Lab Manual¶

Naturally, the ‘y’ laboratory likes to ask ‘why’ questions: Why are some cells more vulnerable to Alzheimer’s disease? Why are some cancers more resistant to treatment than others? More broadly speaking, we seek to develop methods to tackle any interesting biological questions, whenever computation and data might help accelerate biological discoveries and enable potential improvements in quality of life: What can model organisms tell us about human disease? How can we develop better visualizations to aid interpretation and improve the efficiency of not only other computational biologists, but also bench scientists and clinicians?

The key to answering (and asking) interesting questions well in our lab typically requires proficiency in three core areas: programming, statistics/machine learning, & biology. Of course, we recognize that there are few researchers that can claim expertise in all three, but honing our skills and combining our strengths is what we strive to do. Because the questions we are answering require multidisciplinary approaches and experimental validation, collaboration and teamwork are central to our lab’s ethos. To maximize the reach of our work, we care deeply that we write good code, carefully validate methods, make analyses reproducible, and release user-friendly software and tools that can be used widely.

Expectations & Responsibilities¶

Research is often described as a marathon, but everyone has their own individual work styles and approaches for productivity. In our lab, we seek to create an intellectually stimulating environment that is also supportive, balanced, positive, and rewarding. Everyone in the group comes from different backgrounds, personalities, and experiences. Sometimes, this may cause conflict, but we should leverage diversity as a strength—it is always important to be collegial and professional, to view the lab as a team. We are in this together, and hopefully, beyond learning a lot and doing great research, you’ll also make new colleagues and friends along the way.

Towards this end, everyone is expected to:

be honest, ethical, and have integrity (being honest when no one is looking)
be engaged both within the research group and with external collaborators
share your knowledge without judgment (as your seniority and corresponding knowledge grows, so does your responsibility!)
communicate honestly, even when it might be difficult
treat everyone (both inside and outside of the lab) with respect
be a team player and exhibit collegiality: to promote this, everyone in the lab should be addressed on a first-name basis (so, for example, feel free to refer to Vicky as simply Vicky, versus Dr. Yao or Prof. Yao)
be kind (this includes yourself as well—working hard is important, but so is your physical and mental health!)

In addition, we also expect you to be considerate of others, including:

stay home when you are sick: we are lucky, as computational researchers, to be able to work from anywhere, so there is no need to put other people at risk if you are feeling unwell but still able to work; but use discretion and make sure that your responsibilities are still taken care of
try to be punctual: be respectful of everyone’s time; of course, things happen, and if you’re running late, let relevant parties know asap
try to develop independence: everyone should feel free to ask questions, but being considerate of others’ time includes putting in a good faith effort to find solutions before asking
be cognizant of common areas (shared lab office space): this includes keeping shared areas clean and noise levels down; this also includes not wearing strong fragrances and being generally mindful of odors
use and speak English in the workplace: it can often feel more convenient or efficient to communicate in another language, but it is easy for other people to feel excluded (even if that is not the intention) when there are side conversations in a language they cannot understand; as a general rule, when in lab and at lab events, please use lingua franca, aka English (but feel free to teach us useful / interesting phrases in your language if you speak another!)

Roles¶

While everyone should follow these general expectations & responsibilities, below are additional guidelines depending on your role in the lab, as well as the policy for lab meeting, conferences, etc:

Principal Investigator¶

obtain funding to support the function of our lab
support lab members in their professional growth, including planning for career goals, helping design research projects, serving as a sounding board for ideas, writing letters of recommendation, etc.
mediate conflicts should they arise to ensure that the lab is a positive, healthy, safe environment

Staff Scientist¶

focus efforts on priorities defined by the PI, including grant and paper writing, research projects
as needed, help with day-to-day lab management
assist with mentoring of other lab members

Postdoctoral Fellow¶

aim for 2-3 first author papers
provide scientific and technical leadership within the lab
define career goals early on and work towards them
apply for fellowships and help write grants

Graduate Student¶

meet department and graduate school reporting and exam requirements
aim for at least 2 first author papers (probably more for those who are aiming for academia, which we can discuss)
mentor undergraduates
as senior students (roughly defined as post-qualification exam):
- mentor junior graduate students
- help review papers and write grants, as appropriate

