Research Group Handbook

1.    Welcome

Welcome to the Keenum Research Group!! You are about to enter the creative world of science, where everything we do is completely new, and we don’t know any of the answers. Yay! 

The goal of our lab is to develop innovative solutions to challenges that impact environmental systems and to improve our understanding of the physical, chemical, and biological factors that impact these systems. We primarily focus on the role of microorganisms in water and wastewater and use a variety of culture, molecular (i.e. those that target the DNA/RNA of organisms) and bioinformatic methods to characterize these complex environments. 

My goal is to foster a collaborative environment that supports our team’s pursuit of scientific excellence and advancement of the field of environmental engineering. In addition, I encourage all lab members to prioritize personal and professional development while a member of the lab group to support both team and individual success. I strive to maintain an environment that is conducive to learning, developing new skills, and sharing our expertise with others, both within the lab and with collaborators from other fields. This handbook provides a compilation of lab policies, expectations, and resources. 

Quick reference information that you may need can be found below.

Lab website: ishikeenum.com

2.    QuickStart

To onboard, go through the list below in order to set up your computer, accounts, and get acquainted with the lab. If you have any questions, reach out to me or any lab member at any time. 

Important: Before beginning, make sure that I have shared a link to our Keenum Group Google drive, Group Discord, and access to the Keenum Lab calendar. If I haven’t, send me an email reminder.

3.    Learning objectives and mutual expectations

Students who train in the lab will be able to: 

  1. Demonstrate expertise in a variety of experimental techniques relevant to the fields of environmental microbiology, systems biology, and environmental engineering
  2. Critically evaluate scientific literature and formulate unique, novel scientific questions
  3. Design experiments to test hypotheses according to the scientific method, including quantitatively rigorous experimental design, appropriate statistical methods, avoiding bias in data analysis, etc, 
  4. Implement computational biology approaches in one (and hopefully more than one ☺ ) language using various methods, including mathematical modeling, bioinformatics, or statistical analysis 
  5. Establish (or continue establishing) a scientific identity by presenting work at scientific conferences, publishing first and contributing author peer-reviewed papers, and participating in relevant workshops

My expectations of you: 

  • Honesty and integrity. We publish rigorous work in highly regarded and globally recognized scientific journals. One mistake, whether intentional or not, can have catastrophic consequences on every member of the lab. As such, there is never a reason to use questionable data. Throw it out and start again. False or misleading data jeopardizes all our careers. 
  • Respect. Time is valuable – please come prepared and on time to all designated appointments/meetings. 
  • Passionate learning. Be inquisitive, motivated, and creative! I will work with everyone to find a project that excites them. In turn, I expect you to immerse yourself in the subject, read relevant articles, attend related conferences, and anything else to help you learn as much as you can. Most importantly, never be afraid to ask questions. This is your opportunity to learn.
  • Communication. Communicating with me is key to ensure that we are on the same page, whether it be an experiment that went wrong, that you had a bad week, or a personal matter is anticipated to disrupt progress. As long as you keep me updated, we can work together to make sure you are supported in the way you need.

Your expectations of me:

  • Leading by example. If you do not feel the lab meets the standard of a safe and inclusive environment, you can be certain that I will listen to your concerns, work with you to determine the best course of action, and address it to the fullest extent that I am able. 
  • Academic integrity. Any work you produce that is used for publication will receive full recognition in the form of authorship credit on manuscripts and during conference presentations.
  • Lifelong mentorship. As your advisor, I will champion your career in the form of contacts, recommendation letters, and award nominations as loudly and for long as you want my support.
  • Trust. There will never, ever be punishment or judgment for making a mistake! We all do it more than we like to admit. It is critical that we can trust each other in terms of the quality of the work we produce. This means never use data that you are unsure about. Experiments can always be repeated (and often are!). 

4.    Communication and Teamwork

Our team uses a variety of platforms for communication, sharing documents, and advertising our work:

  • E-mail. We will use e-mail for scheduling meetings and conducting any formal communication about research.
    •  Respond to emails from Dr. Keenum and other research collaborators in a timely manner. Aim to respond within 1 business day.
  • Collaboration. Be willing and available to help other graduate and undergraduate students in the research group. You may be asked to supervise student(s) during your program or to be the teaching assistant (TA) for a course. You may also be asked to help with service projects helping rural drinking water and wastewater utilities. We have a group discord that we use to share code, ordering and general lab updates.
    •  Keep Dr. Keenum up to date on your career plans and goals, especially if they change throughout the course of your PhD. This information can be helpful for making sure you get exposure to activities that will be most relevant to your career path.
  • Group Google Drive
    • Use this platform to share documents. Procedures, reference, and other shared documents can be found and uploaded here.
  • You are expected to apply for grant funding, fellowships, and/or awards as advised by Dr. Keenum. I am working hard to obtain funding to support the research and travel of the entire group. I expect you to do what you can to help with this through applying to travel awards, conference awards, fellowships, and other opportunities. When I advise you to apply for an award/fellowship, we can work together to draft your application materials. Grant writing is also an invaluable experience for your professional career.

