Stanford School of Medicine
Developmental Biology–

DevBio Student Handbook

Program of Study - Curriculum

Course requirements for the Graduate Program in Developmental Biology are as follows:

  1. Developmental Biology (DB 210), Spring
  2. Development and Disease Mechanisms (DB 201), Autumn
  3. Advanced Genetics (Genetics 203/ DB 203), Autumn
  4. Frontiers in Biological Sciences (DB215; taken each of the first two quarters during the first year), Autumn & Winter
  5. Research (DB 399; 3 rotations during the first year)
  6. An advanced molecular biology, biochemistry, or biophysics course. Possible courses that would fulfill this requirement are: Graduate Molecular Biology (Biochem 201), Biological Macromolecules (Structural Biology 241), Physical and Chemical Principles of Biochemistry (Biochem 214), Computational Molecular Biology (Biochem 218), Principles of Cell Physiology (MCP 210), Protein and Nucleic Acid Structure, Dynamics and Engineering (Structural Bio 228), Eukaryotic Chromosome (Structural Bio 229). Other courses not listed may be used to fulfill this requirement contingent on prior approval of the Graduate Student Coordinator. Alternatively, this requirement may be fulfilled by acting as a T.A. for Biochemistry 200 or 203.
  7. The Responsible Conduct of Research (Med 255)
  8. At least two additional courses.

Letter grades will be given for all core courses except Frontiers. Students are also expected to attend regular Developmental Biology seminars and journal clubs. In addition to the required courses, many students also take Cell Biology of Physiological Processes (MCP211; offered in the Winter quarter), and may choose from a variety of elective courses that are offered on a rotating basis. The first year students should meet with their Advisory Committees to determine their course schedules. Course requirements are usually fulfilled during the first two years of study and the latter years of the program are devoted to full-time research and work on the dissertation. The University requires that a minimum of three (3) units of coursework be taken with each of four (4) or more Stanford faculty members, not necessarily within the major department.

Students must enroll in a maximum of 10 units.

Courses Offered by the Department

Courses are listed in the School Catalog.

History

One of the major goals of the department is to create a principal center of research and teaching in developmental biology. The establishment of the Department of Developmental Biology has provided a means for assembling a critical mass of scientists who are leading the thrust in developmental biology and who can train new leaders in the attack on fundamental problems of development.

The specific areas of study represented by the fifteen faculty members in the department include vertebrate embryology, developmental genetics with particular emphasis on microbial systems, Dictyostelium, Drosophila, the nematode and vertebrate systems. Research is aimed at a basic understanding of the molecular mechanisms underlying developmental decisions and the resulting morphogenetic processes. The discipline of developmental biology draws on molecular genetics, cell biology and biochemistry.

On October 4, 1985, the Board of Trustees approved the establishment of the Department of Developmental Biology in the Stanford University School of Medicine. The department received authorization to offer degree programs on November 9, 1989. The Arnold and Mabel Beckman Center for Molecular and Genetic Medicine opened in 1989. Housed in the Center are the Department of Developmental Biology and three interrelated academic groups: the Howard Hughes Medical Institute Unit in Molecular and Genetic Medicine, the Department of Molecular and Cellular Physiology and the Department of Biochemistry. The Beckman Center is adjacent to the Medical Center. Housing over 50 faculty members and their research teams, the Beckman Center is an exciting component of the Stanford research community.

Faculty

The department has 15 faculty members that attack the questions of developmental biology through many exciting research studies.

Students

Stanford University has a student enrollment of aproximately 14,000, of whom nearly half are graduate students. The Department of Developmental Biology has a current enrollment of 36 students.

Postdoctoral Fellows

The department welcomes scholars who have recently completed their Ph.D. or M.D. and wish to continue their training and broaden their professional experience. For the scholar, postdoctoral training provides an opportunity both to further professional preparation and research skills and to be exposed to new ideas in a stimulating academic environment. The faculty sponsor works with the postdoctoral fellow to devise a plan of research and to establish goals for the period of training, and provides ongoing consultation.

The postdoctoral fellows in the department provide a reservoir of knowledge and technical expertise. They participate in the many journal clubs and research discussions and are a valuable resource for the graduate student community.

