Student Handbook: First Year
First Year Checklist:
You'll need a UW NetID to access computing resources, including email, online registration, and access to personal records. Create your NetID by visiting this page: http://www.washington.edu/computing/uwnetid/. Your NetID is also your UW email address. For example, if your NetID is "stressedout" then your email address will be "stressedout@u.washington.edu".
Incoming students are expected to begin no later than September 16 (which is when your funding begins), although classes won't begin until September 24. This will give you time to look around the labs and meet faculty and students. Most students will arrive earlier in the month to look for housing and acclimate to Seattle.
The UW will want proof of Measles vaccination before allowing you to register. Please check the Immunization Website for more details.
The UW requires all employees (including students receiving stipends / salaries) to complete an online Affirmative Action Data form: http://www.washington.edu/admin/eoo/aadf/. You'll need to use your UW NetID to access this site. This should be done at some point during your first pay period (September 16 - 30).
Please see Brian Giebel (Foege S-340) sometime during the first half of September to check in & go over program requirements.. There's no need to make an appointment, but giving me a call (206-616-7297) or sending an email (bgiebel [at] u.washington.edu) before you stop by will help, since I'm often away from my desk.
Please see Linda Loveless (Foege S-250 , llov
[at] u.washington.edu) to fill out paperwork. Please be sure to bring either a passport or photo ID and your Social Security Card. International students should bring visa paperwork. Linda will also help you with keys, UW Health Sciences photo IDs (not to be confused with your student ID), and lockers.
The following orientation activities will take place during your first two weeks in the dept:
- Individual meetings with Colin Manoil
by individual appointment -Please email Dr. Manoil with your proposed time (manoil [at] u.washington.edu).
Dr. Manoil, the faculty graduate program coordinator, will help you choose your first lab rotation if needed & discuss the program in general (MSTP students, having already chosen thesis labs, need not attend). Meetings usually take about 10 minutes.
- Department Retreat
September 17 - 19, Semiahmoo Resort
The dept retreat provides a nice opportunity for you to meet faculty and students in a relaxed setting. You will be automatically signed up to attend. The department will provide transportation to the retreat; more details to follow.
Please send a few sentences describing both your research interests & personal interests to Brian Giebel (bgiebel
[at] u.washington.edu). You'll be introduced to the department while at the retreat -- now's your chance to let everyone know about your quirks, talents, and the time you hitchhiked across Bolivia.
- "Choosing an Advisor" Panel Discussion - cancelled
It turns out the MCB program won't be offering this event this year.
- Lab Safety Training
Monday, September 22, 8:00 - 12:00, Physics-Astronomy A-102
You have been enrolled in the standard UW lab safety training session. Please sign up for any optional training that seems appropriate for your anticipated research (Managing Hazardous Chemicals, Bloodborne Pathogens, Biosafety, Field Research).
Please use the following info when signing up for optional training:
Position: graduate student
Advisor: Colin Manoil
UW Box #: 355065
Phone #: 616-7297
- Union Meeting
Tuesday, September 23, 10:00, Foege S-110
UW graduate students voted to unionize in 2004. This presentation will give you an introduction to your rights and benefits as a union member.
- Grad Student Survival Tour
Tuesday, September 23, 11:00, meet at Foege S-110 (following union meeting)
Led by current GS grads, the tour reveals the locations of computer labs, the Health Sciences library, the UW bookstore, and other useful places.
- Faculty Research Presentations
There will be weekly presentations by faculty members throughout Autumn Quarter to provide an overview of their research.
Paydates are generally the 10th (for the second half of the preceding month) and 25th (for the first half of the month) of each month, unless these dates fall on a weekend or holiday. Please check the payroll website for more information. Questions may be directed to Kannie Cheung (kkpc [at] u.washington.edu, Foege S-250) or Gloria Pascual (ditto [at] u.washington.edu, Foege S-250).