Undergraduate Student¶

be able to devote at least 10 hours a week to research during the semester (and 40 hours if working over the summer)
be involved in lab meeting and journal club: present at least once a semester / over the summer

Meeting Structure¶

Lab Meeting¶

Lab meetings will be held weekly and be no longer than 2 hours except in rare circumstances. We will set a recurring day / time / location at the beginning of each semester to coordinate around course schedules / other recurring meetings. All graduate students and senior lab members are expected to attend, be engaged, and participate in the meetings even if they are not presenting.

Try to refrain from using phones, laptops, or any other devices that might be distracting during this time. If there is any confusion during a presentation, don’t be afraid to ask questions as this might start a more meaningful discussion.

Meeting Format¶

Logistical updates (<10 minutes): Mention any upcoming events, new member introductions, new shared resources (or resource limitations)

Journal club (~15 minutes): The presentation rotation order is in ‘shared google spreadsheet’ and will be updated once every semester. The spreadsheet is linked with the lab calendar which will show upcoming journal club presentations as well as who is giving the lab meeting update. For each journal club, prepare a presentation with 3 papers (5 mins each, one of the papers should be ‘new’, i.e., published within the last 6 months).

For each paper, prepare a simple slide deck:

title: paper title, authors, journal, date of publication
overview: a summary figure (e.g., flow chart) from the paper or the key result figure
motivation: why did you pick this paper? Ideally, show the results that inspired you. But also feel free to share whether the paper lived up to your expectations, any potential implications for research in and outside of lab

Try to provide intuition for the methods and results of the paper, rather than focusing on the nitty-gritty details.

Updates (~35 minutes): Lab meeting updates happen on a rough rotation. Every student is assigned a spot in the rotation and can be viewed at any time in the lab meeting spreadsheet. You can choose how you would like to use this time, with some examples below:

feedback session: an opportunity to either get feedback from the entire group on any results / methods, share any problems that might be blocking your progress
practice talks: more time can be devoted to practice talks (or even scheduled for a longer block at another time) as necessary; per the lab policy, for various public presentations (including posters, see Presentations section), practice talks are required. Naturally, these talks are more formal, with a complete slide deck that matches the length requirements for the talk

Individual Meetings¶

Individual 1-1 meetings for all members of the lab will be held weekly with Vicky. Each time slot is 15-30 mins and will be set up at the start of each semester. The purpose of these meetings are to give you a time to plan career-related and project-related strategies and timelines, have a sounding board for new thoughts and ideas, and to discuss/resolve specific obstacles and challenges that may arise throughout the week. This is also a chance for you to give Vicky feedback or bring up any lab policies or personal conflicts that may be hindering your progress and/or general happiness in the lab.

These meetings are a reserved, dedicated time slot, and you are not obliged to use all of them if you have nothing to discuss. They will not be rescheduled by default if there are conflicts (due to travel, illness, etc.), but try to touch base at least once a month. Note that negative results are a very important part of research and are not included in the “nothing to discuss” category. In fact, discussion of negative results is highly encouraged!

Semiannual Development Planning¶

More structured 1-1 development planning meetings will be held every six months for graduate students, postdocs, and staff with Vicky. These meetings are required and will last around 30 minutes. During this meeting, we will discuss and set both short and long term goals.

Prior to the meeting, prepare a document (see SDP example) with the following information (when applicable) since the previous meeting:

accomplishments:
academic milestones (e.g., qualification exam, completed TA / course requirements)
status of any publications, grants/fellowships/awards
presentations (posters and talks)
mentoring / teaching / organizing
obstacles: anything that didn't work out as planned? Potential follow-up steps?
research goals: any research interests that are not currently represented in current projects?
personal/professional goals: what are your career aspirations? Have they changed since the last meeting?
feedback: where have you improved / what have you learned since the last meeting? Where do you think further improvement might be helpful? What can I do to help you improve?

Send this document before the meeting to Vicky on slack (file format: lastname-firstname-yyyymm-sdp.md).