Undergraduate Research Opportunities

Many high school and undergraduate students gain their first research experience working with graduate students and postdoctoral fellows in the laboratories in the department. The department welcomes these students and utilizes their help through work-study, the Undergraduate Research Opportunities (URO) program, the Youth Opportunities Program and independent study.

Administrative Staff

The departmental administrative staff is located in room B300 of the Beckman Center.

Registration

Graduate students are required by the University to register for autumn, winter, spring and summer quarters each year until the degree is received. Registration is also required each quarter in which a Stanford financial award is received. Leaves of absence require approval before departure.

Axess

Axess Application: http://axess.stanford.edu (a SUNet id and password are required)

Axess is a student information system available via the web. It is regularly available weekdays 8:00 a.m.to 11:59 p.m. and weekends 9:00 a.m. to 11:59 p.m. Using Axess, you will be able to complete the following tasks:

New students may use Axess at any time after receipt of the registration packet from the Registrar's Office. You will need a SUNet ID and password, and PIN to use Axess.

Study List

Your study list is the list of courses you are taking in a given quarter. You are required to submit your student list officially each quarter via the Axess Courses/Grades function. Study lists are usually due by 11:59 p.m. on the Sunday after the second week of instruction; late fees are charged for submission thereafter. Refer to the back cover of the Time Schedule (a listing of all courses taught, their meeting times, and locations) for specific instructions on how to file your study list.

Time Schedule

The Time Schedule includes the university calendar and information on registration procedures, payment of fees and course listings. It is published prior to each quarter and is available in Room B300, Beckman Center, the Graduate Student Affairs Office, MSOB, Room 309, the Medical School Student Affairs Office (M-105) and at the University Registrar's Office in the Old Union.

PIN Number

All members of the Stanford community are assigned a University ID number (it's the 8 digit number above the picture on your University ID card) and a 5-8 digit Personal Identification Number (PIN). This ID/PIN combination verifies your identity when you sign electronic forms or request certain computer services. Your ID number is not secret but your SUNet ID/password and PIN must remain confidential. You should receive your ID and PIN number in the mail once your file has been processed. If you have forgotten your PIN, bring a photo ID to the Registrar's Office during business hours or send an e-email to Registrar@leland.stanford.edu. For further information log on to stanfordyou.edu or contact Todd Galitz, Lab Manager in Beckman B-300.

Student ID Number

Your Stanford University ID is a number assigned to your academic record and is required for any inquiries you make. The ID number is printed on your registration commitment letter, your Stanford University ID card, and all enrollment/grading-related documents distributed by the Registrar's Office. Your ID number is unique and considered directory information. The first step in obtaining your ID card is to check with your student services administrator to be sure that your personnel file has been set up, and that you have been assigned an ID number. Once you have your number, you need to bring some form of picture ID with you to the ID Card Office. The ID Card office is located on the first floor of Old Union (Room 141), and its hours of operation are M-F, 8am - 12pm, and 1pm-5pm.

University Bill

After submitting a Registration Commitment, students may receive a University bill. Tuition credits are entered on this bill. Also entered are other University charges such as rent, student fees, late fees, loans, etc. Students receiving a fellowship paid through Stanford may elect to have these charges deducted from their stipend checks and automatically applied to their bill.

If your bill is incorrect or incomplete, it is your responsibility to ensure that the bill is corrected or to pay the correct amount by the payment deadline.

Terminal Graduate Registration (TGR)

Doctoral students are eligible for TGR status when they have been admitted to candidacy, completed all required coursework, completed 135 units, and submitted the Doctoral Dissertation Reading Committee form.

Students registered in TGR status must enroll each quarter in a TGR course (#802 for doctoral programs) in their department, with their advisor as the instructor. There are zero units for this course selection and you will not be eligible to take classes for credit. The purpose is to work on the thesis, dissertation, or other remaining requirements that must be evaluated each quarter for academic progress and graded as follows: "N" indicating satisfactory progress, "N-" for unsatisfactory progress, and "P" for a final grade when all requirements have been completed. A hold is placed on the registration of a student who receives an "N-" grade for two consecutive quarters. Further registration is contingent on approval of an agreement for completing degree requirements by the adviser and the department.

