CFL Graduate Student and Postdoc Handbook

updated August 17, 2023


The objective of this document is to provide a source of information for graduate students and postdocs at the Center for Limnology (CFL). The CFL is a research center within the College of Letters and Science. While there are multiple research labs within the CFL, the walls between the different labs are intended to be low, and all members of the CFL share certain common facilities, research culture, and general expectations. The goal of this document is to clearly lay out general expectations for graduate students and postdocs, and to provide insights into how things work. This will help avoid misunderstandings and make life easier. We do understand that each person and situation is different. If you have concerns or feel that certain practices don’t fit your situation, talk to your advisor. We emphasize that open communication is essential. We also emphasize that this is a working document – please share any suggestions for the handbook. We will continue to revise it based on your input and experiences.

Helpful references and resources

The CFL website is a useful resource and good starting point for finding additional on-line resources:

CFL Code of Conduct:

CFL User Guide: This is an important resource. It has the answers to many of your questions on a wide range of topics. Keep this bookmarked:

Trout Lake Station User’s Guide:

CFL Diversity, Equity & Inclusion Actionable Items google doc. For suggestions, please use the DEI committee’s Suggestion form.

Integrative Biology graduate student handbooks:

Graduate School resources:

Graduate Assistantship Policies and Procedures:

Office of Postdoctoral Studies:

Water@UW-Madison. A portal for water-related activities on the UW-Madison campus with email list, events, activities:

Center for Ecology and the Environment umbrella organization of ecologists on campus, great e-mail list, and nice symposia

Freshwater and Marine Sciences graduate program:

Freshwater and Marine Sciences Graduate Handbook:

Biology colloquium: weekly seminar for Departments of Integrative Biology and Botany on Thursdays from 3:30-4:30 PM

Center for Limnology Operations Staff

Hasler Laboratory of Limnology

Jake Vander Zanden Director

Monet Hutchins – Assistant Director. Overall administration, Hasler lab operations, grants, animal care

Kelly O’Ferrell – Hasler Lab Coordinator. General administrative support and answers for virtually any question

John Burmaster – Financial Specialist, purchasing, travel, reimbursement

Aaron Nolan – Lab and Facilities Manager. Vehicles, boats, facilities, lab and field equipment

Alyssa Luckey Winters – Payroll and Benefits Specialist. Appointments, human resources

Paul Hanson – Research Professor. Computing and servers

Adam Hinterthuer – Outreach and Communications

Trout Lake Station

Gretchen Gerrish – Trout Lake Station Director

Amber Mrnak –Trout Lake Station Coordinator/Outreach/Reservations, administrative support

Jonathan Lytle – Facilities. Physical plant, equipment maintenance and repair

Tom Swedberg – Facilities. Maintenance


Kelin Boldiis– Integrative Biology (Zoology) and Freshwater and Marine Sciences Graduate Student Services Coordinator

Expectations for CFL graduate students and postdocs

Code of conduct – As graduate students and postdocs, you are entrusted with representing the CFL. We expect you to exhibit academic and personal integrity and play a role in ensuring that the CFL is a welcoming and safe environment that fosters equity and trust amongst the community. We do not tolerate racism, sexism, homophobia, or discrimination of any type. The common-sense expectations are documented in the CFL code of conduct, which can be found here: Please be familiar with this important document and refer back to it as needed.

Below we describe some additional expectations of graduate students and postdocs at the Center for Limnology:

Participate in weekly lab meetings – A “lab” is typically identified as a principal investigator (PI) and their staff, postdocs, and students, e.g., The Stanley Lab. During the academic year, labs (either individually or jointly) tend to hold a weekly informal lab meeting for sharing research ideas, catching up, giving practice talks, discussing papers, and professional development topics. Lab meetings are intended for lab members, but are also open to undergraduate researchers, visiting scientists, and others. We expect that you attend lab meeting whenever you are in town and participate by occasionally sharing your work or leading a session.

In addition to lab meetings, we expect that you will participate in other lab group activities – whatever they may be. When graduate students successfully pass their prelim exam or defend their MS or PhD, graduate Students and postdocs from the lab group take the lead with organizing some sort of celebratory event.

Participate in the weekly Wednesday limnology seminar – The CFL holds a regular Wednesday lunch seminar Weekly Seminar during the academic year, which doubles as Zoology 911: Limnology and Marine Science Seminar (cross-listed with Environ St, Botany, Civil Engineering, AOS, Geoscience). All CFL graduate students should enroll in Zoology 911. We expect you to attend if you are in town. As a rule of thumb, we expect each graduate student and postdoc to present a ½ or full slot each academic year. This is a key opportunity to gain experience giving talks and to receive constructive feedback on your ongoing work.