Working Hours¶

During weekdays (excluding holidays and personal time off), lab members are expected to answer emails / slack messages within a day. One of the benefits of academia is schedule flexibility, though with that, occasionally there may be times when you might need to work ‘odd’ hours, including the weekend (e.g., pushing for a deadline). Vicky may send you messages at ‘odd’ hours, but you are not expected to read or reply to the message until the next working day, unless there are exceptional circumstances that we will have discussed in advance. As a rule of thumb, group members are expected to produce the equivalent amount of work based on a 40 hour week (clarifications can be discussed during biannual or individual meetings).

We understand that individuals have different chronotypes and may be productive at different hours of the day. Nevertheless, please make an effort to work during the core hours of ~1pm-5pm to facilitate responsive interactions. In the new COVID era, we have embraced hybrid working models. Please try to work from the office at least 3 days a week. In general, being physically present in the lab is helpful for building community, asking for help, as well as learning from and supporting your peers. Junior students may need more structure and should consider spending a longer time in the office during core hours (either before 1pm or after 5pm) at the beginning.

Vacations & Absences¶

It is important and beneficial for your productivity and creativity to take breaks from work. Rice’s policy is to give graduate students two weeks of paid vacation, in addition to staff holidays, a year. Postdocs and staff members have more, per Rice’s HR. Work-life balance is important, and feel free to use this time to recharge, but please notify Vicky and mark your availability on the lab availability calendar two weeks in advance.

Of course, personal emergencies, sicknesses, etc. may arise suddenly. Please also note these on the lab availability calendar as soon as possible, and let any affected parties know.

Since our work can be easily done remotely, the lab’s travel policy is actually more flexible, especially since, for example, international students may want to travel home for longer. In these situations, a good rule of thumb is that for any time beyond the standard vacation policy, try to be available and productive. Longer vacations and absences need to be pre-approved by Vicky a minimum of one month in advance and also noted on the availability calendar after approval.

Summer Work¶

Some students may be interested in exploring internship opportunities in the summer and should be discussed with Vicky early in the process. Typically, the earliest time students should consider internships is after they pass their qualifying exam.

For students not doing internships, summers are a great time to make substantial research progress. That said, if a student wishes Houston for the summer, they can work remotely for up to 2 months with prior approval from Vicky. While working remotely, students are expected to attend all normal weekly meetings and be available on Slack during core hours (Houston time). Students should use Slack's status feature to mark themselves as working remotely for the duration of their time away.

Papers & Authorship¶

Publishing is the currency of academia and can sometimes be the source of much contention. To minimize ambiguity, frequent communication, both early on and throughout the process, is crucial. Here are some of the guidelines we adhere to in writing papers and determining authorship in the lab:

internal review: as noted frequently throughout the document, lab members are a great resource for each other, and as such, before the final draft of any paper, the manuscript should be circulated for feedback from all other members of the lab; the first author(s) are in charge of soliciting, organizing, and incorporating any helpful feedback
code: all code associated with papers will be made public and must adhere to the coding standards of reproducibility and readability for the lab
coauthor approval: all applications, abstracts, and papers need to get approval from coauthors before submission
preprints: we will submit manuscripts to a preprint server (e.g., bioRxiv, arXiv) at the time of journal submission (there may be exceptions, e.g., at collaborators’ request, though we would encourage them otherwise)
intellectual property: all code, data, manuscript drafts, and grants produced in the lab are the lab’s intellectual property

Authorship¶

Typically, when starting a new project, the trainee taking the lead role can expect to be the first author of the published work; Vicky will typically be the last author. Others who help over the course of the project may be added, depending on their contributions, and placement will be discussed with all other authors. If a trainee takes on a project but subsequently hands it off to someone else, they will likely lose first authorship to the person they pass it on, unless co-first authorship is appropriate.

As with all other things in the lab, we will have candid discussions about authorship—do realize that authorship discussions are ongoing as things can change over time! Projects can take unexpected turns, contributions can shift, and new collaborations can enhance the work. If there are any concerns at any point (if you are not sure about your authorship status or believe that it needs to be renegotiated), please bring it up with Vicky.