Check the UW academic calendar for dates of instruction, registration, and holidays.
Stop by Odegaard Library (ground floor) to get your student ID card. You will need to show legal photo identification in order to obtain your ID card.
Please note that you will be given a student ID number, and the UW uses these, rather than Social Security Numbers, for identification.
You will receive registration information from the UW Graduate School the summer before you begin your studies. You should wait until arrival at the department to register. Be sure not to lose the PAC (Private Access Code) number the Graduate School sends to you with the registration info. You'll use this code to register for the first time and to create a UW email account.
Online registration: Course registration is done online by going to the "myUW" section on the University of Washington home page.
Insurance: Unless you are an international student, you shouldn't sign up for the standard UW student insurance while registering for courses. Insurance is taken care of by enrolling online at the Graduate Appointee Insurance Program website (for bureaucratic reasons unknown to me, international students need to enroll in the insurance plan online via the Benefits Office and also sign up for standard UW student insurance each quarter when registering). Your coverage will begin October 1. Please enroll online by that date so that you don't forget about this.
You will need the 5 digit Schedule Line Number (SLN) which identifies a particular course. These are found on the online time schedule.
Some courses will require add codes; you can get these from the graduate program assistant (currently Brian Giebel, Foege S-340, bgiebel
[at] u.washington.edu) either in person or via email. Faculty codes used to register for research courses (Genome 501, 600, 800) are now available online. If you are registering for a non-Genome Sciences course that requires an add code, you should get the code from the graduate program assistant in that particular department.
Electives: Please keep in mind a graduate school requirement that you complete at least 18 graded credits by the time you take your General Exam, which is done during Spring Quarter of your second year. Some of the core coursework is graded, some is not, so you will need to take some graded electives during your first two years. Generally speaking, any 500-level science course related to your research interests is an acceptable elective. 400-level courses may also be taken for graduate credit. You'll need to check with the Graduate Program Coordinator, Dr. Manoil, to be sure a 400 level course is acceptable. Genome Sciences students often take Biochemistry, Bioengineering, Conjoint, Microbiology, Pathology, Molecular - Cellular Biology, Physics, and Statistics courses, among others. You should check the online time schedule to see what's available.
You're expected to have some background in Biochemistry and Statistics. If not, this can be made up by taking electives in these areas during your first year. Please check with Dr. Manoil for suggestions on which courses might be appropriate for you.
You should sign up for a minimum of 10 credits each quarter (except for Summer, when you should sign up for 2 credits). You'll want to vary your credits in Genome Sciences 501 to accomplish this. For example, if your core courses and electives total 6 credits, register for 4 credits in GENOME 501. Registration for more than 10 credits is fine (up to 18 credits max).
The Genome Sciences core course sequence has recently changed (as of 10/06). The following course sequence is effective beginning Winter 2007.
Autumn Quarter:
- GENOME 501: Lab Rotation (vary credits so that total credits equal a minimum of 10)
- GENOME 520: Seminar (1 cr)
- GENOME 522: Journal Club (1 cr)
- GENOME 523: Research Reports (1 cr)
- GENOME 550: Methods & Logic in Genetics (3 cr)
- GENOME 551: Mechanisms of Gene Regulation in Prokaryotes and Eukaryotes (1.5 cr)
- GENOME 552: Genomics (1.5 cr)
- It's a good idea to avoid taking additional electives during your first quarter, (unless you are part of a program such as Computational Molecular Biology which requires that you do so) but you have the option of doing so if you wish. If you choose to do so, you should discuss this with Dr. Manoil or another faculty member.
Winter Quarter:
- GENOME 501: Lab Rotation
- GENOME 520: Seminar (1 cr)
- GENOME 522: Journal Club (1 cr)
- GENOME 523: Research Reports (1 cr)
- GENOME 553: Advanced Genetic Analysis (1.5 cr)
- GENOME 555: Proteomics (1.5 cr)
- GENOME 559: Introduction to Statistical and Computational Genomics (will be changed to 3 cr), to be taken by students with little computational background. Not for students in the CMB program.
