Lab Philosophy

Nandakumar lab philosophy (for graduate students and postdoctoral fellows)

This is a live document that was developed by JK Nandakumar in consultation with trainees in the Nandakumar lab to describe the academic culture of the lab and the expectations. More broadly, it serves as a lab manual.  We want to have in place the best practices that ensure that our lab continues to be at the forefront of research and in the process provides an enriching and enjoyable learning experience for its trainees, preparing them for the next step in their careers. 

Onboarding document: For anyone joining the lab, welcome to the lab! To make your orientation process as smooth as possible, please go to the template onboarding document, “save copy” from the file menu, and save the file in your name. Then fill in your name and position and carefully read the rest of the document, checking boxes as applicable.  Please approach JK if you have any questions. 

Why do you want to join the lab?

  • The primary motivation for joining our lab must be your passion for conducting research.
  • JK will work with you toward your career aspirations (in no way limited to academia), but during your training period, the expectations are uniform across trainees to make it an equitable experience. 

Lab Culture: Diversity and teamwork breed excellence

  • The Nandakumar lab aspires to be a welcoming, safe, and collegial environment for doing cutting-edge research. 
  • We strongly believe in the saying that we are stronger as a team than individuals because we can add our unique strengths and help each other overcome our individual weaknesses. 
  • The diverse skills, backgrounds, cultures, beliefs, and experiences that each person brings to the lab enrich the experience of everyone and allow for innovations that no single person could bring. 
  • For us to be a team, everyone must get along with each other, at least at a professional level.
  • Essential to our lab culture is to make new members of the lab feel welcome. 
  • We might have different opinions on many issues, but in the lab, we work on doing good science and being good colleagues to each other. 

Is this a job or am I in training?

Academic pursuit: It is a little bit of both. The reason to join the lab is because you love science and want to grow your research skills. The lab provides the environment and resources (intellectual and physical) for you to get this training. There is financial compensation involved but please remember your PI is your mentor/supervisor but not your employer. This is because your compensation either comes from the University (in your 1st year as a Ph.D. student or if you have a Rackham fellowship), the Federal government (if you are funded from an NIH/NSF/DOD grant or fellowship), or other sources (like a fellowship from a private foundation). Your mentor has limited to no say in your compensation amount or items covered in a contract (if any). 

Conflict arising from the current model: The unfortunate status quo is that research investigation in the lab leads to publications, which lead to grants that can fund future research investigations. This cycle is broken if we fall behind on work. Thus, we are all operating under real-life pressures to produce results (i.e., papers). This model poses a conflict with the flexible, open-ended nature of the academic pursuit because it imposes urgency, deadlines, milestones, etc. Another external pressure relates to competition. Getting “scooped” compromises the prospects of publishing your project as planned. These factors often translate to working more urgently and making sacrifices to achieve your training goal. While we cannot overcome this conflict, you should be in open communication with JK whenever these pressures are defeating your primary purpose for being in the lab. 

Ownership of your project

Although we work as a team, strong emphasis is given to each trainee having a primary project. This means it is ultimately the trainee’s responsibility to make sure that their project is going as planned. All the steps described below are secondary to the trainee being enthusiastic about science and taking ownership of their project. At any point you feel like you are losing motivation or need your mentor to be more actively involved in your project, you should bring this to JK’s attention. Although you have one primary project, JK has many (= the # of trainees!). Therefore, despite his best intentions, JK can fall behind on his duties and needs to be reminded and held accountable. Having this open dialog WILL NOT cause any backlash or issues in the long-term relationship with JK. Once a mentor, always a mentor – your mentor will always advocate for you even after you leave the lab. Any previous trainee (or student JK has written a letter for) can confirm this fact. 

Your health is your top priority

From a human standpoint, we are all aware of the importance of staying healthy. Even from the standpoint of your research goal, your mental, emotional, and physical health are your top priorities. Since this is a personal issue, you are oftentimes the first or only person who will know when you have a health concern. Please be proactive in seeking the medical (or other emergency) help that you need. Here are a few resources to help you find help. JK is always welcoming of those who want to share personal concerns with him, but only if that is what you want to do and if you think it will help you. We will work together to the extent you want to accommodate your situation and customize your training to ensure that your training and productivity don’t suffer. The same is true about financial/family situations. If your mentor is the source of the problem, there are resources listed in that link that can help you resolve those issues. The MCDB Grad Studies Chair is another local resource. 