Here are some more detailed guidelines on specific concerns that may come up regarding authorship:

final decisions: if there is any contention regarding authorship, Vicky is the final arbiter (in collaborations, Vicky will be your advocate)
inclusion criteria: there are many resources discussing how authorship should be determined, but at its core, it really is both a meaningful contribution to the intellectual content of the manuscript and writing (including revisions) of the manuscript; this will be discussed early on, but authors can be added later during the process (and will be discussed with all other authors).
tasks that do not automatically result in authorship: as mentioned earlier, the lab is expected to be helpful and supportive of each other; this may include proofreading manuscripts, helping debug software issues; in general these will not (and should not, ethically speaking) automatically result in coauthorships
wrapping up: seeing a manuscript through to publication is important; if one cannot finish in a timely manner (e.g., leaving the lab and no longer working on revisions) and someone has to take over, author order may change and will be discussed amongst all parties
within lab mentoring: when a senior member of the lab mentors a junior member, for the resulting work, the junior member will typically be listed first, and the mentor later (may be co-first depending on the specific situation)
author responsibilities: first author(s) are responsible for the bulk of data analysis, figure prep, writing, and coordination, and coauthors should remain engaged, helpful, and contribute as needed at all stages
finishing up work prior to joining the lab: in the scenario where there is unfinished work from a prior lab, finishing is a good idea, and you are encouraged to do so; however, to make the most of your time in the lab, you should spend no more than 20% of the work week on these projects, and it should taper off after ~3 months (obviously, any time outside of your normal work hours is up to you!). As a rule, you do not need to list Vicky as an author just because you now work in the lab, but please disclose what you are working on so that we can discuss any potential conflicts of interest. If this timeline is not possible, please discuss with Vicky asap, and we can work something out.

Presentations¶

Presenting your work is important for communicating your findings and getting feedback from a broader audience beyond the lab. For both posters and talks, keep in mind that you are representing yourself as well as the entire group. In order to help you do your best and reduce some of the stress beforehand, all students and postdocs must give a practice talk at least 1 week prior to the event (reference presentation tips as you prepare). For major talks (e.g., qualification exams, defenses, major conferences), more time should be allotted as multiple practice talks may be necessary. The presenter is responsible for coordinating schedules in advance and incorporating feedback. Posters must be submitted to slack for feedback a minimum of 1 week before they will be printed.

Conferences & Workshops¶

An added benefit of going to a conference is that you get to learn about what’s going on in the field, get new ideas, meet and network with other scientists, and explore somewhere new! Senior graduate students and postdocs are encouraged to attend 1-2 conferences a year provided they present a poster or give a talk. As a rule of thumb, conferences should be in the continental United States (or international at an equivalent cost) and should correspond to the research projects / grant funding of the lab member.

It is likely that we will discuss potential conferences at the development planning meetings. Typically, the two biggest general computational biology conferences every year are RECOMB and ISMB, but you are of course welcome to identify others you may be interested in attending. As always, discuss with Vicky first, and be sure to clear all abstract submissions with her (and then with coauthors) at least 1 week prior to submission. You should also apply for travel awards—these both look good on your resume and help keep costs low.

In terms of travel expenses, for an approved conference, the lab will typically cover registration, poster printing, transportation (flights, trains, etc), lodging, and in some cases, meals (depending on the grant, the limit for meals varies and it may be easier to just cover a per diem). When selecting transportation and lodging, try to be judicious with lab resources. This includes sharing rooms when possible and choosing less expensive options (balancing with convenience, travel time, and most importantly, safety). When in doubt, ask!

Collaborations¶

As mentioned several times throughout this document, collaboration and teamwork are a core part of our group. Tackling important questions necessitates working as a team within the lab, as well as externally with other experts in statistics, biology, and medicine who can provide domain specific knowledge and directly apply our predictions to real world problems. Fortunately, we have abundant opportunities to pair with experimental and clinical labs to work together and solve common goals. Your role in these projects will vary, but will include elements of methods development and data analysis where you will be the computational expert often guiding downstream experimentation. To maintain trust, increase efficiency, and ensure the quality of our work, it is important to get internal feedback from the lab members before presenting results to collaborators, especially early on.

