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SCI Graduate Student Handbook




1.1 Welcome

Welcome to the Scientific Computing and Imaging Institute (SCI), one of the nation's premiere computational science research groups. In case you haven't heard, SCI is pronounced "ski", as in ski-Utah. We, the faculty of SCI Institute, work diligently to provide a challenging, yet fun and productive environment for graduate research in a number of fields. We have high expectations of ourselves, and consequently have high expectations of the students in SCI. This document is an attempt to outline the resources available to students of SCI, the general expectations and policies of students. Basically, in general we want to describe the life of students in SCI, or at least the life that we should all strive to attain.

This document is written largely by former SCI students, and attempts to maintain the traditions that were started back when SCI was just a handful of struggling students. This document is not designed to address any particular problem, but we felt it would be helpful for new students entering the program to know what SCI is all about.

You may get tired of hearing it by the time you are done, but graduate student life is an unparalleled opportunity to focus on learning a lot about your desired field. It is a time to explore the field, a time to network with others, and a time to build your reputation. Students still have deadlines, but there are also opportunities to explore outside the halls of the Warnock Engineering Building (WEB). You should take time to exercise, hike, climb, ski, or whatever your interests motivate you to do, but in careful moderation of course. Graduate student life is not a time to "find yourself" or vacation. It should be a time where you work harder than you ever have before, and possibly you will never again have the opportunity to focus so intensely.

As a graduate student you have the power to make important decisions that will dramatically affect the quality of your academic experience and your career. For many students this is a distinct departure from your undergraduate experience. As an undergraduate, the writing was often "on the wall" from day one - make a couple of often self-evident decisions ("I like computers, so I think I'll major in CS"), and then just keep putting one foot in front of the other and you would succeed. At graduate school, the experience is much more "what you make of it". Choosing which graduate school to attend, and choosing to join the SCI group were the start of those big decisions, but realize that there are many others that remain: who will you choose as your advisor, what research project will you work on, what level of effort will you put into your work (success is no longer measured in grades, it's measured in terms of positive impact), what will you choose for your thesis topic, how much will you publish, etc. No one will you give these answers, and the "right" choice will vary from individual to individual. As a graduate student at the SCI Institute, you have a unique opportunity to shape your experience. Think hard about the path you're taking, and then make deliberate, well- informed choices at every juncture along the way.

Being a grad student is a stage in your career. Though you may start to find the SCI lab a comfortable place, never slip into thinking of grad school as a career in and of itself. You need consistent focus on the specific tasks that will lead you closer to finishing your research, graduating, and starting the rest of your career.


1.2 How SCI works (grants, advisors, etc.,)

SCI is a big research institute that has 18 Faculty, 50 staff members and 100 students and occupies 3 floors of the Warnock Engineering Building. Being a research institute and not a traditional academic department, students are associated with an academic department (School of Computing, Department of Bioengineering, Mathematics, Electrical Engineering among others), and must follow the degree requirements and other expectations of their home department. Traditional academic departments are funded largely by state funds (tuition and taxes), while research groups (especially the SCI Institute) are funded largely by research grants from government agencies. Research grants are given to particular faculty, or groups of faculty, to solve a particular problem. Faculty employ students and staff to help complete the goals of the research. Unfortunately, it is difficult for us to obtain money that is not tied to specific research goals, so we look for students that are interested in helping to solve the research goals of the grants that we have.

The specifics of research and grants will be described in further detail below. However, it is important to know that everything in SCI with the exception of a portion of faculty salaries, are funded through research. The computer facilities, the support staff, student research assistantships, staff salaries, and everything that makes SCI successful depends on producing world-class, high-quality research. One important exception is the food, which is funded by gifts from generous individuals (typically the SCI faculty), and this will be described in further detail below.

The remained of this document is organized around the relationships that should be maintained by each student. Relationships with your advisor, with your funding agency/project, with the rest of SCI, with your academic department, and with the research community at large must all be maintained with care. Of course, most students also need to maintain relationships with family, spouses, boyfriends/girlfriends, and others. However, advice on how to maintain these relationships is well beyond the scope of this document!

