Aly Lab Manual
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Lab Manual
Table of Contents
Welcome!
Expectations and Responsibilities
• Everyone
• Principal Investigator
• Post-Docs
• Graduate Students
• Lab Manager
• Undergraduate Students
Code of Conduct
• Essential Policies
• Taking Photos & Videos
• Scientific Integrity
• Human Subjects Research
Lab Resources
• Wiki
• Slack
• Dropbox
• GitHub
• Google Calendars
• E-mail
General Policies
• Hours
• PI Office Hours
• Meetings
• Deadlines
• Presentations
• Recommendation Letters
• Data Management
• Open Science
Funding
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Welcome!
It looks like you recently joined the Aly Lab in Columbia University’s psychology department.
That’s great! We’re really glad to have you here, and will do what we can to make your time in the
lab amazing. We hope you’ll learn a lot about psychology and neuroscience, develop new skills
(coding, data analysis, writing, giving talks), make new friends, and have a great deal of fun
throughout the whole process.
This lab manual was inspired by several others, and borrows heavily from them (e.g., this one and
this one). It’s also a work in progress. If you have ideas about things to add, or what to clarify, talk
to me (Mariam, the PI) or the lab manager.
When you join the lab, you’re expected to read this manual and sign a form indicating that you
have done so.
This lab manual is licensed under a Creative Commons Attribution - NonCommercial 4.0
International License. If you’re a PI or a trainee in a different lab and want to write your own lab
manual, feel free to take inspiration from this one (and cite us!).
Expectations and Responsibilities
Everyone
Big Picture
Science is hard. But it’s also fun. In the Aly 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.
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Work on what you’re passionate about, work hard at it, and be proud of it. Be so proud of
it that you have to suppress bragging (but it’s ok to brag sometimes).
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 ok to makes mistakes, but mistakes shouldn’t
be 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 ok 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!
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Support your fellow lab-mates. Help them out if they need help (even if you aren’t on the
project), and let them vent when they need to. Science is collaborative, not competitive.
Help others, and you can expect others to help you when you need it.
Respect your fellow lab-mates. Respect their strengths and weaknesses, respect their
desire for quiet if they need it, and for support and a kind ear when they need that. Respect
their culture, their religion, their beliefs, their sexual orientation.
If you’re struggling, tell someone (feel free to tell Mariam!). 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 you shouldn’t feel shy about asking for help
or just venting.
If there is any tension or hostility in the lab, something has to be done about it
immediately. We can’t thrive in an environment we aren’t comfortable in, and disrespect
or rudeness will not be tolerated in the lab. If you don’t feel comfortable confronting the
person in question, tell Mariam. In any case, tell Mariam.
If you have a problem with Mariam and are comfortable telling her about it, do! If you
aren’t comfortable, then tell the lab manager (for smaller issues) or another member of
the psychology department (for more serious issues).
Stay up to date on the latest research, by using RSS feeds and/or getting journal table of
contents. Also consider following scientists in the field on Twitter
Remember the lab philosophy: “We like to do good science and have fun. At the same
time, but also separately”. 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.
Small Picture
There are a few day-to-day things to keep in mind to keep the lab running smoothly.
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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 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. You do not have to be in at 9am every day – just show up for
your commitments, and work the hours you need to work to get stuff done. (Note: the lab
manager is expected to keep more regular hours than other lab members)
Make sure the door to the lab is locked if no one is inside. Turn off the lights if you’re the
last one leaving for the day.
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.
Dress code is casual (and you can dress up if you want!) but not too casual. When
interacting with participants or presenting your work, don’t wear pajamas and sweat pants
– but jeans are totally fine.
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Be on time. Especially when you are running participants – in fact, 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.
Principal Investigator
All of the above, and I promise 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 letting you
attend conferences 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 (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 ok
– 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 (Mariam) when I’m wrong or when your opinion is different, and treat the
rest of the lab to your unique expertise
Graduate Students
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All of the above, and you will also be expected to…
• Develop your dissertation research. Your dissertation should have at least 3 substantial
experiments that answer a big-picture question that you have. Much of your work has to
be done independently, but remember that others in lab (especially Mariam!) are there to
help you when you need it
• Help mentor undergraduate students in the lab when they need it – either because they
ask, or because I ask you to. Undergrads can also help you collect data.