It is also important to maintain a healthy working relationship with your collaborators—collaborations are often fun and rewarding, but it is also possible to get bogged down with requests that may not always closely align with our overall research goals. As always, Vicky will be your biggest advocate, so be sure to alert her if you have any trouble with time management or other issues / concerns as soon as possible. Things to watch out for: data analysis requests beyond the scope of your project, repeated contact / expectations to work outside of normal work hours, excessive pressure to prioritize the collaborative project, collaborators omitting Vicky from communications, etc. If something does not feel right, do not hesitate to ask Vicky!

As we develop new computational methods, members of the lab are encouraged to think broadly about their downstream applications and identify potential collaborations (internally and externally) that might benefit the community. However, any new collaborative projects (even with existing collaborators) must be discussed and cleared with Vicky first, as this is crucial for navigating funding, authorship, and to keep you on track with your individual goals.

Deadlines¶

While many things in academia and in the lab are flexible, there are still deadlines. We put in place several internal deadlines as mechanisms to ensure the quality of our work (papers, presentations, etc), which are key for developing and maintaining a reputation for high-quality science.

As a helpful summary, below is a listing of major deadlines in the lab:

Abstract submissions: submit to slack for feedback at least 1 week prior to submission
Poster presentations: submit to slack for feedback at least 1 week before printing
External oral presentations (departmental talks, conferences, workshops, collaborator meetings, etc): practice talk at least 1 week before
Major oral presentations (qualification exam, dissertation defense): first practice talk at least 2 weeks before
Code review: should start when paper writing begins, needs to be completed by at least 1 senior member of the lab before manuscript submission
Letters of recommendation: as soon as possible (see Letters of Recommendation for specific suggestions)
Leaving for a new position: at least 3 weeks notice, offboarding should be completed 1 week prior to departure

Health & Wellbeing¶

Mistakes¶

Making mistakes is a part of doing research and a consequence of innovation. In fact, if you are not making mistakes, especially early on, there may be something wrong! Advocating for mistakes does not mean you should not be careful, but rather, you should not beat yourself up or be embarrassed to acknowledge and correct them. As a lab, we should strive to provide open and honest feedback with each other, and this means actively trying to find the weaknesses and mistakes in our own work and kindly pointing them out when you notice them in the work of others. While you should not be overly nitpicky, no lab member is off limits, including Vicky.

Because mistakes may happen any time, it is essential to evaluate and check your work thoroughly. When you discover mistakes, if other people are involved (e.g., collaborators who have already seen the results), the responsible thing to do is figure out which results are impacted and notify them as soon as possible (preferably with a plan to address / fix the mistake). People are typically understanding, and it is always better to be transparent.

Burnout¶

It may sound cliche, but burnout is real! It is important to recognize the signs early and take preventative action. Striking a proper balance between work and play / rest is important for your long term success. In academia, there are crunch periods when you need to work harder and faster, but these should be temporary “sprints” and not a sustained working habit. Make sure to take breaks (at least small ones during a crunch!), do not feel guilty about it, and give yourself time to disconnect on weekends. Even during the workday, feel free to take short walks, go to the gym, take a coffee (or tea) break, go to Rice Village for some snacks, have a casual chat, take a power nap, or just find somewhere to be alone and breathe. Set a work schedule that you can stick with, make sure to get sufficient sleep, and take care of yourself.

Please check in with yourself regularly and watch for the warning signs of burnout, which can include:

losing interest in research / science that you were once passionate about feeling exhausted all the time and dreading the idea of coming into lab (can also be directed towards specific projects)
feeling overwhelmed and in a cycle where you feel you are never making progress
becoming easily irritated at small things, when you were not like this before
never feeling rested, even after taking vacation time
if you are experiencing any of the signs of burnout, please talk to Vicky; it can be as simple as mentioning it during a weekly individual meeting. Know that you can always recover from burnout, especially if you catch it early. Do not fall into the trap of pushing yourself more and more—this will only lengthen recovery time, and you may find yourself in a chronic cycle.