The most important thing to remember is to work hard! The SCI faculty work very hard, and successful SCI students also work very hard. We as faculty have a much easier time when the students are productive, and love to give recommendations to potential future employers when the student has contributed substantially to the research program.


Relationship to Advisor

The most important aspect of student life in SCI is understanding how to work with your advisor. Any of the expectations described in this document may be modified by your advisor. Different advisors may emphasize different aspects of the general descriptions in this document, or in some cases may have different expectations completely. It is essential that you select an advisor that you can relate to and work with, and it is essential to understand their expectations of you.


2.1 Choosing an advisor

There is a large number of SCI faculty, and their research interests span a broad range. You should talk with and get to know several of them before you select them as your research advisor. Making that decision is difficult, and should be thought out carefully. Factors to consider are:

  • Do your research interests align with the faculty member?
  • What is the reputation of the faculty member in your field?
  • Does the faculty member have funding for new students and are you interested in that research project, or do you have other funding mechanisms (fellowship, independently wealthy, working elsewhere, etc.)
  • Do relate to the other students working on the same projects?

Ultimately, you must choose an advisor, and the faculty member must agree to take you on as a student. Each faculty has different criteria for taking on new students, but it is important for you to know what some of them are:

  • Does this student have research interests that are aligned with mine?
  • Can this student make important contributions to the field, and to my funded research?
  • Am I confident that I will have funding for the next 1–2 years (for MS students) or 4–6 years (for PhD students)?
  • Do I have time to advise this student?
  • Does this student have a reputation for doing high-quality work in courses?
  • Is this student ambitious, productive, and willing to follow my direction?

Of course, students have a lot of influence on the answers to these questions. You should work diligently in your first year to make yourself noticeable to the faculty that you would like to work for, and then you should stay diligent and make solid contributions to the research.


2.2 Switching advisors

Occasionally, your first choice of an advisor just doesn't work out. Sometimes this is due to funding problems, but more often it is due to personality mismatches between the student and advisor. It may be worth switching to a new advisor, but this decision should be made carefully, especially if your current advisor has invested a lot of time and money into your career. If possible, you should first talk with your current advisor about possibly switching. You should then talk with other faculty, being very open about the situation. Typically, the old advisor and new advisor will discuss the situation and your progress in the program.

In rare instances, your advisor may ask to step down. Usually this is due to severe lack of progress, and can be avoided by working diligently toward your research goals. In this case, you will need to find another advisor or consider withdrawing from the program. Please don't let it get to this point!


Relationship to Grants/Funding

Unfortunately, students have to eat, need a place to sleep, and may have other financial commitments. Students are paid primarily through four different mechanisms: 1) self funded/externally funded, 2) teaching assistants (TA's), 3) research assistants (RA's), and 4) fellowships. Most students are paid as research assistants for particular research projects. This creates a unique opportunity for students to get paid for completing their degree, but also provides responsibilities that differ from a regular job.


3.1 Responsibilities to grants

Many students in SCI are paid as research assistants to work on particular research projects. You should consider this a "part-time" job, not a stipend. Different faculty have different expectations of RA's, but you should definitely understand where your funding comes from, and know the milestones, deliverables, or other expectations that are associated with it, and most importantly, what the PI of the grant expects from you. Grants have different durations, but are typically 3-5 years long. If you help meet the goals of the research, we will be much more able to receive funding in the future.


3.2 Choosing a project to work on

Funding and your research topics are typically very connected. However, there is often considerable flexibility in choosing from a few different projects, making implementation decisions, and in prioritizing research directions. These decisions should all be made in concert with your advisor. If you have demonstrated skill, your advisor should give heavy weight to your opinions on the final choice, but it is still their call.


3.3 Help write new grants

New grants are being written on a regular basis. Senior students should become involved in the grant writing process, especially if you have any intentions of becoming faculty yourself. If you are interested in writing a grant proposal, you should consider taking the writing class in the School of Computing or Bioengineering, and you should talk to your advisor about potential opportunities. Even if you are not interested in writing a proposal, you just might get asked to help out anyway.


3.4 Fellowships

One way to partially sidestep the grant process is to receive a fellowship. A fellowship is like a grant directly to you that funds your specific research. Students with a fellowship have a lot more flexibility in choosing what research to work on, but still need to work with their advisors on the research subject. Students with a fellowship may also be expected to contribute to particular grant projects that pay for computers or other resources that apply to your research.