- any desired elective, so long as the total number of credits is at least 10
Spring Quarter:
- GENOME 501: Lab Rotation
- GENOME 520: Seminar (1 cr)
- GENOME 522: Journal Club (1 cr)
- GENOME 523: Research Reports (1 cr)
- GENOME 560: Statistics for Genome Sciences (1.5 cr)
- GENOME 561: Population Genetics (1.5 cr)
- any desired elective, so long as the total number of credits is at least 10
Summer Quarter:
- GENOME 600: Independent Study / Research (2 credits)
- you may sign up for additional courses if they are vital to your research; please inform the graduate program assistant if you plan to do so
Tuition: Tuition is covered by the department or individual labs, except for approximately $288 in student fees (including the cost of a U-Pass) each quarter, which are the responsibility of the student.
Funding: In addition to the tuition waiver, GS grad students also receive salaries / stipends of $26,676 per year. While the gross salary is the same for all students, net amounts vary according to the funding source.
Information on how to find outside funding sources is available on the UW website.
Taxes: With the disclaimer that I am not a tax expert and am not offering financial advice, here's essentially how it works:
Federal taxes aren't withheld from stipends funded by NIH training grants, since these aren't considered "salaries" per se, but students will owe taxes on this income in April. Generally, students who are US citizens / permanent residents receive the majority of their funding from these sources during their first two or three years in the program. Funds from non-training grant sources are often used to supplement the amount provided by the training grants, and these are generally taxable. For example, you may receive $20,000 of your salary from a training grant -- federal taxes aren't withheld from this. They will, however, be withheld from the remaining amount. Clear as mud. Stipend amounts are listed on form 1098.
International students and U.S. citizens / permanent residents who have been in the program for longer than 2 years are generally funded via research assistant appointments through their thesis labs. Federal taxes are withheld from these salaries, so while gross pay is the same, the net salary will be less. The benefit of sorts is that you won't have to come up with all this cash at tax time.
The simplified version: Students funded by RA appointments pay taxes now; students funded by training grants pay taxes in April.
Options: Some students funded by stipends have found it useful to have a small amount deducted each pay period in order to avoid having to come up with taxes owed in April. Others have made quarterly payments. Some have simply paid in April. There does not appear to be a right or wrong way to do this.
Payroll Office: Shawna Litterski in the UW Payroll Office may be able to answer additional questions. You may contact her at smlitter (at) u.washington.edu
Moving Expenses: You may want to consider deducting moving expenses when figuring your taxes.
IRS publication 970 spells out the rules (in a confusing way). Their chart indicates you must pay taxes on your stipends, but not for funds spent on textbooks or other supplies.
More tax info is available on the UW website.
Update 1/31/08:
The UW currently waives the non-resident tuition differential for out of state students. While this has been a long standing policy, there is no guarantee that this will always be the case. In order to protect yourself and the dept from some future bit of fiscal madness coming out of Olympia, you should take steps to establish Washington state residency, including obtaining a Washington driver's license or state ID, upon arrival.
You will need to apply for resident status in your second year by filling out the application posted here: http://www.washington.edu/students/reg/residency.html. The verbiage on the website makes it appear impossible that residency will be granted. However, here's clarification from the Residency Office (unfortunately not posted on their website):
"I know the website makes it seem if you take more than 6 credits a quarter, you cannot become a resident. This is due to the presumption you are only here for educational purposes. A student is able to overcome this presumption by obtaining all of their Washington legal ties within the first 30 days, plus having a fulltime job and financial independence. Although TA/RA's are on record as only working 20 hours a week, we are aware that these students typically work more than 20 hours a week. Therefore, we consider a TA/RA who has had an appointment for one year as overcoming the presumption they are here for educational purpose, thus they are allowed to apply (and usually obtain) in-state resident status."