Rotations

Research rotations are an important part of the graduate training program. The purpose of laboratory rotations is to broaden the student's research experience and to familiarize students with the ongoing research projects in a variety of different laboratories. While a primary function of rotations is to help students choose a Ph.D. advisor, students should also use the rotations to learn as much as possible about research in developmental biology at Stanford.

First-year students spend one quarter in each of three different labs, working closely with the professor, graduate students and postdoctoral fellows on research projects. The Fall quarter rotation must be in a laboratory within the Department of Developmental Biology. Rotations during the Winter and Spring quarters may be in any laboratory within the Biosciences at Stanford. It is the student's responsibility to contact appropriate faculty members to arrange lab rotations. During the fourth quarter, the student chooses a permanent laboratory in which to carry out his/her dissertation research.

Teaching

There is no formal teaching requirement in the Department of Developmental Biology. Students interested in gaining teaching experience may serve as teaching assistants in several courses, with approval of the course instructors and after consultation with the Advisory Committee.

Advisory Committee

Upon entering the department in the fall of the first year, the new student is assigned an Advisory Committee of three faculty members. This committee will include the student's first rotation advisor and the First Year Student Coordinator (William Talbot). The Committee is responsible for advising students on courses to take, choices for laboratory rotations, and other issues that may arise during the first year.

Seminar Programs

Developmental Biology seminars are listed in the Medical Seminars Calendar.

Frontiers in Biological Research Seminars

The Departments of Developmental Biology and Biochemistry each sponsors a biweekly departmental seminar series held on alternating Wednesday afternoons. The "Frontiers in Developmental Biology" and "Frontiers in Biochemistry" seminar series bring outstanding developmental biologists and biochemists, both nationally and internationally recognized, to Stanford to present their work. To recognize and promote participation by the students, the departments jointly offer one unit of credit for a seminar course, "Frontiers in Biological Research" associated with these seminar series. In this course, students will read and discuss literature related to the topic being presented. Students have the opportunity to meet with each speaker after the seminar for an informal discussion.

The Frontiers in Developmental Biology seminars take place at 4 pm in Clark Auditorium in the Clark Center. Pre-seminar reception begins at 3:30 pm. A meeting with the speaker follows in the Developmental Biology library (Room B302) after the seminar.

Lectures by Students and Postdoctoral Trainees:

An important aspect of the training of every graduate student is the development of speaking skills. The department provides numerous opportunities for trainees to speak about their research in a seminar setting. Once students begin their dissertation work in the second year, they will be asked to give a talk in the department about once a year. Student talks can be given in one of the many research interest groups such as; the Microbial Data, "Dev Bio Departmental Data Club ("3D"), RAVE or at the departmental conference. This is a valuable experience because all members of the department, including faculty attend the seminars. These seminars will be concerned with ongoing and unfinished work and consequently are expected to generate considerable discussion. The speaker must organize the work, present it clearly, answer questions, and discuss other ideas raised by the listeners.

"Dev Bio Departmental Data Club ("3D")

Discussing Developmental Data: 3D is an informal research meeting at which graduate students and postdocs present their latest results and ideas to the entire department. These lunch-time discussions are lively and informative, reflecting the enthusiasm and cutting-edge research of graduate students, postdoctoral fellows, and faculty of the Department.

Journal Clubs

Most students participate in journal clubs that meets on a regular schedule to discuss published reports from the literature. The goal of these Journal Clubs is to teach students to read, analyze and criticize scientific papers. Students are exposed to a broad sampling of research interests and experimental approaches. All students participate actively in critiquing the papers, and each student is given the responsibility for leading discussions several times throughout the year.

Microbial Data Club

The Microbial Data Club is an informal gathering of approximately 50 graduate students, postdocs and faculty who have a research interest in prokaryotic and eukaryotic microbes. The "Bug Club" meets the second Thursday of every month from 6-8 pm in the Developmental Biology library. Dinner can be purchased inexpensively for the first half-hour. Two talks of about 20-30 minutes are presented and there is plenty of time for questions. In the past year, participants from the following departments have taken part: Biological Sciences, Biochemistry, Developmental Biology, Genetics, and Microbiology and Immunology.