• Present your work at departmental events, at other labs (if invited), and at conferences
• Apply for grants (e.g., NRSA or NSF grants). It’s a valuable experience, and best to get it
early.
• Think about what you want for your career (academia – research or teaching, industry,
science writing, something else), and talk to Mariam about it to make sure you’re getting
the training you need for that career
• Make sure you meet all departmental deadlines (e.g., for your exams and thesis) -- and
make sure Mariam is aware of them!
• Prioritize time for research. Coursework and TAing are important, but ultimately your
research gets you your PhD and prepares you for the next stage of your career.
Lab Managers
All of the above, and you will also be expected to…
• Work on your own research project (developed with Mariam’s help)
• Help new lab members adjust to the lab by answering whatever questions they have that
you can answer. If you can’t answer, direct their questions to Mariam
• Maintain IRB protocols for the lab (writing them, renewing them), archive old consent
forms, keep any required paperwork up to date and organized
• Oversee the hiring, scheduling, and training of undergraduate research assistants
• Maintain the lab website and lab wiki, update the lab manual, add lab events to the lab
calendars, manage the lab Dropbox, check the lab e-mail address
(alylabcolumbia@gmail.com; take care of any e-mails that you can, forward the rest to
Mariam)
• Give new lab members access to the lab wiki, lab GitHub, lab calendars, and add their
experiments to the lab Dropbox
• Assist with the recruitment and scheduling of participants, including patients
• Assist lab members with data collection and analysis (behavior, fMRI, and/or patient
studies)
• Be in the lab on a regular basis -- more than other lab members, your presence in lab when
others are around is essential. This means you probably shouldn’t work 7pm to 3am –- try
9am to 5pm or 10am to 6pm, with flexibility depending on your out-of-work schedule
(e.g., doctor appointments)
Undergraduate Students
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All of the above, and you will also be expected to…
• Assist other lab members with data collection and analysis (unless you are working on your
own independent project under the mentorship of another lab member, in which case you
should work on that)
• Develop your weekly schedule by talking to your graduate student mentor or your postdoc mentor. You should be coming in every week, and scheduling enough time to get
your work done
• If you are earning course credit for research, you must also attend lab meetings when your
schedule permits, present at one of these lab meetings, and submit a write-up of your
research by the end of the semester
Code of Conduct1
Essential Policies
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 Columbia University policies on discrimination and
harassment, which you can (and must) read about here. Essential policies of Columbia University
can be accessed here.
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, 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 Mariam immediately. If
Mariam is the cause of your concern, then reach out to the department chair or another trusted
faculty member in the department.
Taking Photos & Videos
We respect the privacy and comfort of lab members by only taking photos or video recordings of
them with their explicit knowledge and consent. This is especially important in situations where a
lab member would otherwise not be aware of you taking a photo and therefore cannot object if
they do not want you to – e.g., if they are wearing one of our VR headsets or are being scanned.
To avoid ambiguity about when a lab member is vs is not aware of photos being taken, we ask
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This was adapted from the code of conduct found here and here.
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that everyone obtain consent from lab members before taking photos or videos, and obtain
consent again before posting any images on social media. This is done to respect others’ privacy
and acknowledge that people have varying degrees of comfort related to being photographed
and especially with having those photographs shared on social media.
The goal of this is to foster an environment where everyone feels safe to be who they are, take
risks, and have fun, without worry or self-consciousness. If someone wants to be photographed
doing something fun or silly in lab events, and consents to be photographed, by all means go
ahead! Just please respect the privacy of those who do not want that.
On a related note, you cannot photograph your participants during an experiment. We do not
have IRB approval to do this. If you would like a photograph of someone demonstrating your
experiment, ask a lab member if they would feel comfortable being photographed while
demonstrating what a participant does in an experiment.
Scientific Integrity
Research (Mis)conduct
The lab, and Columbia University, is committed to ensuring research integrity, and we take a hard
line on research misconduct. We will not tolerate fabrication, falsification, or plagiarism. Read
Columbia’s policies on the conduct of research carefully (main page here, institutional policy here,
more information here).
A big problem is why people feel the need to engage in misconduct in the first place, and that’s
a discussion that we can have. If you are feeling pressured to succeed (publish a lot, publish in
high impact journals), you should reach out to Mariam 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: you’re here to arrive at the truth, to get as close as we
can to facts about 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.