One important advantage of a fellowship is that they typically pay more than a research or teaching assistantship. They are also prestigious to list on a resume or vita. Fellowships are available from the National Science Foundation, the Department of Energy, and other sources. Students in their first two years should work with their advisor (or any faculty member if they have not chosen an advisor) to determine which fellowships to apply for.

Note that, due to the competitive nature of these awards, you will most likely need help in the application process in addition to support from an advisor. The university has programs dedicated to helping you find and apply for fellowships, and departments often offer classes or mentoring programs to help you with this process.


3.5 Teaching Assistantships

Teaching assistantships (TAs) provide an opportunity for you to interact with other students (typically undergraduate or early graduate students) in an academic setting. TA duties vary, but typically include staffing lab/discussion sessions, grading papers, contributing test questions, holding office hours, and sometimes even delivering lectures. Being a teaching assistant can be a great opportunity to develop teaching skills, and will really increase your understanding of the subject.

It is important to be a TA if you are considering a career in academia, and you should take as much responsibility for the class as possible. Your degree may even require a certain amount of TA experience; make sure to understand your requirements and plan accordingly. You may also be asked by faculty to be a TA for a class where you have particular expertise. TA funding is rarely available for students merely because they cannot find funding for other projects to work on. If you are interested in being a TA, work with your advisor to find a course and work out the timing so that you can get the best experience.


Relationship to SCI Institute


4.1 Contributing to SCI

Demos One of the hallmarks of the SCI Institute is the presentation and communication of our research to others in our field and to the community at large. Two components of these communications are (1) demonstrations ("demos") of our research for visitors, and (2) the development and release of research software. Demos are often presented in the Evans and Sutherland conference room (3rd floor) or the Coon lab (4th floor). SCI faculty members give dozens of demos each year to an array of visitors ranging from grade-school students to prominent CS and Medical researchers to high-ranking government officials.

Students should consider preparing their work to be presented in a demo format for some of these visits. If you are a student who studies/works at SCI, you are strongly encouraged to participate. If you are a PhD student you are even more strongly encouraged. If your research has a visual component (i.e. you create or utilize visualization tools) you should expect to demo your work at some time during your tenure at the SCI institute. Demos are a prominent public face of SCI research, and you should strive to have your work included.

If, however, you find it difficult to fit your work into a demo format, there are several opportunities to share your work with other researchers and the public. The most prominent being SCIx. The SCI Institute hosts a bi-annual, SCIx event where every student at the SCI institute is expected to present a portion of their work. SCIx occurs on even numbered years. Posters and demos (created by you and other students) are placed throughout the 2nd, 3rd, and 4th floors. The event is open to the public, who can tour the facility, read posters, talk to the students, scientists, developers, and faculty associated with the research, and observe several demos. All are expected to participate in the event in some meaningful way. It is up to you and your advisor to determine what your level of participation will be.

Contributing software Writing software is another important component of research at SCI. Research is improved when software is shared and developed in cooperation with others. It is very likely that you will have to write some software to complete your research, but you must resist the temptation to code up absolutely everything for yourself or by yourself, effectively creating your own separate world in which to operate. Your goal as a student is to do research, not software development. Leveraging other people's code whenever possible is ultimately better for you and for the rest of SCI. Much of the software written at SCI is released as open-source, so your coding efforts are likely to have a broader impact when you contribute to an existing project, rather than starting one from scratch.

The common good Demos and software are a great examples of the "chip-in" mentality that has helped make SCI great. Students are strongly encouraged to help build common infrastructure (software, hardware, and so forth) and to share tools and techniques among each other. In addition, any of members of SCI may be called upon to help with other large projects that are for the common good, which could include involvement in social events or committees, presentations to local schools in the valley, or an occasional meal with a visiting professor or dignitary (paid for by the Institute, of course).

Whether is through contributing a demo, contributing to shared software, or through other means, every SCI member should strive to make a positive mark on the SCI Institute's shared infrastructure. Of course, as with most other aspects these activities should be undertaken with the approval of (and usually encouragement of) your advisor. Your advisor should help decide the right balance between short-term research results and longer-term infrastructure improvement.


