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Ph.D. Program - New Students

Getting started

General information

http://www.stanford.edu/dept/DoR/GSH/

This is the Stanford graduate student handbook, a very useful reference for graduate life at Stanford. Included in this manual is academic and financial information, resources for housing, social and spiritual activities, general university policies, and campus maps.

You may also find it useful to have a map of nearby store locations. (coming soon)

SUnet ID

http://www.stanford.edu/group/itss/services/sunetid/.

In order to use any of the electronic services at Stanford, you need to get a SUnet ID - the login name you will use to identify yourself with Stanford computer systems . Like everything else this can be done over the web. You will be asked to provide your Student ID (sometimes called SU ID ) and your PIN .

Your student ID is a unique number assigned to your academic record. It is imprinted at the upper right on the mailing label of the admission packet sent from the Graduate Admissions Office. It will be on your university ID card.

Your PIN is a five-digit number initially set to the month and day of your birth preceded by a leading zero. For instance, if you were born on May 9, your PIN is 00509. Note the two leading zeros since the first character of the PIN is 0 and the numeric representation for May is 05. You'll probably change your PIN right away since this obviously isn't very secure! If you should have any trouble with your PIN, e-mail Registrar@leland.stanford.edu.

Axess

https://axess.stanford.edu

This is the University's web based administrative system. It is useful for interacting with the university in ways such as:

  • Giving an official response to your admissions offer by clicking on the Admissions Response link on the Axess front page. Replying electronically will ensure that you can do the following right away:

  • Apply for housing

  • Register for each term; sign up for classes; view course grades

  • Let the university know your address for official correspondence.

Finances

Student stipends and financial aid are not shown on the initial bill UNTIL THEY ARE OFFICIALLY REGISTERED. Once registered for the quarter, stipends/ grants/ aids are activated and reduce the large amount you apparently owe. If you have questions about financial aid or your student bill after you’ve registered, please call Maureen. For the first 3 years, a graduate student will typically be on a departmental fellowship. In the fourth and fifth years, graduate students may switch to bi-weekly pay and your checks can be directly deposited into your bank account.  

Taxes

Graduate students are required to file estimated quarterly taxes by September 15th, January 15th, April 15th, and June 15th, as taxes are not automatically deducted from the stipend check.   If estimated payments are not made, students will incur a financial penalty. Please file for both Federal (http://www.irs.gov) and California state taxes (http://www.ftb.ca.gov/forms/index.html) using (in most cases) forms 1040ES and 540ES, respectively.  Computer programs such as TurboTax can help you determine how much money you owe per fiscal quarter and will provide you with the necessary forms. Rules are different for international students.

The following resources may be helpful:

Make sure your mailing address is correct in Axess so that you receive your earnings statement, which will arrive by the end of January.

Courses

Units for individual courses may vary depending on how the course is organized each year. You may register, depending upon your financial aid package, between 10-15 units per quarter. Please select the 'Curriculum' menu option for more information.

The “Time Schedule”, a catalog of courses offered each quarter, goes online approximately one month before the start of classes. The Time Schedule can be found on the left-hand menu in Axess. The deadline to register is usually 2 weeks after the official first day of classes. The academic calendar, which lists academic dates and deadlines, can be found at http://registrar.stanford.edu/academic_calendar/index0708.htm.

Students may find information and assignments relevant to the courses in which they are enrolled at Coursework.

Safety Training

General safety training is required of all students. All students planning to work with animals must all take the animal safety training. If you will work with human subjects, you are required to take the HIPAA training. If you will be working with blood, you must take the bloodborne pathogens training under the 'Training' tab on Axess. If you plan to work with radioactivity, you must attend Radiation Training. A list of other training courses can be found on Axess under the 'Training' tab, or at the EHS website.

 

Choosing a thesis lab

Rotations

A minimum of two one-quarter laboratory rotations will be required of all students during the first year. Students must choose a thesis advisor prior to the end of summer quarter of first year, but not before the end of winter quarter of first year .

Rotation advice:

  • Set up your rotations as early as possible

  • Talk to as many principal investigators (PIs) as possible, both about their work and the work of other potential labs.

  • Attend multiple lab meetings in various labs of interest. This allows you to see the culture of the lab without committing to a full rotation.

  • Get the "dirt" on that lab from the other students in the department

  • Don’t be afraid to expose yourself to new and different areas of science that appeal to you.

  • Rotations are a low-risk time to try new fields.

 

Advice on choosing a thesis lab

Your thesis lab is where you'll be spending a lot of time over the next few years, so do your best to find a place that feels comfortable for you. Besides the scientific questions being answered in the lab, there are many intangible items that enhance your learning experience. Gain information by talking to as many current and former lab members, other students, and PIs to get information about a lab.

Typical questions to ask others and yourself when choosing a lab include:

  • What is the PI's mentoring style? PI’s integrity dealing with people and publishing papers?

  • How does the PI choose and distribute projects among lab members, and the role the student plays in decision-making?

  • How much time does the PI spend with lab members?

  • Does the PI help his/her people get good postdoc positions/jobs? Does s/he give career advice?

  • How does the PI handle collaborations?

  • What is the student:postdoc ratio? Few students and many postdocs have a different feel than many students and few post docs.

  • What the lab's publication record? Have there been authorship conflicts? If so, why?

  • How supportive is the PI of lifestyle choices (spouse, children, homosexuality, other important non-lab commitments)?

  • Are the people in the lab happy? Do they get along well and work together?

  • How many hours do people work in the lab?

  • Will the PI be moving the lab during your thesis?

  • What is the financial situation of the lab?

  • What is the average time to completing a Ph.D. degree in the lab?

Thesis Examinations

Qualifying Exam

Besides coursework, students are required to do a two-part qualifying exam based on the student’s thesis proposal. The written exam (Part I) will consist of answering five questions in a two-day period (Usually the second week in July). Part II of the Qualifying Exam (Orals-thesis proposal defense) will be completed before December 17th, fall quarter of the second year. The examining committee will consist of two faculty members from the Immunology Program and will not include the student’s thesis advisor. A third committee member may be chosen from outside the program. The composition of this committee will be chosen by the student and must be submitted to the program administrator in October of your second year.  After successfully passing Part I and II of the Qualifying Exam Process, you may apply for Ph.D. candidacy (please fill out the pdf forms, “Application for Ph.D. candidacy” and the “Doctoral Dissertation Reading Committee” form).

Presentation Requirements

In addition to the qualifying exam, students are required to give a presentation based on research done in one lab rotation in late July-early August to the Predoctoral Committee.   These presentations are not graded, but are a wonderful mechanism of receiving advice and feedback on graduate degree progress.

Thesis Defense

Before finishing the program, students will give a presentation based on their Ph.D. research and submit a written dissertation, which is the result of independent investigation, and which constitutes a contribution to knowledge in the field of immunology. The presentation is the equivalent of the required University oral examination, and is taken only after the student has substantially completed his or her research. The examination is preceded by a public seminar in which the candidate presents the research. The oral examination is conducted by a five-member dissertation reading committee whose composition is discussed in the Stanford Graduate student handbook.   A checklist has been provided by the program to help you plan your thesis defense.