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),
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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. The lab’s GitHub is
https://github.com/alylab.
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.
Authorship
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 considered anyone involved with initial research design, data collection and
analysis, manuscript 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."
At the start of a new project, the student or post-doc taking on the lead role can expect to be first
author (talk to Mariam about it if you aren’t sure). Mariam will typically be the last author, unless
the project is primarily under the guidance of another PI and Mariam is involved as a secondary
PI – then Mariam will be second to last and the main PI will be last. Students and post-docs 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. If a
student or post-doc takes on a project but subsequently hands it off to another student or postdoc, they will most likely lose first-authorship to that student or post-doc, unless co-firstauthorship is appropriate. 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.
Old projects
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If a student or post-doc collects a dataset but does not completely analyze it or write it up within
3 years after the end of data collection, Mariam will re-assign the project (if appropriate) to
another person to expedite publication. If a student or post-doc voluntarily relinquishes their
rights to the project prior to the 3-year window, Mariam will also re-assign the project to another
individual. This policy is here to prevent data (especially expensive data, e.g., fMRI) from remaining
unpublished, but is meant to give priority to the person who collected the data initially.
Human Subjects Research
Adherence to approved IRB protocols is essential, and non-adherence can lead to severe
consequences for the entire lab (i.e., we may lose permission to run any research on human
participants). All lab members must read and comply with the IRB consent form and research
summary for any project that they are working on. If you are not on the IRB, you cannot run
participants, look at the data, analyze the data, or be in any way involved with the project.
Lab members must complete CITI Training and save their certificate. To be added to an existing
IRB, talk to the lab manager and present them with your CITI certificate. If your project does not
fall under the scope of a current IRB protocol, talk to Mariam and the lab manager about writing
a new one or filing an amendment to an existing one. You must ensure that you have IRB approval
to run your study before you begin (which means that you either submitted an IRB protocol that
got approved, or your name was added to an existing or amended IRB).
If a participant falls ill, becomes upset, has an accident with lab equipment, or experiences any
problems while you are conducting your research, you must notify me and the lab manager as
soon as possible. We may need to report this information to the IRB and/or funding agencies.
Lab Resources
Wiki
The lab wiki (https://osf.io/mdh87/wiki/home/) 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-today 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 lab manager to be added as a member.
Slack
Slack will be used as the primary means of lab communication. There are two Slack workspaces
for the lab: one just for us (alylab.slack.com) and one shared with Chris Baldassano’s lab
(alyssano.slack.com). Use the former if there are things to share that are only relevant with the Aly
Lab. Use the latter if there are things to share with the broader Alyssano labs.
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Notes for the Aly 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, #code-tips for
sharing wisdom on code writing or asking (and answering) the coding questions of others, #fmrimethods for sharing wisdom on fMRI data collection / analysis or asking (and answering) the fMRI
questions of others, #stats to ask and answer questions about statistical analyses, and #random
for non-work-related chatting that is best kept out of the work-related channels.
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 Mariam isn’t responding on Slack, e-mail her.
Full-time lab members should install Slack on their computers and/or phones. Part-time lab
members should also check Slack regularly. You should of course feel free to ignore Slack on
evenings and weekends – and Mariam probably will, too!
Dropbox
The lab has a shared Dropbox account that is used to store experiment code, so that you can run
your experiment on any computer that has access to the lab Dropbox folder. The lab Dropbox is
also used to store documents and files for general lab use (e.g., IRB documents, stimuli,
demographics forms, etc), though the lab wiki will also have that information. Contact the lab
manager when you want to add something to the lab Dropbox.
GitHub
The lab’s GitHub (https://github.com/alylab) should be used to share code, stimuli, and data with
the world. Only share data after you’ve spoken to Mariam (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 other lab
members check it if possible. Ask the lab manager to get access to the lab’s GitHub.
Google Calendars
The lab has many Google calendars.
1. Aly Lab calendar: used to keep track of lab events, including any lab meetings just for our
lab, and birthdays!
2. Alyssano Lab Meeting calendar: used to keep track of joint lab meetings with the Baldassano
lab.