5.    Lab safety

Safety comes first, always. Putting ourselves and our peers at risk is unacceptable practice and will not be tolerated. Anyone found to violate our safety procedures more than once will be asked to leave. 

Our lab is certified to handle Biosafety Level 2 (BSL2) pathogens. Familiarize yourself with what that means here, and if you feel you need additional safety precautions, discuss with me so we can get those set up for you ASAP. Among other requirements (such as air filtering/turnover rates), here is a quick reminder for day-to-day ways this is enforced:

  1. Closed-toe shoes and clothing that covers your entire legs must be worn in the lab at all times
    1. The door to the hall must be shut (never propped open)
    1. Appropriate ppe, including eye protection and lab coats, must be worn when working with BL2 pathogens
    1. Absolutely no food or drink in the lab area 
  • Contact information (self and emergency) for all lab members can be found here.
  • Before beginning any lab work, students must complete all safety training modules. 
  • Some trainings are renewed annually; keep an eye on your email to stay up to date.

6.    Laboratory policies

A. Lab meetings

Lab meetings will be held weekly, and everyone is expected to attend. Each week, someone will present a project update according to our rotating calendar. The purpose of lab meeting presentations is to provide a safe space to present research progress, practice scientific communication, troubleshoot as a group, and work through ideas together. Critical feedback is always welcome, but will only be tolerated if conveyed in a positive and constructive way. Although this is meant to be a low-stress activity, there are a few guidelines that everyone is expected to follow:

  • Presentations should be clear, concise, and organized
  • They do not need to be polished as one would find in a scientific conference, but the presenter should come prepared with the topic they would like to discuss
  • Attendance is mandatory. If you are not able to come one week, email me ahead of time to let me know
  • All presentations should be archived in the lab-meeting-slides folder here with the title format: YYY-MM-DD_YourLastName_PresentationTopic

B. Journal club

Journal clubs are typically held every other week – this gives us a chance to critically evaluate relevant papers, and keep up to date with new literature. Below are some guidelines to follow:

  • Each journal club has a designated leader. The leader chooses the paper for the week, and leads us through a discussion of the results
  • Papers should be posted in the slack, copied into this folder, and a link should be updated in the lab_meeting_schedule excel file, one week prior to your journal club
  • Priority should be given to papers relevant to your project and those more recently published
  • Leaders should come prepared to present the full paper in the form of powerpoint slides. Paper presentation should be concise and last no more than 10 minutes. Choose relevant figures and tables to present – not every panel needs to be included.
  • Attendance is mandatory. If you are not able to come one week, email me ahead of time to let me know. Everyone should come prepared to discuss the paper
  • All presentations should be archived in the journal-club-slides folder here with the title format: YYY-MM-DD_YourLastName_LastNameOfFirstAuthor

C. 1-1 weekly meetings

Every non-undergraduate member of the lab has a scheduled 1-1 meeting with me weekly for one hour. This time is meant to be yours where you have my undivided attention to fully focus on your project, discuss results/next steps, and/or help you navigate milestones and other concerns that you may have. To get the most out of these meetings, follow the following guidelines:

  • You are expected to put together powerpoint slides for our weekly meetings
  • Slides should be sent to me no later than 6am on the morning of your meeting, or before
  • All slides should include a discussion of what was done the week before, any challenegs that arose, and what is planned in the week ahead
  • As long as 1-1 meetings go as planned, annual or bi-annual project reports are not needed, but will be reassessed regularly with the lab

Note that while meeting once a week is the minimum required, I am always happy to meet more than that for anyone who would find that beneficial, if something more urgent has come up, or to get a new member situated and up and running in the lab.

Undergraduate meeting schedules vary depending on project-specifics. However, most undergraduates should accept similar meeting structures.