Most of you will end up needing to work with radioactive materials in the course of your thesis work. To become qualified to do so, you will have to undertake formal radiation safety training, and it is best to do that in your first year. Otherwise, you might well end up not being allowed to perform key experiments in your thesis research. Training is offered by Environmental Health; you should check their website for a schedule of courses offered.
On the other hand, if your thesis is very unlikely to include any experimental work (such as if it is to be entirely computational), then you might not need this training and do not have to take it now.
You may be required to attend other lab safety courses; these will be scheduled for you by the Graduate Program Assistant.
Asbestos Training :
The UW now requires all staff and students to complete asbestos training each year. This can be done online in a few minutes at: http://www.ehs.washington.edu/pubcookie/train/asbestosg/index.shtm
All students should apply for outside funding. This should ideally be done early in your first or second year. Your own fellowship will look great on a resume and will also make your thesis advisor very happy...
Funding sources include:
NIH grants home page - the basic gateway into NIH grants of all types - has information links to forms, instructions, processes etc. See the left side of the page for 'types of grants', F series
http://grants1.nih.gov/grants/oer.htm
Predoctoral NIH fellowship (F31) detail instructions - review for the full scoop on how to complete these forms, what gets included in the applications, where
they get sent and most important, the deadlines: Dec 8, Apr 8, August 8 - Please remember to contact the Genome Sciences grants team 6 weeks before the deadline
http://grants1.nih.gov/grants/guide/pa-files/PA-07-106.html
To target your NIH search for funding even more specifically, check out the specific NIH institute that might support your work. Review the NIH roadmap (http://nihroadmap.nih.gov/) and then check out the NIH home page for institute list: http://www.nih.gov/icd/index.html
National Science Foundation funding opportunities can be found at: http://www.nsf.gov/funding/
Community of Science - a search engine for all types of funding opportunities. The site has a search wizard that lets you refine your search to closely match the type of program and research you want to do:
http://www.cos.com/
Many non-profit organizations are using a web portal for application submission called Proposal Central. This website shows a list of upcoming application deadlines, the sponsors, and provides links to the sponsors so you can find out more. https://proposalcentral.altum.com/
And finally, there is the primary federal application portal, grants.gov.
http://www.grants.gov/
You are required to attend these weekly departmental functions: Research Reports, Genome Sciences Seminars, and Journal Club. A listing of topics and speakers can be found on the Genome Sciences homepage.
First year students generally rotate through three labs, with the option of a 4th rotation over Summer Quarter if need be. If you decide to do a 4th rotation, please check in immediately with Dr. Colin Manoil (manoil [at] u.washington.edu).
Please follow this link for a complete listing of Genome Sciences Training Faculty.
When you begin a lab rotation, you should immediately meet with the faculty member to find out what her/his expectations are for your rotation. Be careful not to focus solely on other courses and neglect your lab rotation. This is an important part of your training and you will be expected to spend a significant amount of time in the lab and interact with other lab members as well as the PI. You should meet again with the PI after a few weeks, to be sure you are meeting expectations.
The open rotation / transfer policy gives you the flexibility to do your third rotation with a faculty member from any participating department (Biochemistry, Immunology, Microbiology, Pathology). This program also gives you the option of transferring to one of these programs if you find it to be a better match for your interests. For more information, check the School of Medicine website.
The Department has recently decided to have first year students give a brief (10 minute) presentation discussing their lab rotation research each quarter. These will be scheduled as part of the Research Reports series during the last two weeks of the quarter. Please check the Research Reports schedule for your presentation date.
Your first Journal Club talk should be given Spring Quarter. Journal Club provides a forum for information exchange and for practice in organizing and presenting research material. Journal Club presentations should provide a critique of published experimental or theoretical work. Generally it is only possible to adequately present the material in one or two papers. While it will be necessary to give an introduction which draws upon earlier work, the presentation should not be simply an overview of an area of research.