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3. Aly Lab – Travel Schedules calendar: used to indicate travel dates (e.g., “Mariam away” for
August 1-7), so that other people know when you aren’t available. You are not obligated to
put down your travel dates, but they are useful for planning purposes (e.g., Mariam will know
not to bother with lab meeting if no one is around; or if she is writing a grant, it helps to
know if you will or won’t be available to provide data, etc).
4. Aly Lab K-Space calendar: used to reserve time in the lab’s desk in K-Space in the Jerome L.
Greene Science Building (MBBI). This desk is useful to use if you will be at MBBI for extended
time and need a place to work (e.g., between fMRI scans, or between a scan and a talk).
5. Aly Lab Running Rooms calendar: used to reserve time in the experiment running rooms
6. Aly Lab MacBook calendars: used to reserve one of the two MacBook laptops. Laptops should
be used for running experiments first and foremost (e.g., patients, fMRI). If they are available
and not in use for an experiment, you may also use it for meetings, etc.
E-mail
We have a lab listserv for sending e-mails to the entire lab when necessary (alylab@columbia.edu).
Contact the lab manager to get added to the lab listserv.
We also have a lab listserv for sending e-mails to the lab meeting group. Everyone on
alylab@columbia.edu is also on alylabmeetings@columbia.edu; but there are some people on the
lab meeting listserv that aren’t members of the lab, and are just interested in attending our lab
meetings. Talk to the lab manager if you want to be added to the lab meeting listserv.
Everyone on alylabmeetings@columbia.edu is also on alyssano@columbia.edu. This latter listserv
is for joint lab meetings between the Aly Lab and Chris Baldassano’s lab.
There is also a lab e-mail account that only the lab manager and Mariam can access
(alylabcolumbia@gmail.com) -- people often contact the lab (e.g., if interested in participating in
studies) through that email address.
General Policies
Hours
Being in lab is a good way of learning from others, helping others, building camaraderie, having
fast and easy access to resources (and people) you need, and being relatively free from
distractions at home (e.g., your bed or Netflix). That said, hours in academia are more flexible than
other jobs -- but you should still treat it as a real job (40 hours/week) and show up to the lab. My
primary concern is that you get your work done, so if you find that you are more productive at
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home (lab-mates can be chatty sometimes), feel free to work at home occasionally. If you have no
meetings, no participants, and no other obligations that day, it might be a good day to work at
home – but you can’t do this all the time, and I expect to see everyone in the lab on a regular
basis.
The only exception to this is lab managers / research assistants, who must keep more regular
hours and be in lab 5 days a week (excluding vacations, doctor appointments, family issues, etc).
I expect lab managers / research assistants to be in about 8 hours a day, starting around 9am or
10am and ending around 5pm or 6pm.
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.
I’m a night owl and sometimes work 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 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.
PI Office Hours
In addition to weekly meetings (see below), and occasionally dropping by the lab, you can find
Mariam in her office. Her door is almost always open; if it is, feel free to ask for a chat. She will
always say yes, though sometimes she can only spare a couple of minutes. If her door is closed,
assume that Mariam is either gone, in a meeting in her office, or does not want to be disturbed –
so please send a message (Slack or e-mail) rather than knocking.
Meetings
Weekly Lab Meetings
Weekly lab meetings (~1.5 hours each) are meant to be a forum for trainees to present project
ideas and/or data to get feedback from the rest of the group. Projects at any level of completion
(or even not yet started!) can benefit from being presented. These lab meetings can also be used
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to talk about methods, statistical analyses, new papers, and career development. For paper
discussions, everyone must come to lab meeting having read the paper and prepared with
comments and questions to contribute. Some weeks we may explore a particular issue and have
people read different papers – in that case, come to lab meeting having read your paper and be
prepared to summarize it for the group.
Each trainee (RA, students, post-docs) is expected to present at least once every semester. These
meetings are informal, and you can do what you wish with your slot – just be prepared to
contribute something substantive. Lab members are also expected to attend every meeting
(obviously, illnesses, doctor appointments, family issues, etc are a valid reason for missing a
meeting). Undergraduate students are encouraged to attend as often as possible (assuming it fits
in their course schedule).
Occasionally, we may have joint lab meetings with other faculty in the department – these may
be combined with our weekly lab meeting or an additional meeting. We will also use lab meetings
(or ad-hoc scheduled meetings) to prepare for conference presentations and give people
feedback on job talks or other external presentations. Lab meeting agendas and notes will be kept
in the #lab-meetings channel on Slack.