Participate in CFL community activities – Participation comes in many forms and includes the following: being an active participant on the CFL committees, participating in outreach and other activities, attending relevant seminars, interacting with visiting scholars, and mentoring undergraduates and their research. You will hopefully participate in some or all these activities, depending on your situation. Participation generally involves modest time commitments.

Work together and collaborate – We expect you to help each other and to share your expertise with your fellow CFLers. If you encounter problems that you cannot figure out, please do not hesitate to ask someone (staff, advisor, labmates, officemates) for help. This can often lead to collaboration and exciting new synergies. Collaboration is a very positive and important part of the academic experience. In addition to your first-authored thesis papers, you are likely to also participate in collaborations that result in non-first authored publications.

Present at scientific meetings – You are expected to attend and present at regional, national and/or international conferences. One conference per year (excluding your first year) is typical. We ask that you apply for travel funding (JJD travel award, graduate school travel awards), and your advisor is committed to covering remaining travel costs. Please see John Burmaster before making travel arrangements. You will need to get a fund number from your advisor. Use to get reimbursement for expenses.

Communicating your results –There are many valuable ways of communicating your research – present at a scientific meeting, give public talks, tweet, write articles for non-scientific audiences. But the dominant currency of science remains the scientific paper. Publications give you legitimacy as a scientist and provide the basis for preparing a press release that will get the message out to a mass audience. Once you’ve built your scientific foundation, communication that extends beyond the traditional scientific papers will naturally follow. As a research center, the core of our work is to conduct research and communicate it.

Balancing your main project and other opportunities – During the course of your degree or postdoc, a variety of opportunities will emerge. You may be asked to collaborate on a side-project, participate in a University service opportunity, join a working group, conduct fieldwork internationally, assist a colleague with field sampling, etc. Please discuss these opportunities with your advisor. Your advisor understands that collaboration, international experiences, and co-authorship on papers are all important to your development as a scientist. Your advisor will want you to carefully consider how the opportunity will advance your career, your overall experiences, and the advancement of science. Will the benefits from the experience outweigh the time away from your dissertation work? You are likely the best judge of this. Your advisor’s degree of enthusiasm for such enrichment activities will largely depend on your other commitments, and whether you are making strong progress with your research! Recognize that you are expected to focus on your thesis and dissertation first and foremost. If you are not making strong progress, your advisor’s enthusiasm for your exciting opportunity may be low. On the other hand, if you are making strong progress with your research, the sky is the limit! Making progress with your dissertation work generally opens the door to more and additional enrichment opportunities.

Grants and awards – Obtaining funding is a critically important part of conducting science. While PIs generally provide funding and guarantee financial support, we strongly encourage graduate students and postdocs to gain experience obtaining and managing your own funding. Doing so will help you develop these valuable skills. Examples could include applying for a NSF postdoctoral fellowship, a Smith Postdoctoral Fellowship, a NSF GRFP, EPA STAR Fellowship, a National Geographic grant, and many, many others. There are also a number of internal funding opportunities through the CFL (Anna Grant Birge scholarship, Charlotte Stein Travel Award) and Integrative Biology (JJD travel award, student awards).

If you are planning to submit a proposal through the university to an external funding organization, please arrange a meeting with Monet Hutchins several weeks in advance of the deadline to discuss the budget and the logistics of proposal submission, which are often complicated and can’t be done at the last minute.

In addition to grants, awards are also important for building your credibility and your CV. There are many award opportunities within UW-Madison, scientific societies, and beyond. We encourage you to keep track of opportunities to be nominated for awards and share these with your advisor.

Activity report– soon after the beginning of spring semester, you’ll be asked to do a Graduate Student/Postdoc Activity Report. This provides you with an opportunity reflect on progress and goals, and a chance to provide an update to your advisor. These reports play an important role. Once they’re all received, CFL PIs meet and discuss the progress of each graduate student and postdocs. Following this, advisors and graduate students/postdocs are to meet for a yearly performance review to discuss the big picture – how things are going, progress, and goals.