D. Data storage and organization

Data documentation and good bookkeeping is the most important (and challenging) part of 

conducting reproducible research, and should be taken with the highest level of care. Even unintentional mistakes can have catastrophic consequences on careers. It’s critical that we can trust each other’s work, that results are reproducible, and that projects can be passed down without losing information. Below are our guidelines to ensure this:

  • Written notebooking: 
    • Everyone will be provided a written lab notebook to document experiments in real-time. 
    • Written notebooks are considered the property of the lab, and are used to supplement our online system.
    • These should never physically leave the lab space
  • Electronic notebooking: 
    • The Projects folder should be treated as our electronic lab notebooking system.
    • Everything must be fully documented, organized according to common lab standards described, and deposited in the appropriate Projects folder in Drive. This ensures consistency, facilitates project transitions between members, and backs up our data.
    • All projects, and associated experiments, are indexed according to a specific documentation system that must be kept to date. 
  • Computational projects must be initiated with a Github repo and pushed regularly (at least once a week)
  • I strongly encourage you to back up your files in real time with Google. 

7.    Discrimination, harassment, and lab community

This lab is an open, safe, and inclusive environment for every single member. As such, we have no tolerance for direct or indirect discrimination of any kind, including but not limited to race, ethnicity, gender identification, sexual orientation, disabilities, and religious beliefs. Any student who violates this code of conduct will be asked to leave immediately, with no exceptions.

Science, by nature, requires as broad a variety as possible of viewpoints and opinions to find ground truth; therefore, filtering participation, by definition, results in a non-optimal solution to any question we might ask. We strive to bring as many backgrounds, viewpoints, and personalities into our lab as possible by proactively engaging underrepresented communities. To combat unconscious bias, we use group interview formats; in this way, we hope that the bias of any one individual will be balanced by the rest of the group. This only works if everyone makes their candid opinions known- in other words, speak up! We can tackle bias most effectively only once it is in the open. Likewise, come with an open mind to the opinions of others; apply your scientific curiosity not only to your projects, but to the community we are building. You will inherit the relationships you build during your time in this lab for the rest of your scientific career, so take this opportunity to make sure your network is as wide and diverse as possible.  

Just like lab members, the lab itself deserves respect. Please treat the lab as you would your own personal property. Store all reagents in their appropriate location and put everything away after using it. Turn equipment off and clean up common areas after you are done. Running a lab takes money, and the less we have to spend on maintenance the more we have to do cool science.

8.    Weekly hours and time off/vacation

We do not actively track weekly hours or vacation time. Accordingly, there are a few policies to keep in mind: 

  • You should treat your PhD/MS program like a full-time job. Subject to the exact expectations outlined in your contract, you should expect to work approximately 20 hours per week on research or teaching assistantship assignments during the school year and 40 hours per week during the summer. During the school year, you will also be enrolled in course and/or research credits, to which you should expect to devote the remaining 20 hours of a typical work week. 
  • Weekly progress is assessed during our 1-1 meetings. As long as we are making sufficient progress, you can structure your time as you see fit and work best. 
  • Although we don’t enforce strict schedules, we believe that both lab dynamics and learning opportunities are amplified by spending time with each other. The more overlap people have, the better and stronger a community we can build, and the more organic collaborations can form. 
  • If progress declines for a prolonged period of time without adequate communication, we will have an open conversation to discuss ways to address this, which may include anything from taking a vacation to recharge, to enforcing more strict hours.
  • Vacations are also not tracked directly – however, I expect you to take ~ 13 days off a year. All vacations must be submitted via email to the PI at least 2 weeks ahead of time so that she knows you when you are out of town. This is critical for safety reasons and to make sure lab processes keep running smoothly.

9.    Yearly evaluation

Each fall we will review this document prior to meeting to discuss your progress, goals, funding, and reflect on our mentoring relationship and communication (including completing the CEE PhD student-advisor form).  This is an opportunity to discuss any concerns that you have with respect to my role as your advisor. I would like to hear whether you feel that you need more guidance from me, or if you feel that I am interfering too much with your work.  At this meeting, I will provide feedback to you about your progress. It will be my responsibility to explain to you any areas where I feel you need to improve.

This meeting is also an opportunity to tell me if you are unhappy with any aspect of your experience as a graduate student here. Remember that I am your advocate, as well as your advisor. I will do my best to help you with any problems you might have with other students, professors, or staff.  

10. When you need things from me

  • Give Dr. Keenum 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 Dr. Keenum at least two weeks’ notice (preferably more) to do something with a hard deadline that requires a moderate amount of time (e.g., a letter of recommendation).
  • For manuscript submissions and revisions (i.e., which either have no deadline at all or only a weak deadline), send drafts to Dr. Keenum as soon as you have them, and bug her to give you feedback if she hasn’t responded in 2 weeks, email again!

11. Research Posters and 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, 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.