Individual Meetings
At the beginning of each semester, we will set a schedule for weekly meetings. Each full-time lab
member (RAs, graduate students, post-docs) will have a one-hour slot set aside to meet with
Mariam. If scheduling conflicts arise (e.g., because of travel), we can try to reschedule for another
day that week. If there is nothing to discuss, feel free to cancel the meeting or just drop by for a
brief chat.
Mariam will meet with undergraduate students every other week (or according to need); postdocs and graduate students should meet with their undergraduate mentee on a regular basis.
Deadlines
One way of maintaining sanity in the academic work is to be as organized as possible. This is
essential because disorganization doesn’t just hurt you, it hurts your collaborators and people
whose help you need. When it comes to deadlines, tell your collaborators as soon as possible
when you know when a deadline is, and make sure they are aware of it the closer it gets. Don’t be
afraid to bug them about it (yes, bug Mariam as well).
Give Mariam at least one week’s notice to do something with a hard deadline that doesn’t require
a lot of time (e.g., reading/commenting on conference abstracts, filling out paperwork, etc). Give
Mariam at least two weeks’ notice to do something with a hard deadline that requires a lot of time
(e.g., a letter of recommendation). For manuscript revisions and invited paper submissions (which
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have hard-ish deadlines), give her as much time as you can, because these will require multiple
back-and-forths.
For manuscript submissions (i.e., no hard deadline), you can still bug Mariam to give you feedback
if she hasn’t responded in a week or two – papers are important!
Presentations
Learning to present your research is important. Very few people will read your papers carefully
(sad, but true) but you can reach a lot of people at conference talks and posters. Also, if you plan
on staying in academia, getting a post-doc position and getting a faculty position both
significantly depend on your ability to present your data. Even if you want to leave academia,
presentations are likely to be an important part of your job. Additionally, every time you present
your work, you are representing not just yourself but the entire lab.
It is therefore highly encouraged that you seek out opportunities to present your research,
whether it is at departmental talk series and events, to other labs (within or outside of Columbia),
at conferences, or to the general public. If you are going to give a presentation (a poster or a talk),
be prepared to give a practice presentation to the lab at least one week ahead of time (two weeks
or more are advisable for conference presentations, and many weeks ahead of time are advisable
for job talks, which require much refining). Practice talks will help you feel comfortable with your
presentation, and will also allow you to get feedback from the lab and implement those changes
well in advance of your real presentation.
Templates for posters will be available, and you can use those as much or as little as you’d like.
Some general rules for posters should be followed: minimize text as much as possible (if you wrote
a paragraph, you’re doing it wrong), make figures and text large and easy to see at a distance,
label your axes, and make sure different colors are easily discriminable. Other than that, go with
your own style.
Mariam is also happy to share slides from some of her talks if you would like to use a similar style.
You’ll get a lot of feedback on your talks in any case, but other people’s slides might be helpful
to you as you are setting up your talk. As with posters, feel free to go with your own style as long
as it is polished and clear.
Recommendation Letters
Letters of recommendation are extremely important for getting new positions and grants. You
can count on Mariam to write you a letter if you have been in the lab at least one year (it’s hard
to really know someone if they have only been around for a few months). Exceptions can be made
if students or post-docs are applying for fellowships shortly after starting in the lab.
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If you need a letter, notify Mariam as soon as possible with the deadline (see Deadlines for
guidance), your CV, and any relevant instructions for the content of the letter. If the letter is for a
grant, also include your specific aims. In some cases (especially if short notice is given), you may
also be asked to submit a draft of a letter, which will be modified based on Mariam’s experience
with you and anything else that has to be added. This will ensure that the letter contains all the
information you need, and that it is submitted on time.
Data Management
Storing Active Datasets
Lab data can be stored in one of three places:
1. Lab server(s): fMRI data, behavioral data, and (separately from data and coded so that data
are not identifiable) electronic consent forms, demographics forms, questionnaires
2. Shared Dropbox folders (not the Aly Lab Dropbox) can be used to share small datasets
and/or code with collaborators
3. Habanero (Columbia’s new HPC cluster) can be used to store small amounts of data as
you are running analyses on it – it is not for permanent storage, as we only have a limited
amount of space there
Although the servers are backed up, the backup is only on-site – so make extra backups! Each lab
member should back up raw data on an external hard drive, as well as the code needed to
reproduce all analyses. You should not store data locally on your computer (but having data in a
Dropbox folder synced to your computer is ok).