Interactions with your advisor – It is important for you and your advisor to be on the same page about communication style and expectations for meeting. This is something the two of you should discuss and agree on when you start. It is important for you to meet with your advisor regularly, and your advisor is almost always happy to meet for advising (sometimes schedules and deadlines make this challenging, so bear with them). This holds for committee members as well, but your advisor will almost always be your main point of contact. Regular meetings allow for proper communication. It is your responsibility to arrange meetings to share results and get feedback, since you know best when you need input or feedback. The details will vary among advisors. For some graduate students, regular weekly meetings are preferred, though there is no hard and fast rule for meeting frequency as the optimal meeting interval depends on the student and the situation. If your advisor does not have set office hour slots for graduate student/postdoc meetings, contact them to set up a time slot. If a regular ‘on the books’ meeting would be helpful, request it. Sharing results via email or Slack is also an effective way to get quick feedback.

If you need something or would like to meet, do not hesitate to simply ask your advisor. Email is often the best and fastest way to reach your advisor given travel and meeting schedules.

Reference letters – Writing reference letters for jobs and awards are an important part of the job of faculty. Please request the letter at least two weeks before the deadline and provide the position description, your application including cover letter, and your CV. This will allow us to tailor letters accordingly. Tell us if there are certain details you’d like us to highlight, or if there are specific questions the reference letter should address. If you don’t have confirmation that the letter has been submitted, send an email reminder 2-3 days before the deadline.

Vacation and leave – Information about leave for postdocs can be found here (see LINK below).  UW does not have formal vacation time or sick leave for graduate student research assistants, but you should take a reasonable amount of vacation or sick leave as needed. There is no overtime or comp time. You absolutely should take vacations – it is important to inform your advisor before taking an extended vacation.

Samples – All samples that you collect as part of your research must be labeled with your name and that of your advisor. Include a dispose by date. This is vitally important when the time comes for you to leave and get things in order. After you finish you will need to dispose of samples and clean up any messes.

For graduate students

Here we outline information that is specific to CFL graduate students. CFL graduate students can earn MS (Master of Science) and PhD (Doctorate) degrees through the Freshwater and Marine Sciences (FMS) or Integrative Biology GraduatePprogram. The overall experience of CFL graduate students is essentially the same regardless of whether they are enrolled in the Integrative Biology or FMS Graduate Program. The overall requirements of graduate study include coursework, an annual committee meeting, an oral and written preliminary examination (PhD only), submission of a thesis, and a thesis defense. Specific program requirements are available on the FMS/Integrative Biology/Graduate School websites and spelled out in great detail in handbooks for each program. And if these resources don’t do the trick, try contacting Kelin Boldiis, the graduate coordinator for FMS and Integrative Biology. It is the responsibility of the graduate student to assemble their graduate committee, organize the necessary meetings, and ensure that all milestones are being met. Graduate students should schedule a committee meeting annually.

A typical MS thesis consists of 1-2 published chapters. MS students form a committee of three, including the student’s advisor. Committee meetings are to be held annually. The MS is typically completed in 2 years (occasionally 2.5 years for a two-chapter thesis).

For the PhD, the student forms a committee of five, including the student’s advisor. The committee meets annually after the first year. The prelim exam is held during the second year, or early in the third. The procedure is as follows: the student provides a thesis proposal to the committee. Two weeks later, committee members provide questions for a week-long written exam administered by the advisor. Two weeks after the written exam is a three-hour oral exam in which the candidate presents and defends their research proposal to the committee. After successful completion of the preliminary exam, the candidate is expected to hold a committee meeting annually. The thesis defense is typically at the end of year five, but timelines vary among students depending on circumstances. A PhD is typically comprised of three to five chapters, with each chapter being equivalent to a manuscript for a scientific journal.

MS and PhD theses should be sent to the committee two weeks prior to the defense.

Every semester, the CFL faculty offer a graduate seminar Zoology 955: Limnology Seminar. Topics rotate and span a broad range of topics. We expect all graduate students to participate unless there is a very specific reason not to. Graduate students should also enroll in Zoology 911: Limnology and Marine Science Seminar every semester.

CFL graduate students are encouraged to take Zoology 750: Problems in Oceanography (cross-listed with several departments), also known as the Sapelo course. This latter class is offered in alternate fall semesters and is often cited by program alumni as a highlight of their graduate career.

Incoming graduate students who do not already have a MS degree may be encouraged to complete the MS degree en route to completion of the PhD. This creates a mechanism for graduate students to complete a research product and submit a paper for publication by the end of year two, before proceeding to the PhD. The MS outputs count towards the requirements of the PhD. This route generally results in more rapid progress and an additional concrete benchmark towards completion of the PhD.