Work ethic

Ultimately what matters is what you learned and produced (i.e., papers) in the lab and not the hours spent. However, it is also true that the only way to learn and produce is to put in the hard work. The Nandakumar lab strives to offer flexibility in how trainees go about their work in the lab such that they can achieve their goals of having a rich learning experience and productivity. It is important to have a mutually agreed upon policy for the sake of equity – everyone should be held to the same bar so that some people don’t feel like they are working hard but others not doing the same are being held to a different standard. Considering these factors, the Nandakumar lab has the following paradigm for work in the lab so that you can achieve your training goals:

  • Flexible schedule: If you enjoy a flexible work schedule, i.e., you like taking multiple breaks (anything  >30 min), then it becomes difficult to clock hours in the lab. It is then expected that you would work outside of the generic eight-hour weekdays/weekends-off schedule to accomplish your goals while enjoying the flexibility that academia offers you. This is the schedule JK follows for his work but that is his personal preference.
  • Fixed schedule: If you like the 8-hour/day 40-hour/week schedule, then we need to prioritize time management. For e.g., a 2-hour incubation is not 2 hours of work. Instead, that is time that should be spent reading the literature, starting another experiment, etc. Thus, this option sacrifices flexibility. But you still have the flexibility to have longer/shorter days in a week (based on what your experiments ask for) so that you aim for the same weekly aggregate of hours. 
  • Custom schedule: Each of us faces unique challenges and circumstances in life. If neither of these schedules works for you, you should work with JK to develop a custom schedule that helps balance your life and work in the best way possible. 
  • Regardless of the schedule you pick, working smart will let you get more bang for your buck (i.e., more results per hour of work). Working smart would mean that you spent sufficient time reading about your planned experiment, discussing your design with others including your mentor, and carefully planning out (and writing) every step of the protocol. 
  • Regardless of the schedule you pick, your “work” hours include the time you spend on non-research-related academic duties such as teaching, coursework, and service. However, we should not lose sight of your primary goal in the lab, which is to accomplish your research ambitions. So you should budget your time/effort in your lab accordingly.
  • If your training is bound by a legal employment contract, then its terms will prevail over the options listed above.

Open communication is key to success – Meetings within the lab and with JK

  • Please communicate with JK about any issues that arise including feeling demotivated about your project, wanting a new direction/project, sensing a lack of support, feeling like the lab is not conducive to learning or a safe space to fail in, or is toxic to your progress, etc.
  • The Nandakumar_Lab_Events_Calendar on Google Calendar will have all Nandakumar lab events. 
  • We hold data meetings where every lab member will present every ~3 weeks (i) the goals set past week (ii) the data from that week and (iii) plans for next week. If you are unable to attend or present, please email JK and let him know why you are not able to participate. 
  • We hold literature meetings/journal clubs every ~3 weeks. We have a schedule rotating through the entire lab, assigning one person to pick papers for any given journal club. That person sends the paper and assigns figures to the lab well in advance (1 week – to give people enough time).
  • At the start of each weekly group meeting, we do a “Guess what I learned this week”. This is an exercise to motivate all of us to read more (see section below for details). The idea is that from your browsing of the major journals and “alerts” specific to your field, you would have discovered at least one paper (can be more!) that you want to inform the lab about. We will go round the table and (at least) each person not presenting data that day will say what paper (authors, journal, title, year) they want to highlight and briefly (1-2 minutes) share what they learned. Everyone, including undergraduates, is welcome to share something that they learned. The more we read and hear about cool research, the more we would want to do our own cool research. 
  • You are encouraged to set up a time to meet one-on-one with JK every Friday, although the format is not as formal as the month-end meeting (see below). For any one-on-one meetings, you should feel free to keep the office door open or shut for the conversation and request any other accommodations to help make you comfortable during the meeting (e.g., want me to wear a mask).
  • Once every month (in the last week of the month) we will have one-on-one meetings in JK’s office  (~1 hour long) where you will present the progress you have made in the last month (using a .pptx and your notebook). This is a nice, formalized way for us to keep track of how a project is progressing with time. These discussions are documented in a live Google doc so that we can track goals and results from previous months all in one place. From the last meeting, you will have bullet points for your proposed experiments for the month. In preparation for your next month-end meeting, you will write a detailed summary of your progress under each bullet point. This writing exercise serves at least three purposes. It allows you to reflect on your monthly progress and assess your effort and experience in the lab. It allows you to practice scientific writing. Finally, it provides JK with a coherent summary of your progress, allowing him to provide more constructive feedback during the Friday month-end meeting. At the meeting, we will discuss your progress summary and brainstorm to come up with the bullet points for the next month. You and JK will update the document with the new aims so that it serves as a guide for your experiments and a template for writing down your progress a month from then. Not everyone might meet with JK on the same Friday. We would split into groups such that only a small group (3-4 students) would meet one-on-one with JK for a month-end meeting on a given Friday. 
  • Once every semester, you will present an hour-long formal presentation on your project and its progress to the lab. Like with any formal presentation, it is expected that you will provide sufficient background on your project, followed by results, a discussion of what they mean, and what the future directions are. This exercise serves at least three purposes. It allows you to assimilate ideas and data from many experiments, helping you track the evolution of your project (toward becoming a paper). It allows you to give a comprehensive description of your project so that the lab can provide useful feedback. It helps you practice your presentation skills in front of an expert yet friendly audience. 
  • JK is accessible in person and/or by email/Slack (all 7 days) – his response time is generally <24 hours. If you haven’t heard back in 48 hours, please send him a reminder. When JK contacts you, a similar response time is expected. It is not expected that you will respond to messages at night or on weekends unless it is something you want to do. Please discuss any other boundaries for when it is not acceptable for JK to contact you with emails or Slack messages.