Data Organization
If you have already run several independent projects and have a data organization structure that
works well for you, feel free to use it. If not (or if you are looking for a change), the following
structure is recommended (based on Neuropipe):
•
projectName/subjects
o individual directories for each of your participants
o projectName/subjects/{subj}/analysis
▪ subject-specific analyses (e.g., 1st and 2nd level analysis – at the run level and
experiment level)
o projectName/subjects/{subj}/data
▪ raw data for that participant, with the following directories…
• behavioralData (for, well, behavioral data)
• eyetrackingData (if applicable)
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•
•
•
•
•
• nifti (raw nifti files / raw MRI and fMRI data)
• rois (participant-specific ROIs)
o projectName/subjects/{subj}/design
▪ timing files for that participant, with different directories for the different
GLMs you’re running (and the different runs in the experiment)
o projectName/subjects/{subj}/fsf
▪ if you’re using FSL, put the .fsf fies here. If you’re using SPM or something
else, save the files for setting up preprocessing and GLMs here
o projectName/subjects/{subj}/scripts
▪ Matlab, Python, R, or bash scripts that you used for that participant. You
should keep the ‘template’ scripts elsewhere, but you can store scripts you
modified specifically for that participant here
projectName/scripts
o template scripts and that you may modify for each participant, as well as scripts
and functions used for all participants and group analyses
o recommend making subdirectories for each type of analysis (e.g., behavior, pattern
analysis, functional connectivity, univariate)
o if you have scripts that are the same for each participant, you can have symbolic
links for them in your participant-specific scripts directories
projectName/results
o figures with main results, powerpoint or keynote presentations, manuscripts if you
wish
projectName/notes
o detailed notes about the design, analysis pipeline, relevant papers, etc
projectName/group
o group analyses
o recommend making subdirectories for each type of analysis (e.g., behavior, pattern
analysis, functional connectivity, univariate)
projectName/task
o code for your behavioral experiment, stimuli, piloting information
o if you are running your presentation code out of Dropbox, it will still be good to
have a copy of the code here (but you can keep the stimuli only on Dropbox if
you’d like)
When you leave the lab, your projects directories should be set up like this, or something similarly
transparent, so that other people can look at your data and code. You must do this, otherwise
your analysis pipeline and data structure will be uninterpretable to others once you leave, and this
will slow everyone down (and cause us to bug you repeatedly to clean up your project directory
or answer questions about it).
Archiving Inactive Datasets
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Before you leave, or upon completion of a project, you must archive old datasets and back them
up. We will develop the instructions for this when we reach our first inactive dataset ☺
Open Science
We’re all for open science, so lab members are encouraged (well, required) to share their code
and data with others, whether they are in the lab or outside of it. Within lab, you can share your
code and data whenever you like. But do not share your code or data with the outside world until
you think (and Mariam agrees) that the lab has finished working with it. This gives us an
opportunity to work with the data to meet our needs (including grant needs!) before releasing it
for other people to use. Generally, we will try to make our data and code publicly available within
one year of publishing the results (longer if work on the dataset is ongoing). Currently, the best
option for sharing smaller datasets might be the Open Science Framework, and the best option
for sharing MRI datasets is OpenFMRI (let the lab know if you find others).
We will also share our work with the world as soon as we ready, which means preprints! The lab
policy is to upload a preprint of a manuscript simultaneously with initial submission to a journal.
The preferred preprint servers are bioRxiv and PsyArXiv. We will also put PDFs of all our papers
on the lab website, and you should share PDFs of your paper with whoever asks.
Funding
Funding for the lab currently comes from Mariam’s start-up package from Columbia University,
as well as a few grants. If you need to buy something, or have to charge a grant for something,
let Mariam know and she will oversee the process.
At some point, you will likely be asked to provide a figure or two for a grant Mariam is writing,
and/or provide feedback on the grant. Relatedly, you are entitled to read any grant Mariam has
submitted, whether it is ultimately funded or not. Aside from being a good opportunity to learn
how grants are written, this will also allow you to see her vision for the lab in the years ahead. Feel
free to ask Mariam to see any of her grants.
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