The paper to be presented should be chosen, and the presentation developed, in consultation with the thesis advisor or another faculty member who knows the topic better. First year students will be contacted by a faculty member who will help them prepare for this presentation.
Even the most experienced person requires a considerable amount of time for preparation; the paper should be chosen at least two weeks in advance.
Toward the end of spring quarter, you will choose a Thesis Advisor. Normally, the advisor will be one of the full-time Genome Sciences faculty (Akey, Berg, Braun, Brewer, Dunham, Eichler, Felsenstein, Fields, Furlong, Gallant, Green, Hall, King, MacCoss, Manoil, Monnat, Nickerson, Noble, Olson, Pallanck, Queitsch, Shendure, J. Stamatoyannopoulos, Storey, Swanson, Thomas, Trask, or Waterston). However, if the desired training opportunity is not available within the department, a request for supervision of thesis research by an adjunct or affiliate faculty member is allowed. It should be recognized that, unlike regular Genome Sciences faculty, adjunct faculty members are not under any obligation to sponsor Ph.D. theses, since they have primary responsibilities in other departments.
Once you've selected a chosen a thesis lab, you and your advisor should sign the Summary of Mentor Responsibilities form and submit this to the department grad program assistant. This new requirement is intended to ensure faculty members are aware of their responsibilities to the student.
You are encouraged to read the UW Graduate School's guide, "How to Obtain the Mentoring You Need: A Graduate School Guide".
Things to consider when choosing a Thesis Advisor -- articles posted on ScienceCareers.org:
Choosing a Thesis Lab
Finding the Perfect Advisor
At the end of the year, you will receive feedback from a faculty committee regarding your performance in courses and lab rotations.
Your Supervisory Committee is comprised of a minimum of 4 faculty members chosen by you (including your Thesis Advisor). Your committee should ideally be in place by the end of Summer Quarter after your first year in the program , although there is some flexibility with this. The Graduate School provides information on Doctoral Supervisory Committee roles and responsibilities.
One of your committee members is the Graduate School Representitive, whose primary role is to act as your advocate in making sure exams are conducted fairly. The procedure for selecting the GSR has changed, as of January 2005.
Criteria for selecting the GSR include:
- s/he must hold an Endorsement to Chair a doctoral supervisory committee
s/he must present no conflict of interest (budgetary relationship, adjunct appointment, or the like) with the departments of either the student or the supervisory committee chair (dissertation advisor)
- Affiliate faculty may not serve as GSRs.
The GSR's role is to:
- represent the broad concerns of the University with respect to high standards of scholarly performance;
provide, for The Graduate School, a non-specialist’s view of the quality of the student’s work, ensuring that the student’s mastery of the subject matter is broad and comprehensive;
assure that all procedures are carried out fairly and according to the guidelines of The Graduate School;
present no conflict of interest (budgetary relationship, adjunct appointment, or the like) with the departments of either the student or the supervisory committee chair (dissertation advisor);
participate in conducting both the General and Final examinations;
- provide a report to The Graduate School immediately following the examinations (this form is sent to the GSR one week prior to the examination along with an explanation of examination responsibilities)
Please consider the following requirements when considering potential committee members:
- At least one member of your Supervisory Committee must be a core Genome Sciences faculty member (Akey, Berg, Brewer, B. Byers, Dunham, Eichler, Felsenstein, Fields, Furlong, Gallant, Green, Hall, King, MacCoss, Manoil, Monnat, Nickerson, Noble, Olson, Pallanck, Queitsch, Shendure, Sibley, J. Stamatoyannopoulos, Swanson, Thomas, Trask, Waterston).
The doctoral supervisory committee consists of a minimum of four members, at least three of whom (including the Chair & GSR) must be members of the Graduate Faculty with an endorsement to chair doctoral committees. You may check Graduate Faculty status & chair endorsements on the Graduate School's faculty locator.