12. Requirements for Ph.D. Students

Graduate Committee

  • During your second semester, you should form a graduate committee consisting of four faculty members: at least 3 CEE faculty and at least one from outside the department. Your committee members should be selected to complement my expertise and your dissertation topic.  
  • It is critical and your responsibility to establish a productive relationship with your committee members. You should plan to reach out to your committee once per semester to update them on your research progress. This can involve you making a short presentation and getting feedback. Be respectful of your committee members time when planning for these meetings. 

Qualifying Exam and Proposal Defense

  • Written qualifying exams will be determined by your graduate committee. It should be completed no later than one semester after you complete 18 credit hours. This will typically be your forth semester. This is a formal Pass/Fail exam. 
  • The General Environmental Engineering part of the Comprehensive Exam will be based on information covered in the following courses: CE3501 Environmental Engineering Fundamentals CE4501 Environmental Engineering Chemical Processes BL3310 Environmental Microbiology, BL3400 Principles of Ecology, or BL5451 Aquatic Ecology CE5501 Environmental Process Engineering
  • Your proposal defense exam will take place after your Qualifier with your graduate committee. You will provide your committee with a written document (i.e., dissertation proposal) and then present and defend this proposal. This is a formal Pass/Fail exam. 

Publication Expectations

  • I expect your final PhD dissertation to be composed of a minimum of 3 peer-reviewed journal articles (one or two of these may still be in review at a peer-reviewed journal at the time of your defense). 
  • I will help you to plan manuscript #1 in more detail. You will be expected to take a greater leadership role in planning manuscripts #2 and #3. Of course, you may plan to publish many more manuscripts if you choose and this will make you more competitive in the job market after graduation. 
  • Your dissertation proposal will also include a critical review of the literature that will be included in Chapter 1. If your literature review provides a novel addition to the field, you may wish to publish this as a manuscript in a peer-reviewed journal. 
  •  

13. Expectations for Masters Students

Research based masters degrees are incredibly valuable if you are interested in research and want to learn about the scientific process. 

Graduate Committee

  • During your second semester, you should form a graduate committee consisting of four faculty members: at least 3 CEE faculty and at least one from outside the department. Your committee members should be selected to complement my expertise and your dissertation topic.  
  • It is critical and your responsibility to establish a productive relationship with your committee members. You should plan to reach out to your committee once per semester to update them on your research progress. This can involve you making a short presentation and getting feedback. Be respectful of your committee members time when planning for these meetings. 

Degree Progress

  • Students must take or be comfortable with the material in the following courses: CE3501 Environmental Engineering Fundamentals CE4501 Environmental Engineering Chemical Processes BL3310 Environmental Microbiology, BL3400 Principles of Ecology, or BL5451 Aquatic Ecology CE5501 Environmental Process Engineering. We will discuss your plan individually as it will vary based on your degree background. 

Publication Expectations

  • I expect your final thesis to be composed of a minimum of 1-2 peer-reviewed journal articles (these may still be in review at a peer-reviewed journal at the time of your defense). 
  • I will help you to plan manuscript #1 in more detail. You will be expected to take a greater leadership role in planning manuscripts #2 and #3. Of course, you may plan to publish many more manuscripts if you choose and this will make you more competitive in the job market after graduation. 

14. Expectations for Undergraduate Students

Undergraduate research varies widely in format, and can include projects that span the summer, the school year, or both and may be paid or for credit. You should discuss the exact expectations for your position with Dr. Keenum.

If you are being paid hourly, be sure to log your time. During the school year, you can work no more than 20 hours per week. During the summer, you can work no more than 40 hours per week. It is your responsibility to keep track of these hours and not exceed them. You should be clocking in for all of the following activities:

  • Doing lab or field research (including cleanup after lab work and recording data)
    • Analyzing data
    • Creating research products (poster, paper, etc.)
    • Individual meetings with Dr. Keenum
    • Group meetings 
    • Small research group / project meetings
    • Preparing for meetings
    • Webinars / training opportunities encouraged by Dr. Keenum
    • Reading literature related to your research
    • Doing training / problem-solving related to your research (for example, training/tutorials related to using an R package for your research)

I strongly encourage you to generate one or more research products to communicate the findings of your work to others. This will typically take the form of a poster or presentation, and you may be given the opportunity to co-author a journal article, depending on the scope of your project. Good opportunities to present your include:

• MTU’s Undergraduate Research and Scholarship Symposium

Check MTU’s Undergraduate Research Website frequently for more information about these opportunities.

In addition, if you wish to work hourly over the summer, you are strongly encouraged to apply to programs that support this work, such as the following:

Coordinate with Dr. Keenum to develop your application for these programs.