Hopkins Track Overview

Hopkins Marine Station PhD Requirements 

Hopkins First Year Advising Committee and Co-Mentorship Program

Hopkins’ students are encouraged to meet with their host lab at Hopkins during the weeks before the start of Autumn Quarter. During this time, students are required to select a mentor in addition to their primary research advisor (referred herein as a co-mentor). The role of the co-mentor is to provide support and guidance in navigating academic studies and to achieve professional goals. 

Co-Mentor Eligibility

Faculty at Stanford and outside of Stanford are eligible to serve as co-mentors. When feasible and applicable, trainees are encouraged to partner with Stanford faculty on the main campus as a means to become better integrated within the campus community. Faculty may be active, emeriti, or retired. A co-mentor may be a member of a graduate student’s dissertation Reading Committee other than the primary advisor or another faculty member that the trainee already has a relationship with. Co-mentors may also be other professionals including academic staff (e.g. senior research associates and lecturers), non-academic staff in professional development supporting roles, and professionals at a range of institutions (e.g., Monterey Bay Aquarium, MBARI, MBNMS, and NGOs)*.

Role and Responsibilities of Co-Mentor

Co-mentors are expected to meet with trainees to discuss their work (e.g. research, teaching, training), professional development and/or career opportunities. The role of the co-mentor is to act as a coach, to provide advice, guidance, feedback and connection to professional networks and opportunities. They can also act as a champion to offer encouragement and support. When relevant, co-mentors may serve as facilitators to connect trainees with colleagues, campus academic resources (e.g. Office of the Vice Provost for Graduate Education, Office of Postdoctoral Affairs, the Center for Teaching and Learning, research facilities), or external networks to support their personal development and growth, and professional goals. The co-mentor is not responsible for serving in an official advisory role for the trainee (see below) or providing the type of information that is available to trainees from the Biology Student Services Office. Co-mentors may help trainees consider and weigh potential consequences of decisions and actions to avoid the pitfalls and possible surprises that may occur. Co-mentors and trainees are expected to meet on a regular basis (at least once per quarter) for a casual check-in meeting to talk about their progress and professional development; this frequency of meeting facilitates building a meaningful relationship.

Role and Responsibilities of the Mentee

Trainees are active partners in the mentoring relationship. They are responsible for identifying initial goals and measures of success for the mentoring relationship, these can be refined over time in continuing discussion with the co-mentor. Trainees should be open to and seek feedback. They should take an active role in their own development and provide feedback to the co-mentor with the goal of building a mutually beneficial relationship. Trainees should schedule and attend mentor conversations.

Mentoring Plan

It is recommended that the trainee and co-mentor work together to develop a mentoring plan to define expectations for the relationship. This plan may include the format and frequency of the meetings, and mutually agreed upon goals and expectations for the coming months.

Factors to Consider When Selecting a Co-Mentor

There may be several factors that influence the choice of a co-mentor. Co-mentors may be selected based on their research interests, teaching interests, professional experiences, leadership and mentoring roles or other personal or professional characteristics that would make for a positive relationship. Trainees will work with their advisors, or with HMS Co-Directors and HMS committee chairs, and the Student Service Office in the Biology Department to identify a co-mentor. The existing mentoring BFF (Biology First-year Facilitator) Program serves as an excellent example for a co-mentoring program that can be adapted for this purpose. First year graduate student trainees working with BFF faculty mentors can consider extending their relationship for another year to satisfy the co-mentoring requirement.

Distinction between a Co-Mentor and Co-Advisor

Co-mentors are not responsible for monitoring the trainee’s academic requirements and responsibilities, or providing funds, resources, or facilities for the trainee to complete their research and/or degree. By contrast, a co-advisor serves in an official university role to advise and/or provide resources (e.g. funding, space) for trainees. If a trainee has a primary research advisor and a co-advisor, the trainee may opt to have the co-advisor serve as their co-mentor if the co-advisor agrees to serve in this role.

First Year Advising Committee

In addition to the selection of a co-mentor, students must select an advising committee consisting of three faculty members. The First Year advising committee may or may not include the co-mentor. The purpose of this committee is to advise the student on their academic activities during the first year. The committee will discuss several topics with the student: recommendations for courses to take during the first year, plans for teaching assistantships, fellowship applications, general research areas of interest, and rotation plans (if applicable). The student can call on members of this committee throughout the first year to request further guidance on these topics as the year progresses.