4.2 Interactions with other SCI students

You may have interacted with groups at other universities with limited collaborative relationships. The SCI Institute is proud of its track record of both internal and external collaborative success. Interacting with other students is strongly encouraged and is a basic part of how research works in the SCI group. Learn something about what your peers are working on! Talk to your neighbors. The typical classroom ethics of "don't collaborate with your neighbor" don't really apply in graduate research outside of the classroom and certainly not within SCI. However, there are a few instances where you should be careful. First, we cannot grant two people degrees for the same ideas so you need to ensure that you have unique research ideas. Second, do not publish the ideas of others without their consent and hopefully their involvement. In an environment such as SCI where ideas are shared freely, it is important to be careful that other participants are not left out of publications inappropriately. If you are unsure of where basic ideas in your work came from, talk it over with the other students and faculty with whom you may have brain-stormed. As always, the Golden Rule applies: err on the side of giving credit to others, because you would prefer others to do the same in return.


Relationship to Academic Departments

Your degree will not be granted by SCI, but by a traditional academic department such as the School of Computing, the Department of Bioengineering, and so forth. It is essential to understand the requirements of your particular degree program, and to understand that SCI cannot override those requirements. However, it is also important to be aware that your advisor may impose additional requirements (courses, writing assignments, or other requirements) that must also be met. In general, SCI students should be "multi- disciplinary", and should take courses that ensure they have a broad background in computing and application domains.


Relationship to Research Community


6.1 Publishing

Publishing strong papers is a very important facet of the SCI public image. It is important for your career to write high quality publications that appear at a variety of quality conferences and journals. Papers should not be submitted for publication without the consent of your advisor or other SCI faculty. In most cases, your advisor or another faculty member should be a co-author on publications. Some PhD students may publish sole-authored papers near the completion of the PhD program, but this should still be done with the agreement of your advisor.

High quality publications take a large amount of time to prepare before they can be submitted. Please be conscientious of the time constraints of the faculty when planning to submit, and please allow plenty of time to ensure that the publication properly reflects the quality of the work being done at SCI. Do not ask for extensions of deadlines or request other special favors without agreement from your advisor or another faculty member. Remember, there is absolutely no shame in pulling the plug on a paper if it isn't going to be finished and polished by the deadline! Keep iterating and improving the work. Chances are, you're not going to get "scooped", and your final paper will be much stronger because of the extra time, consideration, and effort.


6.2 Attending Conferences

If your paper is accepted to a conference, you might be asked to present the paper at the conference. You should plan on giving at least one to two practice talks before the actual conference, so prepare the presentation well in advance. Giving good presentations is an acquired skill, and it is vital for your career. You should not be afraid to ask other students and faculty for their feedback at your practice talks.

Typically, you will only be funded to attend conferences where you are presenting a paper. However, there are exceptions. Sometimes, you may be able to attend a conference to learn about topics related to your research, and sometimes you may attend a conference or other meeting as a representative of SCI and/or your research project. Conferences are an important time to meet others in the field, develop relationships with future employers, and to stay current on the state of the art. Ultimately, it is up to your advisor whether you should attend a conference, and this is based on many factors, such as grant budgets, appropriateness of the conference to the grant and your research area, and so forth. If a conference looks interesting to you, you should certainly try to read the proceedings, even if you cannot attend in person. Some students will want to attend conferences under their own initiative and with their own funds, which can be an enjoyable "road trip" when it is not too far away.

In general, your advisor will assist with supporting your travel and attendance at conferences. This means both financial assistance and assistance in preparing the presentation and advising you on how to get the most from your conference experience.