RAVE

Research About Vertebrate Embryos (RAVE): Every month Bay Area labs working on vertebrate development meet to discuss ongoing research projects utilizing fish, frogs, chicks, mice, and humans. Two half-hour research talks are usually presented, with lots of time for questions and discussion. Meetings alternate between Stanford, Berkeley, and UCSF.

Pizza and soft drinks provided. Meeting times and topics posted near B307 and on departmental bulletin boards. Contact the Kingsley laboratory for more information.

Group Meetings

Each faculty member in the department schedules weekly group meetings in which the students and postdoctoral fellows take turns presenting their experiments and/or discussing papers from the literature.

Student Symposium

Every 2-3 years, students and postdocs organize a two-day symposium focused on a particular topic in Developmental Biology. Expert scientists in the field are brought together to probe the subject in depth. The Symposium will be held on April 17-18. Previous symposia topics include: "Cell Migration During Development", and "Evolution of Genetic and Developmental Programs". And "Cellular Asymmetry".

"Cookies" and Social Hour

Two long-standing DB traditions are snacks provided by the department at 4:30 p.m. on Mondays and on Wednesdays when there is no seminar, and a Social Hour held Friday afternoons at 5:30 p.m. (sponsored by different lab groups on a rotating basis). Both gatherings are held in the 3rd Floor lobby.

Qualifying Exam

Procedures

The research proposals should be approached as a 3-year, one-person project (similar to the basis of a postdoctoral fellowship application). A short presentation before the examination committee may be requested. Visual aids (e.g., slides or overheads) are acceptable. Below are more detailed instructions on writing the proposals:

Research Plan. Organize Sections A-D of the Research Plan to answer these questions. (A) What do you intend to do? (B) Why is the work important? (C) What has already been done? (D) How are you going to do the work? Do not exceed 20 double-spaced pages for Sections A-D. You may use any page distribution within this overall limitation; however, the advisory committee recommends the following format and distribution:

A. Specific Aims. State the broad, long-term objectives and describe concisely and realistically what the specific research described in this application is intended to accomplish and any hypotheses to be tested. One page is recommended.

B. Background and Significance. Briefly sketch the background to the present proposal, critically evaluate existing knowledge, and specifically identify the gaps that the project is intended to fill. State concisely the importance of the research described in this application by relating the specific aims to the broad, long-term objectives. Two to three pages are recommended.

C. Progress Report (second proposal only). A progress report is required for proposed thesis research. Use this section to provide an account of preliminary studies pertinent to the proposal. Six to eight pages are recommended. For the first proposal that does not have a progress report, use the additional pages for Section D.

D. Experimental Design and Methods. Outline the experimental design and the procedures to be used to accomplish the specific aims of the project. Include the means by which the data will be collected, analyzed, and interpreted. Describe any new methodology and its advantage over existing methodologies. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims. Although no specific number of pages is recommended for this section, the total for Sections A-D may not exceed 20 double-spaced pages.

After the presentation, the committee will ask questions broadly related to the proposal. The student is expected to understand and be able to clearly explain relevant biochemistry and genetics principles and procedures. In addition, the student may be asked to justify the particular approaches presented in each proposal. A working knowledge of the scientific literature relevant to the planned experiments will be expected. The questions may cover related material from previous courses or from laboratory rotations. The examination results in a Pass or a Fail. If a student fails, he or she may be allowed to remedy deficiencies. This could include any of the following: rewriting of the proposal, a second examination on the same topic or on another topic, the presentation of a seminar, or the successful completion of additional coursework. The Committee on Graduate Studies will recommend the student for admission to candidacy only after successfully passing the qualifying examination.

Timetable for completion of the Ph.D. in Developmental Biology

The Ph.D. thesis and oral examination are expected to be finished within five and one-half years from the date of entrance into the graduate program. The following process is designed to facilitate this expectation and to promote faculty participation.

Dissertation Committee

The dissertation committee will consist of four faculty members. These will include the student's thesis advisor, another departmental faculty member who will serve as chair, and two other faculty members who can come from either inside or outside the department. The student subject to prior departmental approval will choose committee members from outside the department.

The dissertation committee will initially be the same as the committee for the qualifying exam, but can be changed by the student, subject to prior departmental approval, to best reflect the research interests of the student. The dissertation committee will follow the student's progress from completion of the qualifying examination to the dissertation defense. The membership for the dissertation committee should not be changed after the penultimate meeting, scheduled approximately six months before the expected date of completion of the dissertation.