Mental Health¶

Academia (and grad school in particular) is a notorious breeding ground for anxiety, depression, and other mental disorders. It takes discipline, and sometimes courage, to prioritize your mental and physical health. Know that as a lab we care first and foremost about your wellbeing. Please call 911 if you are in immediate danger, including but not limited to self harm. Rice University offers confidential professional mental health services that are free for students through the Rice Counseling Center, and a 24 hour emergency phone service by calling (713) 348-3311. Postdocs and other staff members can begin seeking help for free through the Rice Employee Assistance Program.

If you find yourself with any health concerns, especially if they are impacting your work or are caused by any member of the lab, feel free to discuss privately with Vicky. Furthermore, be vigilant in recognizing signs of distress of your fellow peers in the lab and gently take action to help them by expressing concern directly or relaying your concerns to Vicky. Please help maintain the lab culture of kindness and consideration.

Ethics¶

While many things in our lab (and even guidelines in this document) are quite flexible, unethical behavior is taken very seriously and will not be tolerated.

Code of Conduct¶

To ensure a safe and welcoming environment, we expect everyone (including visitors and rotation students) to agree and abide by the lab’s code of conduct. This code will be enforced. The lab is dedicated to providing a harassment-free experience for everyone, regardless of sex, race, religion, gender identity and expression, sexual orientation, age, disability, or physical appearance. We will not tolerate harassment of lab members in any form. Sexual language and imagery is generally not appropriate for any lab venue, including but not limited to, lab meetings, presentations, or discussions. However, we do work on biological problems, which, for example, can involve discussion of reproduction, and if these work-related discussions are kept professional, they are not considered inappropriate.

Harassment includes offensive verbal comments related to one’s sex, race, religion, gender identity and expression, sexual orientation, age, disability, or physical appearance (including body size); sexual images in public spaces, deliberate intimidation, stalking, following, unwanted photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome attention (sexual or otherwise). We expect members to follow these guidelines in all in-person, phone, or online communications, lab-related events, university events, conferences, etc. Members asked to stop any harassing behavior are expected to comply immediately.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please notify Vicky immediately. If Vicky is the cause of your concern, Dr. Eugene Ng (eugeneng@cs.rice.edu) is a good informal point of contact; he is a neutral party not affiliated with the lab and has agreed to mediate should issues arise.

Students should also be aware when seeking support on campus that most employees, including Vicky, are required by Title IX to disclose all incidents of non-consensual interpersonal behaviors (e.g., sexual harassment, assault, stalking, relationship violence) to Title IX professionals on campus who can act to support that student and meet their needs. For more information, please visit safe.rice.edu or email titleixsupport@rice.edu.

Research Integrity¶

Integrity is one of the core values of the lab, and we naturally expect members to always act ethically while conducting research in the lab. We are in a position of privilege as scientists, and with that comes a duty to maintain public trust in our external and internal communications. In a world that is increasingly distrustful of science and medicine, maintaining high standards, political neutrality in our results, and our integrity is of the utmost importance. Furthermore, as computational scientists that study diseases, we must always consider the real world implications of our results and strive to thoroughly test findings that may directly impact human health.

To this end, you should not, under any circumstances:

falsify results, intentionally manipulate data, or misrepresent them in figures to fit a predefined narrative (e.g., deliberate data inclusion / omission)
plagiarize or directly copy the work of others and present it as your own—this includes taking credit for work done by your fellow lab members or collaborators
lie about your credentials or any other information on applications and forms

We recognize that as ethical questions arise, answers may not be immediately obvious, and there can be ambiguity. In these situations, please raise questions with the group, so that we can discuss and figure out the best course of action together. Science is ultimately the pursuit of truth and trying to make sense of the natural world. Please do your part to be good stewards, giving credit where it is due, testing and evaluating findings carefully (being careful not to overfit), sharing results, and striving for reproducibility.

Acknowledgments¶

This document was inspired by and benefitted from several other lab handbooks: Casey Greene, Luis Pedro Coelho, Tiffany Lowe-Power, Olivia Rissland, Savio Chan, and Elana Fertig.

Last update: 2022-04-23