Community validation of scientific work is of fundamental importance. With this in mind, Master and Doctoral Students can expect to have the opportunity to attend scientific conferences at national or international levels under the following conditions:

Selection of conference:
  1. The conference should be applicable and meaningful within the student's field of study, as judged by the student's SCI advisor.
  2. The responsible SCI advisor will decide on the suitability of any proposed conference based on discussion with the student.
to qualify to attend a conference, a student will normally participate by:
  1. Presenting a peer reviewed paper or presentation with the student as an author,
  2. Preparing and presenting a peer reviewed poster with the student as an author,
  3. Serving on a panel or in a tutorial session,
  4. Serving as a student volunteer, or
  5. Attending conferences for other reasons at the discretion of their advisor.
Additional guidelines:
  1. Once a student has obtained permission from their advisor to attend a conference, they should submit a request through the travel request form at, and then coordinate their travel plans with the SCI Administrative team.
  2. Students are strongly encouraged to apply for any external travel support that is available.
  3. Students should be prepared upon their return to report to the group on meaningful results or information gleaned from the conference.
  4. Whenever possible, a conference presentation should lead to the preparation of a journal article on the same material.


6.3 Collaboration

Another hallmark of SCI is collaborating with researchers across many different departments, other institutions outside the University of Utah, or both. It is important that these relationships are handled carefully, and of course only with the blessing of your advisor. A collaborator could be a future employer, reference writer, or funding agent. Please help us show others the great research that we do.


6.4 Internships

We encourage students to do summer internships at places where they can pursue research related to their field. Your advisor or other SCI faculty may be able to help you locate internships in industry, national laboratories, or other places. Typically, internships are performed in the summers during the first few years of PhD study, as the final years are focused on your PhD topic. An internship is by no means required, but can be valuable experience and provide important contacts for your future career.


Personal Life


7.1 Vacations

Students are officially entitled to 25 days of time off per year, including sick time. This time does not accrue from year to year. Most students take considerably less time away from SCI. Any time off should only be done with approval of your advisor, and the PI of the grant you are funded through if that is not your advisor. See also the vacation policy at the end of this document.

There is also a standard SCI policy regarding the time students can expect to have for vacation and any sick time they require.

  • Supervisor/graduate student advisor must approve time off. Send request for time off to you supervisor and the supervisor will forward their approval to payroll reporter.
  • When possible, submit all vacation requests two weeks prior to date requested.
  • We reserve the right to adjust scheduling if the request falls during deadlines or other critical times.
  • Graduate students, Research Associates and Faculty are allowed 25 days of vacation and sick time per calendar year. (it does not accrue)
  • Please notify supervisor and payroll reporter when you are sick.


7.2 Family emergencies

In most cases, important family emergencies can be accommodated. Please talk with your advisor about the situation, and if at all possible do this before leaving.


7.3 Working from home

Most students should plan to spend considerable time in the lab. We work very hard to provide nice facilities for students, and you should take advantage of those in every way. It is also very important time to network with your fellow students and , share ideas, and live the life of SCI. To a surprising extent, key insights in research problems come from spontaneous interactions and white-board discussions. If you hide away in isolation, you are "out of the loop" in a very real way, and you are missing out on the life blood of the SCI group.

However, students with families or other relationships may want to work from home during the evening hours instead of coming back to the lab. Most of the SCI facilities are accessible over the Internet. However, you will be expected to provide your own computer and network connection for working from home.


7.4 Enjoying Utah

Graduate students often have very flexible schedules, and you are attending graduate school in a very beautiful part of the world. This brings a number of opportunities and challenges. The opportunities are obvious: hiking, skiing, rock climbing, camping, mountain biking, and so forth. The challenges are to not get too distracted by all of these activities. Please enjoy the activities in Utah, but please do it in moderation and only when you are caught up on your responsibilities and are productive in your research.


7.5 Life after SCI


7.5.1 Ongoing collaborations

We hope that you will continue to maintain a strong relationship with your advisor and the SCI Institute after you graduate. If you become faculty somewhere else, you will likely attend the same conferences and work on similar projects to those at SCI. If you go to industry or a national lab, you may have opportunities to fund research here at SCI. We welcome these ongoing collaborations with SCI alumni.


7.5.2 Donor support

Remember all of that pizza that you ate while you were at SCI, and all of the nice parties at the faculty houses? Food of this type cannot be paid from research or state funds, so we rely on donated gift funds for all of these activities. Most of these funds are donated by SCI faculty from their personal income. Donations from SCI alumni are a wonderful way to pay back the institute for the perks that you enjoyed while you were here, and will help provide that environment for the next generation of SCI researchers. Any amount will be appreciated, but if you make it big please remember us back at Utah that helped you get there!