Publication expectations – As noted above, a key expectation is the production of scientific papers. We expect students to write and submit thesis chapters for publication as they go, rather than letting them pile up and then submitting papers after they’ve defended and departed the CFL. We expect graduate student to submit chapters for publication by the time of thesis defense. Our point here is that graduate students are expected to defend a near-complete and published/publishable product. Peer review publications are the benchmark for scientific achievement and demonstrate that you are able to complete projects, a skill that is relevant and applicable to any career path student may take. Also, be sure to give your committee members the opportunity to review these manuscripts before you submit them for publication. They may or may not provide feedback, but it is wise to give them the chance to provide input before the paper shows up in your dissertation.

We expect most graduate students to make teaching (TA) contributions while at the CFL. Ecology of Fishes Lab (Zoo 511), Limnology Lab (Zoo 316), and Introductory Biology (Zoo 151-2 and 101-2) are the most common teaching assignments. The number of semesters a student TAs will depend on their specific funding situation, and the degree to which the student wants to gain teaching experience. Many MS students TA for 2 semesters, while PhD students TA up to 3-4 semesters. There are other valuable teaching opportunities, such as giving guest lectures, assisting with graduate seminars, and serving as course instructor (for example, sabbatical replacements).

For postdocs

Here we lay out work and productivity expectations for postdocs. As a rule of thumb, you should spend at least 80% of the total time that you work on the project funding you, and no more than 20% on other tasks, such as old manuscripts, job applications, etc. This 80% is a long-term average. We understand that there will be times when more than 20% is necessary for outside tasks, but this means that there have to be weeks during which 100% is devoted to the project.

As for productivity, a rough rule of thumb is that you would submit around one first-authored paper (from postdoctoral work at UW-Madison) in your first year, and at least two first-authored papers in each of the following years. Of course, we view this as a rule of thumb.

We understand that collaborating outside of your project, participating in proposal writing, and teaching are all important to building your record, experience, and professional network, and we are supportive of that. It is important to ensure that side projects and completing old papers does not occur at the expense of the main project that provides postdoc salary. To avoid this, good communication is important. Please discuss opportunities with your advisor when they arise, and understand that they will expect your main focus, especially during the initial phase of your postdoc, to be your postdoctoral project. Your advisor’s view on side projects will depend on the progress with your main project.

Trout Lake Station

Trout Lake Station (TLS) is an integral part of the CFL. Individual CFL graduate students and postdocs will use TLS in very different ways. For some, it may provide a base for a writing retreat, or a single field outing. Others may spend entire summers at Trout Lake and use the station as the base for all their research. In either case, it is important to understand TLS and how it works, and to coordinate with the appropriate TLS staff to ensure that you have the equipment you need, know the rules, and can co-exist with TLS staff and other users.

Because all TLS staff live off-site, graduate students tend to play a key leadership role among those living on site. As such, graduate students are expected to provide both personal and academic leadership for the many undergraduates that live on station during the field season.

When you leave

When you depart, you will likely continue to collaborate and interact with colleagues at the CFL. Here we lay out several rules that are especially relevant at the end of your time at the CFL.

  • Do not leave your samples behind at the CFL. This includes in freezers. All samples must be labeled with your name, PI name, and dispose by date. Communicate with your advisor your plan for disposing of your samples after you’re done.
  • Clear your desk space when you leave so that it is usable for another student.
  • Provide information needed to gain access to data, code, and other files from your research to your advisor, including full documentation. Archive your data through LTER and EDI.
  • Please have your MS or Ph.D. thesis bound and give a copy to the Hasler Lab and TLS libraries
  • Be sure to remove all limnological equipment (‘limnotrash’) that you’ve deployed in the field.

Many high-quality research findings from CFL graduate students and postdocs are never submitted for publication. In other words, lots of great research never sees the light of day. When this happens, we fail to contribute to advancing science and aquatic conservation, which is the reason why we do all this work in the first place. For this reason, we emphasize that you should submit your manuscripts for publication in a timely fashion. Our hope is that you will submit your papers and serve as the corresponding author. Where progress is not being made, we offer the following guidelines. Your advisor will communicate with you before taking any steps:

  • We expect that manuscripts that have not been submitted before you leave, and that require only minor revisions before submission, will be submitted within six months of your departure. After that, your advisor will assume the role of corresponding author, and will submit the manuscript on your behalf, without changing the author list or author order.
  • We expect that manuscripts that have not been submitted before you leave, and that require substantial revisions and maybe additional analyses before submission, will be submitted within twelve months of your departure. After that, we reserve the right to take the role of corresponding author, including inviting new co-authors to assist with the remaining analyses, changing the author order, and taking over as the lead author if necessary.

For comments or suggestions regarding this topic, contact the Jake Vander Zanden. For edits to this page, contact Kelly O’Ferrell.