A majority of the voting members must be members of the Graduate Faculty.
If your Thesis Advisor is an affiliate faculty member, you will have to either:
1) have a co-chair who is a core or adjunct faculty member, or
2) Have at least two core faculty members on your committee
- Although not required, it is a good idea to add an additional committee member (bringing the total to 5) both for the added expertise, and to avoid scheduling problems, since the Graduate School requires that at least 4 members of your committee be present at your General and Final Exams.
Please give the names of your committee members to the graduate program assistant (currently Brian Giebel in Foege S-340), who will file the paperwork with the Graduate School. It is important to note that the Graduate School strongly encourages the committee to be in place at least 4 months prior to the General Exam.
MD / Ph.D. students should consider applying for Poncin Fellowship funding, to begin your second year in the program. Please contact the MSTP office staff for more information.
Please be sure to read through this entire section before making any travel arrangements.
1. Determine who pays:
If you are:
a) currently supported by a training grant or other UW fellowship, or
b) an international student currently receiving departmental funding
then funding is available to you to travel to a conference where you are presenting a poster or giving a talk. Please check in with Brian Giebel ( bgiebel [ a t ] u.washington.edu, Foege S-340) to determine the amount available to you.
Students supported by training grants accrue travel funding as follows:
Genome Training Grant: $800 per year
Genetics Training Grant: $300 per year
Departmental or other UW support: $300 per year
Please note that training grant travel funds can only be used while you are supported by the grant. They cannot be accessed thereafter.
If your funding is coming from your mentor's research grant, your travel funds will need to come from that source. In this case, you do not need to check in with Brian - the person in your lab responsible for purchasing can make your travel arrangements.
The UW Graduate School also offers very limited funding: $300 for domestic travel, $500 for international. Please see Brian to apply.
2. Book your travel:
The department must pay for flights and conference registration up front. Please do not pay for these items on your own and then ask to be reimbursed.
Once you have checked in with Brian Giebel (if your travel is being paid by a training grant) and are ready to book your travel, please follow the steps below.
Please be aware that if you take personal time before or after the conference and this results in a higher airfare, you may be asked to reimburse the difference to the university.
Contact the current agency of choice, Tangerine Travel (http://www.vacation.tangerinetravel.com/group+and+corporate+travel/). Please be sure to let them know this will be paid by UW Genome Sciences. Once you’ve been emailed an itinerary, please send this to Brian - or have the travel agent include him on the initial email - so that he may fill out the purchase order paperwork.
To pay for your conference registration, provide the registration info needed (either to fill out a form or enroll online) to Brian.
3. Reimbursement:
Please note that we will need a copy of your flight itinerary and conference schedule in order to process any reimbursements.
Lodging and meals will be reimbursed after your return from the conference.
Meals will only be reimbursed if they are not provided by the conference, and will be reimbursed at standard per diem rates (http://www.washington.edu/admin/travel/contracts.html#meal.lodging.rates). Since per diem rates are used, you do not need to save meal receipts. If you choose to skip a conference dinner, etc, you cannot be reimbursed for that particular meal.
If your lodging costs are higher than the allowable per diem rate, please include a brief explanation (e.g. it was the designated conference hotel, only place you could find space, etc) along with your receipts.
You will need to provide receipts for ground transportation.
Insufficient Academic Progress:
You should meet a minimum of once per year (twice per year recommended) with your supervisory committee. If the committee is concerned about your research progress, they will suggest ways to get back on track.
If problems persist, your mentor may opt to put you on academic probation. This involves notifying the
Graduate
School
with documentation of the circumstances. It does not normally affect your funding or registration.
If problems continue past this point, you may be put on final probation. Students are normally on final probation for one quarter only. After that point, the department will either recommend that you be removed from academic probation or that you leave the program.
First year students who do not reach faculty expectations in coursework or lab rotations may also be put on academic probation.
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