Following the literature and other people’s research

The most important part of lab research apart from experiments is reading the literature. Reading papers allows you to gain an understanding of your project and the latest and greatest in science, and generate new ideas. An excellent time to read is when your experiment has a wait period. 

  • At the very least, we should make all kinds of PUBMED and BiorXiv alerts for your project keywords and check these alerts every day. Other than that, having alerts from Nature, Science, Cell, NS&MB, Structure, eLife, PNAS, EMBO, G&D, Mol. Cell, NAR, JBC, Mol. Cell. Biol. is a great way to keep up with the literature. 
  • Attending seminars/talks is another way of quickly grasping a lot of data, and sometimes, getting new ideas for your own project. You should at least try to attend all talks from your department/program, those relevant to your research, and the ones JK emails you about. The onboarding document has details.
  • Attending one conference a year is standard to increase your knowledge and networking in the field. You could alternate between a local conference and an international conference in alternating years. 

Being organized 

  • Please keep a detailed laboratory notebook. We are currently using Benchling (electronic) for this. You should be comfortable with this software and seek help from your labmates if you have questions. You are welcome and encouraged to also have a written lab notebook for calculations, writing down active protocols, etc. It should have page numbers, and no page can be torn out. It should always be in the lab. Every experiment you do (including making a simple buffer or dissolving antibiotics) should be documented in your (hard-copy or electronic) notebook with a date. In addition to this being a resource for you and other members of the lab (after you leave), Federal agencies mandate keeping notebooks for several years past the experiment so that they can inspect them in case of an audit. 
  • Organizing reagents is another essential key to your success, but more to the long-term success of a lab. Please label all tubes/samples. Any tube in general storage areas (4C, -20C, -80C, liquid N2 dewars, shakers, etc.) without labels could get discarded as we wouldn’t know who they belong to. For current experiments at the bench, you can use simpler labels (e.g., 1,2,3), but anything stored long-term (i.e. >1 day) must be properly labeled. This also applies to bottles on your bench.  
  • Primers should be in a primer box. Label the box with your name, and primer box #, and store at -20C.
  • Please label plasmid tubes not only on the top (with a cryo-resistant label) but also on the side with an EtOH-resistant marker. You should store plasmids in a separate box. For every plasmid that has been sequenced completely for the gene/genes you cloned in, you should store it in a separate box labeled with your name and ‘sequenced plasmids box #’ at -20C. It is important to not place DNA clones that have not been completely sequenced in the ‘sequenced plasmid box’. 
  • Please store the Sanger DNA sequencing alignment software files for all completely sequenced clones with appropriate names (e.g TPP1-F150A-Flag) and make a note in your notebook as to which clone # (e.g. clone 4 of TPP1-F150A-flag) is the fully sequenced clone. If anyone wants to see your sequencing data (even many years down the line), you should be able to show them the complete alignment. If other programs serve the purpose, they are fine too. If you simply do the alignment online and don’t store the results on your hard drive, PLEASE print out the alignment and make a folder for yourself with full alignments for every completely sequenced clone. 
  • Every completely sequenced plasmid should also be documented in a Google spreadsheet format. You want to put details (e.g. what was cloned, how it was cloned etc.) into this form. Have a similar Google spreadsheet for all primers (name and short description if name not self-explanatory). You want to forward JK the Google links so that he can maintain a full list of primer/plasmid files for the lab.
  • Computer files must also be organized and saved on our lab server. The university is changing the way this is done. We will wait till they tell us how the new system works before having all of us keep our data on this server. The lab can also provide you with external hard drives for you to make a second copy.  It is also a good idea to back up the same data on your computer (or on the lab laptop). The more backups we have the better we protect ourselves from losing precious data. 