By the end of the last quarter of year three, the student in consultation with the research advisor should present to the student's dissertation committee for its review and acceptance a plan and timetable for finishing the Ph.D. During the third quarter of years four and five, the student should similarly meet with the dissertation committee to report on her/his progress. For each of these meetings, the student should prepare an outline of the research plan to hand out to the committee members in advance. In a minority of cases, completion of the Ph.D. by the end of the second quarter of year six may not be anticipated at either of these committee meetings. In these cases, the student in consultation with the research advisor should present to the committee for their approval a revised plan for completion. This plan is to include meetings with the student's committee every other quarter and the expected sources of stipend support after the second quarter of year six. Should the source of this stipend support not be obvious, the student in consultation with the research advisor will submit to the committee a written request to the Department for that support.

Dissertation Defense Committee

When the student, advisor, and Dissertation Committee agree that the student has completed work of sufficient novelty and quality to merit the Ph.D., the student will write a dissertation. When the dissertation is acceptable to the advisor, it will be presented to the Dissertation Defense Committee. The student will then defend this dissertation at the University oral examination.

University regulations specify the composition of the examination committee and the format of the dissertation defense. It will consist of at least five members, four examiners and a committee chair. The chair must be from an outside department and may not have a full or joint appointment in the same department. The department requires that the student present a formal seminar to the members of the department. The formal seminar is held immediately prior (on the same day) to the dissertation defense. The dissertation is expected to be an original contribution to scholarship, to exemplify the highest standards of the discipline, and to be of lasting value to the intellectual community. University guidelines for presentation of doctoral work are described in Directions for Preparing Doctoral Dissertations. These guidelines should be read carefully before final preparation of the manuscript to avoid costly and time-consuming revisions.

Published papers may be included in dissertations; however, they must meet the University's format guidelines. Manuscripts and figures submitted for publication during the doctoral program should be retained for later reformatting and inclusion in the dissertation. Dissertations must be in English.

The Doctoral Dissertation Reading Committee approves the dissertation. Each member of the dissertation committee signs the signature page of the dissertation to certify that the work is of acceptable scope and quality. One reading committee member reads the dissertation in its final form and certifies that departmental and University specifications have been met.

Deadlines for submission of dissertations are strictly enforced. Students who submit their dissertations after the deadline in a given quarter may obtain a Statement of Completion from the Graduate Degree Support Section; official conferral will occur in the following quarter.

Doctoral Dissertation Reading Committee

The Doctoral Dissertation Reading Committee consists of the principal dissertation adviser and two other readers. At least one member must be from the major department. At least two members must be on the Academic Council. (Approval for appointment of a reader who is not on the Academic Council may be given by the Graduate Degree Support Section if that person is particularly well qualified to consult on the dissertation topic.).

The reading committee is endorsed by the chair of the major department on the Doctoral Dissertation Reading Committee form. This form is submitted to the Graduate Degree Support Section before approval of Terminal Graduate Registration (TGR) status or before scheduling a University oral examination that is a defense of the dissertation, whichever comes first in the program.

University Oral Examination:

A University oral examination is a requirement of the Ph.D. program. The purpose of the examination is to test the candidate's command of the field of study and to confirm fitness for scholarly pursuits. The University oral examination will be administered according to the following guidelines:

  1. The chair must be an Academic Council member from a department not represented by members of the examining committee.
  2. At least four examiners are required, three of which must be on the Academic Council. A fourth member who is not on the Academic Council may be substituted if he or she contributes an area of expertise not readily available from the faculty and if approved upon petition to the Graduate Degree Support Section.
  3. The student's candidacy must be valid and registration is required in the quarter in which the oral examination is taken. The Doctoral Dissertation Reading Committee form must be on file in the Graduate Degree Support Section before oral examinations that are a dissertation proposal or defense.
  4. The student's department delivers to the chair a University oral examination schedule, University Guidelines for Oral Examination Procedures, and an abstract for oral examinations that are a dissertation proposal or defense.
  5. The oral examination results are validated by the chair and reported to the department and the Graduate Degree Support Section within five days of the examination.
  6. University procedures are followed in communicating with students who do not pass the examination. Copies of this correspondence will continue to be sent to the Graduate Degree Support Section.