8.1 Computer accounts/help

Upon joining SCI, an account will be created for you to access the many computing resources available to SCI members. These include: emailHPC Systemsversion control (svn and git) among others. The page, has a growing, dynamic set of links, documents, and resources for all aspects of life at SCI. It is accessible from within SCI, or externally with a password.

The SCI computer facility is a shared resource that everyone depends upon for conducting their research. Do not use more than your fair share of resources: disk space, sysadmin time, matlab licenses and so forth. If you need help, send an email to This email address is being protected from spambots. You need JavaScript enabled to view it.. Please do not drop by the offices of the system administrators or call their cell phones unless it is a true emergency with broad impact. If you need help with the software side of these computational resources shooting an email to This email address is being protected from spambots. You need JavaScript enabled to view it. is the best way to go.

You are welcome to use SCI email to maintain family and other personal contact, and to use a very modest amount of resources for personal use. The computer facilities are for research, which takes priority over personal uses of the machines.


8.2 Desktop systems

SCI Support can help you set up the computer that your adviser will provide you. They support Windows, OSX and OpenSUSE 13.1 and higher. You are free to install any other operating systems like Ubuntu (which is not supported by SCI support) as long as you manage your computer and do the necessary system and security updates to keep the SCI network secure. The page also has information about setting up printers which are available on each floor of the building.


8.3 Lab Access

After 6 p.m and during the weekend, you will need to use a key to access the SCI floors, open lab doors and for the elevator which Deb will give you upon joining SCI. Also, after 10 p.m. the Warnock Engineering Building will be locked. You can ask Deb to configure your university ID card to allow you to enter the building at any time.

If you are the last to leave your lab at night. Please close the doors and turn off the light in your lab.


8.4 Supplies

SCI maintains a stock of paper, pens, whiteboard markers, and other items necessary for your research in the cabinets in the SCI front office. Please utilize what you need. If you need supplies that are not stocked, talk to one of the admin staff as appropriate.


8.5 Kitchen

The SCI Institute maintains a kitchen to make it easier to eat while working hard on projects. There is coffee, tea, milk and sodas available for SCI institute members and visitors.

It is important to be considerate when using the kitchen: clean up the microwave, do not leave food to rot in the refrigerator, and generally clean up after yourself. Also given that SCI has about 200 people and only one fridge, please do not bring more than one day's worth of food.


8.6 Help with writing and presenting your research

As a graduate student, you will be writing papers, making posters and video to promote your work. The following people can help you with those:


8.7 Paychecks

Paychecks are distributed on the 7th and 22nd of each month into your SCI (or Departmental) mailbox. You are strongly encouraged to sign up for direct deposit of your paycheck into your account. If you have your paycheck deposited directly, you avoid possible delays in getting the paper check.


8.8 Other Resources

The following resources are also available:

  • Three conference rooms that can be booked by sending an email to This email address is being protected from spambots. You need JavaScript enabled to view it.Ed Cask can assist you if you need help using the projector and other equipment in the conference rooms.
  • A small gym on the 2nd floor and male and female showers on each floor.
  • A nursery for SCI mums on the 4th floor of the building.
  • A small library on the 4th floor. Please return the books you borrow from the shelves when you are not using them.


8.9 Mailing lists

Finally a list of mailing lists is available at Some of the popular ones are:

  • This email address is being protected from spambots. You need JavaScript enabled to view it. : General questions for SCI Administration
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : Travel related requests
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : Place an order
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : Reserve a conference room
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : General questions for SCI IT Staff
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : Technical support/assistance
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : For software related questions.
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : To reserve a conference room, send an email to conference.
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : SCIs OS X mailing list for all you mac users.
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : If you have a question for SCIs student activity committee, send an email to sci-sac.
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : To send a SCI-wide email, address it to sci.
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : Bike mailing list.
  • This email address is being protected from spambots. You need JavaScript enabled to view it. : Beer mailing list.
  • This email address is being protected from spambots. You need JavaScript enabled to view it.: Ski mailing list.
  • This email address is being protected from spambots. You need JavaScript enabled to view it.: Yoga mailing list