Actively pursue funding opportunities

Although your mentor is primarily responsible for securing funding, there is a huge incentive for students to also capitalize on such opportunities. Fellowships embellish your CV and make you a stronger candidate for future jobs. In addition, they serve to supplement the lab’s existing financial resources, allowing us to do more science and train more trainees. Multiple training grants have supported students in the lab or are potential funding sources, such as the NIH T32 grants for (1) Genetics, (2) Aging, and (3) Chemistry-Biology interface. New Ph.D. students who are eligible typically apply to one or more of these training grant positions. Other fellowship opportunities are the NIH F31 grants for students, and the NIH F32 and American Cancer Society fellowships for postdoctoral fellows. The decision to apply for trainee fellowships is made mutually.

Integrity of research

  • You will have a one-on-one meeting with JK to discuss the integrity of research and other ethics-related topics when (or before) you join the lab but you should feel free to discuss such topics ANYTIME. 
  • We strive to hold ourselves to the highest ethical standards when it comes to designing experiments, generating data, presenting data, and publishing data. At ANY point you feel we are deviating from this mission, you should immediately bring this to your JK’s attention.
  • Authorship: This has always been and will continue to be a sticky issue. Although there are no published or strict rules for how authorship or its order is determined, it is ultimately a decision made by JK after considering the paper itself and discussions with each of you who would be on that paper. Here are the general principles used in our lab to determine authorship. If you contribute significantly to the ‘idea’, the actual bench work (i.e. data in figures), or writing, you will be an author on the paper. However, the order of authorship will be decided based on relative contributions, that can be subjective. You should make clear what you think your contributions are and where you belong on that list. Sharing first (or second) authorships is quite common these days. Many of us have mixed feelings about this. Although it is not the best or most sincere distribution of credit, it is often a way to break a deadlock and publish a paper – the ultimate goal of all authors on that paper. 

Being a good lab citizen

  • If you are the last to leave the lab, please check that all 4C, -20C, and -80C fridges/freezers are closed. 
  • Please do not leave your dirty glassware in common spaces including sinks. Please follow the rules of dishwashing in the lab. 
  • Please inform JK in advance. about reagents running out. If we do run out of a reagent that is important for your experiment, please borrow the reagent from another lab and return their reagent when it arrives. We don’t want your research to stop if you can find the reagent in the building or on campus. 
  • Please check every month for old plates, tubes, etc. in common storage areas and discard samples you don’t need. 
  • Please be willing to help a lab member with their work/writing/presentation. 
  • We must have fluid communications within the lab, at least around research. When conversing about research, it is best practice to use English (even if it is not your preferred language of communication) for multiple reasons. First, it allows everyone in the lab to be included in the scientific discussion (if you are talking about a broken centrifuge or a contaminated reagent, everyone in the lab should be able to learn about that). Second, almost all the papers we read are written in English and all the scientific writing you will do in your training will be in English. Therefore, it seems most effective to orally communicate in English. For non-scientific discussions with those in the lab or visiting it, you are welcome to speak in the language of your choice/comfort. 
  • We should always be willing to share reagents and equipment with other labs, but please confirm with JK before you approve of something major (e.g. expensive reagents/equipment like FPLC).
  • Once again, please make new members of the lab feel welcome. 
  • Any kind of personal/professional/experimental crisis occurring in the lab must be resolved ASAP. Please bring any such incident immediately to JK’s attention in person or by calling him. 
  • Since most of our research is funded by taxpayer money, we should always be cognizant of the cost of reagents/experiments and minimize wastage or careless spending. 

Absence and vacation policy

Having a break from work is essential not just for the sake of the break, but also for us to recharge and give our projects a fresh thrust when we return. So, you must take a vacation when it is due. 

  • If you will not be able to come to the lab for some reason, please email JK and any other person you are working with about this. 
  • Although the lab is a rich resource, if you prefer doing important reading in the library/coffee shop/home, please let JK know. Please also mention how you are best reachable and if you could come to the lab that day if there is an urgent need. 
  • A good time to take a break is when you just submitted your paper, or you just completed/published a project. Another good time is if when you submit an experiment that will only yield results after a few days/weeks. Another good time to take a break is when you feel it is needed to prevent burnout. 
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