Oral examinations should be scheduled at least ten days before the examination date to allow sufficient time to send announcements to the Stanford Report.

Conferral of Degrees:

The Notice of Intention to Complete Advanced Degree Requirements form is submitted to the Graduate Degree Support Section to initiate approval for conferral of all graduate degrees. It should be submitted preferably in the second week, but no later than the last day of classes of the degree quarter, as listed in the University Calendar. Requests for conferral are reviewed by the Graduate Degree Support Section and the department to verify completion of degree requirements. In Summer, Autumn, and Winter Quarters degree certificates are sent to students within two weeks of the conferral date.

The Graduate Degree Support Section should be notified in writing when conferral plans change. Students who withdraw their conferral request or who fail to complete degree requirements must file a new Notice of Intention for a subsequent quarter. A new Notice of Intention must be filed for each degree and conferral quarter.

Spring Commencement:

Commencement ceremonies are held each June for students who have received degrees in the previous Summer, Autumn, Winter and Spring quarters. Students who wish to receive their diplomas at June commencement must submit a Notice of Intention by February 1 to allow adequate time for preparation of the diploma. Information on Commencement activities and distribution of diplomas is sent by the Registrar's Office in early April to addresses provided on the Notice of Intention. Students who wish to participate in commencement activities in advance of conferral of their degree may obtain a Graduate Student Petition to Walk Through Commencement Exercises from the Graduate Program Office from May 1 until the day before commencement. A Walk Through petition should be requested only if there is no possibility of completing degree requirements for June conferral.

Financial Aid Stipends:

Entering students are normally offered research assistantships, fellowships, or traineeships that include payment of a stipend and tuition. Students are strongly encouraged to apply for predoctoral fellowships from the National Science Foundation by November of their first year in residence. Applications are available in October and due in November. Check with the Graduate Support Section of Financial Aid for further details. Students are also encouraged to apply for other outside fellowships. The Awards Data Base available on Folio (a computer on-line system) contains information on over 1,200 awards of academic interest. Departmental funds are used to supplement support from all sources to the university annual required level and to pay for health insurance. Student fees, late fees, etc. are the responsibility of each student. Students may receive stipends quarterly or semi-monthly depending on their funding source.

For those students on fellowships who are paid quarterly, the stipend checks are usually issued the day before classes begin. Checks are sent to the "mailing address" listed in axess.

Students who are paid semi-monthly will be paid on the 7th and the 22nd of the month (or on the preceding work day if these dates fall on a weekend or holiday). Checks are sent to the department. Semi-monthly paychecks may be directly deposited in local banks upon request to the departmental business office staff.

Outside employment is discouraged.

Tuition

Tuition is fully covered by research assistantships or traineeships at 9 units. Tuition paid by the department is paid directly to the University. Students will receive tuition credit on their University bill.

Tax

Health and Safety:

Stanford University's health and safety mission is to provide a safe and healthy environment for faculty, students and staff and to assure compliance with federal, state and local regulations. The University Environmental Health and Safety (EH&S) office manages health and safety programs for the School of Medicine such as:

Each person working in a lab is required to be trained in the specific hazards of his or her job. Laboratory safety is a component of the orientation to a research lab. It is the Principal Investigator's responsibility to provide training for lab equipment, procedures and chemicals. EH&S provides two mandatory training sessions.

EH&S, through the Health Physics Department, provides mandatory training for use of radioisotopes as part of Stanford's licensing agreement with the State of California. New students need to contact Health Physics and complete the following before they can work with any radioactive material:

In conjunction with the Medical School's Health and Safety Program office, EH&S provides mandatory Lab Safety Training. The office also assists in resolving safety problems and provides each department Safety Team with safety information and regulatory compliance strategies. EH&S provides a variety of environmental health and safety services:

The department has developed a Health and Safety Team made up of representatives of the research and administrative staffs and students. The principal investigator on the team is Dale Kaiser. Their initial goals will focus on compliance issues, education and training, disaster preparedness and accident reporting. They also maintain copies of the Radiation Safety Manual, Stanford Biohazardous Materials Guidelines, Stanford Safety Manual and Material Safety Data Sheets (MSDS) and department training records.

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