Students and First Year Advising Committees are advised to remember the university requirement that every Ph.D. student university-wide must complete four courses of 3 or more units with four separate faculty members. As some Hopkins students take relatively few courses, Hopkins’ students are advised to devise a plan for fulfilling this requirement in their meeting with the First Year Advising Committee. We view this requirement very broadly, and any four courses of 3 or more units each, not necessarily in Biology, can satisfy this requirement. The Bio 302-303-304 course counts as one of the four courses. The four courses must be completed by the end of Spring Quarter of the second year. Enrolling in units for TA service can potentially count as one of the four courses if necessary. For NSF-eligible students, the student will also discuss with the First Year Advising Committee whether to apply for the NSF fellowship in the first year or in the second year. Students will meet with the First Year Advising Committee at the end of the first year to discuss the first year’s progress and to complete the First Year Evaluation Form. A good time for scheduling this end-of-year meeting is immediately after the First Year Seminar.

For Hopkins’ students, the First Year Advising Committee provides the main academic advising during the first year (with supplementation by the BFF and the co-mentor, who are sometimes also members of the First Year Advising Committee).

Biology First-year Facilitator (BFF) Program

Faculty mentorship in the BFF program is focused on helping students integrate into the department culture through non-judgmental advocacy. This is facilitated by meetups in casual environments once a quarter. BFFs also support students as they manage their lab rotations and choose appropriate coursework. Emphasis is placed on cultivating a supportive relationship between faculty and student during what is often a stressful period of transition. In August, faculty indicated their interest in diverse areas of mentorship. Students then rank their preference for mentors based on shared interests. Mentors will ideally be faculty the student does not plan to rotate with to avoid conflicts of interest.

The first meetings should take place during orientation week or the first week of classes. Students must verify online that they have met with their BFF no later than one month into the quarter. Students will meet with BFFs during the Autumn, Winter and Spring quarters.


All courses must be completed prior to Spring Quarter of the 4th year, except for the required first year courses as noted.

  • BIO 301 (Autumn) or BIO 302, 303, 304: Current Topics and Concepts in Population Biology, Ecology and Evolution – students must enroll in Autumn, Winter and Spring quarters of 1st year Students should consult with their advisor asto which course series to take during the first year on campus

  • Ethics Requirement: MED 255: Responsible Conduct of Research (offered every quarter) OR Bio 313 (strongly recommended) must be completed by the end of the first year.

  • Two additional Hopkins Marine Station courses (BIOHOPK). These may include BIOS mini courses offered at Hopkins.

  • In addition to the courses listed above, students may be required to take a set of courses to be determined by the advising committee.

Please note that there is a university requirement that all Ph.D. students must complete at least three units of work with each of four Stanford faculty members. Three units of work can include lectures, labs, seminars, teaching, research, directed readings and independent study.

***New Optional Course Available***

BIO 305: Managing Your PhD

Curriculum is targeted for different periods of your PhD training, Autumn quarter: 1st years, Spring quarter: 4+ years. The course will focus on 5 themes for effectively managing your PhD: professionalism, scholarship, well- being, and community-engagement and career development. We will meet every other week and have an active discussion-based class meeting for 1.5 hours.

Professionalism: Personal conduct in a professional environment.  Professionalism skill development includes personal accountability, time management and working effectively in groups.

Scholarship: Your knowledge of, and achievement in, a field of study as evidenced by presentations, written work and publications. 

Well-being: Being in a state of comfort, health and happiness.  Attention to personal well-being is necessary to achieve long-term goals through persistence and resilience. 

Community-engagement: Research and education are funded by the public.  Academics are responsible for communicating the importance of their work to the public through outreach and community engagement.

Career development: The PhD is a stepping stone to a career.  Students are encouraged to consider how their PhD studies prepare them for the job market and a career that is personally fulfilling and broadly impactful.

Lab Rotations

Hopkins PhD students may rotate with and select as the primary Ph.D. advisor any faculty member with a primary appointment in one of the Biosciences Home Programs. While rotations are not required in order to choose the primary advisor, they are certainly possible. Many students collaborate with faculty in addition to their primary advisor in order to increase breadth and depth. This is usually accomplished with the advice and encouragement of the primary Ph.D. advisor.

Seminar Presentation

The seminar requirement is fulfilled by presenting a 20-minute talk. This seminar is typically given at Hopkins but does not have to be. The student must arrange for at least two faculty members from the Department of Biology to attend the seminar and evaluate the presentation. Evaluation will consist of meeting with each faculty member within one week following the seminar to obtain comments. If the faculty members approve the presentation, they will sign the form at this time. In some cases, they may require an additional talk before signing. The Seminar Evaluation form must be submitted to the Student Services Office no later than May 15 of the first year.

First Year Paper

Each student must prepare and submit a paper before the end of the first year that will be evaluated by the advising committee. This paper should be a step toward the development of a dissertation proposal and may consist of an analysis of new data or a literature review and synthesis. This can be satisfied in a number of ways that all involve new writing, undertaken since entering the Stanford program. These may include:

  • A new draft research manuscript; a previously published paper is not acceptable because it may have received much editorial modification in the review process.

