the lab, including any lab outings.

If you notice someone being harassed, or are harassed yourself, tell Avram immediately. If Avram is the cause of your concern, then reach out to the department chair or another trusted faculty member in the department.

Lab Resources

Wiki

The lab wiki is, well, a wiki for the lab. It has all of the information you need to get started, including tasks that need to be done upon arrival, day-to-day housekeeping duties, forms and flyers, programming and stats tips, information about accessing the high-performance computing cluster and lab servers. Edit it when you obtain information that will be useful for others to know! Ask the research assistant(s) to be added as a member.

Slack

Slack will be used as the primary means of lab communication (holmeslab-yale.slack.com)

Notes for the Holmes Lab Slack. When posting messages or looking for updates, check the appropriate channel: #general for lab announcements, #lab-meetings for notes or communication related to lab meetings, #papers for sharing links to lab-relevant papers and discussing them, #script_and_pipelines for sharing wisdom on code writing or asking (and answering) the coding questions of others, #training-opportunities for learning about training and workshops, and #random for non-work-related chatting that is best kept out of the work-related channels. Please feel free to create your own channels as needed.

Try to keep each channel on topic, so that people can subscribe only to the channels that concern them. For messages to one person or a small group, use direct messages. If you have to send attachments (e.g., papers) or send messages that include out-of-lab recipients, use e-mail. If it’s an emergency and Avram isn’t responding on Slack, e-mail or call him.

Full-time lab members should install Slack on their computers and/or phones. Part-time lab memers should also check Slack regularly. You should of course feel free to ignore Slack on evenings and weekends – and Avram probably will, too!