  • Some other piece of new writing, such as a review paper from a course, or an initial literature review of a potential thesis topic. In this case the paper should ordinarily be not less than 10 or more than 20 double-spaced pages in usual sized font, plus references. It should be written in the style of a standard scientific paper.

The paper should be read, commented upon, and agreed to as satisfactory by two faculty members. The First Year Paper Evaluation form and a copy of the first year paper must be submitted to the Student Services Office no later than May 15 of the first year.

Hopkins Committee Meeting Guidelines: Second Year and Beyond

The graduate committee exists to provide students with guidance in their thesis work, and to certify that they meet the standards of the program (i.e., successfully defending their thesis proposal, writing and defending a doctoral thesis). To those ends, the Hopkins faculty have established the following procedures:

  • Approximately a week before a committee meeting, the student should provide a short outline/precis of what they will be presenting to the committee at the meeting. The idea is to give the committee members a heads-up as to the topics the student wishes to discuss so that they can give some productive thought to those items before the meeting. If applicable, this precis should include a short discussion of how the plans formulated at a prior meeting have unfolded.

  • Within a week or so after the meeting, the student should send the committee members notes from the meeting. The idea here is to have some record of what was decided at the meeting, a record that can be very useful in keeping everyone on track by providing continuity from meeting to meeting.

  • The student should arrange with one member of the committee for that member to serve as committee chair. The chair must be someone other than the student’s advisor. The chair is responsible for keeping the records of the committee meetings, completing the department Committee Meeting Form, and (if needed) reminding the student to deliver the before- and after-meeting documents. The chair also runs the meetings.

  • Typically, a meeting starts with a presentation by the student, followed by constructive discussion of science and the student’s progress. Sometimes it’s better if the student is allowed to make their entire presentation before opening the meeting to discussion. That ensures that all of the student’s thoughts/issues/concerns are presented before questions take the meeting on some tangential path.

  • The meeting then finishes with two rounds of discussion. (1) The student leaves the room, and the committee discusses the student’s progress. The summary of that discussion is then conveyed to the student when they come back into the room. (2) The advisor then leaves the room, providing time for a discussion of any concerns the student or committee might have about the student/advisor relationship. If there are concerns that require further attention, the student and the committee chair should work together to begin the process of addressing those concerns.

  • Beyond this, the details are up to the student and their committee to determine, including how long the pre’cis and notes should be, length of the student’s presentation, etc. These, and similar details, should be worked out on a case-by-case basis.

Committee Meeting Schedule

  • 3rd Year: due by May 15

  • 4th Year and beyond: due by May 15.

    • The 4th year committee meeting written progress report should describe the following:

  1. Progress towards goals

  2. A timeline to graduation within 5.5 years

  3. A timeline towards publication(s)

  4. If applicable, a written petition for extending the time to graduate beyond 5.5 years with an explicit anticipated date for graduation; a petition could be for health, personal or scientific reasons.

The meeting must also include a formal slide presentation and timeline to degree completion with specific milestones outlined. Career planning should begin at this meeting.

  • 5th Year and 6th Year: due by November 15 and May 15. Beginning in the Autumn Quarter of the 5th year students will need to have committee meetings twice a year, every 6 months until degree completion. These meetings should include an updated progress report of work done and the timeline of experiments to finalize degree completion, which must occur no later than the winter quarter of 6th year (5.5 years total in the Ph.D. program).

Graduate Student Symposium

All second-and-fourth year students are required to present at an annual student symposium (typically in February).

Second Year Students

The first half of the symposium will give second-year graduate students a forum to present plans for their graduate work. Because each student’s research is different, there is no one-size-fits-all plan for these talks. But in general, these 20-minute presentations are meant to answer the questions: What broad area of marine biology am I pursuing my PhD? What is known about this now? What am I planning broadly to contribute? What preliminary or initial data do I have?

Fourth Year Students

The presentation for fourth-year students comes in two parts:

  1. Each student will prepare a written overview of their doctoral research, including progress to date and plans for the final thesis. The document should be single spaced, 11-point (or larger) font, and should not exceed 3 pages (including figures and tables, but excluding references). In addition to this research overview, each student will submit an up-to-date CV, and the research overview and CV should be submitted no later than one week before the symposium date. Please combine the research statement and CV into a single PDF file, and email it to the co-directors.

  2. In the second half of the symposium, each fourth-year student will present to faculty and a general audience a 20-minute report on their PhD research. Along with the written research overview, this is intended to give each student a chance to pull together their data and analyses to date, lay out initial conclusions, and explore what they mean in the context of their overall research interests and goals. As with the research overviews, these talks give students a chance to concentrate on what progress they have made along the complex path of their PhD, and what they are particularly excited about. Laying out plans for finishing the thesis should be a part of these talks, but should not be the main topic.

 After the symposium, both second and fourth year students will meet with Hopkins faculty to receive feedback on the content and presentation of their talks.

For more information, please see the 2021-2022 PhD Handbook