Current Graduate Students

Please visit the below separate pages for these topics:

• Academic Advising: contact information for the Bioengineering graduate academic advisors
• Career Advising: career advising resources and professional and career development opportunities 
• Degree Programs: information about each degree program offered by the Department of Bioengineering, including curricular and courses requirements for each program
• Financial Support: information about PhD financial support, departmental and university financial support policies, and masters students obtaining funding for their graduate education
• Teaching Resources: information about Teaching Assistant (TA) positions in the department, including how to apply, responsibilities, and the PhD teaching requirements
• Bioengineering Graduate Society (BEGS): engage with other students in the department through social and professional events organized by BEGS

Graduate Student Handbook

Below please find helpful information to assist students during their graduate studies in Bioengineering.

RESOURCES

Campus Offices 

 

• Academic Integrity Office: “promotes and supports a culture of academic integrity in order to reinforce quality teaching and learning” at UC San Diego. The website includes information about:
  • How to “Excel with Integrity”
  • ChatGPT in Education
  • The Academic Integrity Review process
• Campus Card Office: provides ID card services. Every registered graduate student is eligible for an official UC San Diego ID card. You can find more information on their website about:
  • How to obtain a physical ID card
  • How to replace a lost, damaged, or stolen ID card
  • List of discounts available when you show your ID card to participating stores, museums, and performing arts centers
• Career Service Center: offers a range of programs and services to support student career and professional development. Please see our Career Advising page for more information. 
• Division of Graduate Education & Postodoctoral Affairs (GEPA): provides support and services related to graduate education on campus.
• GradLife supports graduate student life on campus through a number of resources, programs, and events hosted throughtout the academic year. 
• Financial Aid Office can assist students with questions related to FAFSA, loans, and scholarships.
• International Students & Program Office (ISPO) provides expert level knowledge in immigration services and advising for international students. Questions about visas should be directed to ISPO. Please visit their website for information on advising services and the latest updates about:
  • Visa advising service
  • The latest updates on visa regulations 
  • CPT and OPT requests
  • Reduced course load requests
• Office for the Prevention of Harassment & Discrimination (OPHD): “educates the UCSD community about issues of bias, harassment, and discrimination, and assists with the prevention and resolution of these issues.” Visit their website to learn more about:
  • UC San Diego’s Nondiscrimination Policy
  • How to make a report
  • Mandatory Graduate Student Training
• Office of the Ombuds: “provides a confidential, safe space for UCSD community members to talk about concerns and problem-solve issues arising from interpersonal and group conflict.” Visit their website to learn more about:
  • Mediation Services 
  • Confidentiality and Neutrality Statements 
  • Navigating difficult conversations

 

Housing & Transportation

 

Below please find additional information about graduate housing options and general transportation around UC San Diego and the San Diego metropolitan area.

Housing 

• On-campus housing is available for graduate students through Housing Dining Hospitality (HDH) Graduate and Family Housing. Please see their website for information about:
  • Housing availability and waitlists
  • Rate and leasing terms
  • Community events
• Off-campus options can be found through Off Campus Housing Services.  

Transportation Services
All campus transportation and related services are handled by the Transportation Services Office, including:

• Campus Shuttles that service different areas on and off campus 
• Mobility Services to help campus community members with a disability travel between ADA compliant locations 
• Parking Permits for the campus community
• The U-PASS (a student bus pass) that provides rides on local public transportation 

 

Library Services

 

• Library Services: are available online and in-person at the main Geisel Library Building and the Biomedical Library Building. More information about their service can be found on their website, including: 
  • Borrowing books and requesting interlibrary loans
  • Technology lending
  • Reserving computing lab and study spaces in the library 
• Subject Librarians: can assist with questions related to specific subject areas and can assist with pulling past PhD dissertations and MS theses for students to read.

 

Mental & Physical Health and Wellbeing

 

Below please find a list of campus offices and services related to student mental and physical health and wellbeing. 

• Counseling and Psychological Services (CAPS) offers students free and confidential counseling and psychological services, as well as groups, workshops, and open forums. Please visit their website for more information about:
  • How to schedule an appointment
  • Workshop and open forum times and locations
  • iFlourish self care resources
• Center for Mindfulness: provides mindfulness and compassion practice and support, including programmatic offers, free live practice sessions, and resources. 
• Student Health and Well-Being: provides support services in Student Health, CAPS, and Health Promotion. 
• UC San Diego Recreation: “engages the campus community to pursue lifelong wellbeing, growth, and success.” They offer a number of different opportunities, including:
  • Instructional in-person and online courses
  • Intramural sports and sports clubs
  • Climbing and outdoor adventuring
  • Wellness services like nutritionists and personal trainers.
• The Zone: promotes a healthy Triton community through programming centered around healthy living and well-being resources for students

 

Student Support Services and Resource Centers

 

Below please find a list of support services for students as well as information about the various resource centers on campus.

• The Hub’s Basic Needs Center provides resources for food and housing insecurity and financial wellness. They offer a number of different services and referrals to help students have “access to nutritious food, stable housing, and financial wellness resources.” This includes:
  • Food security resources on campus and through the city, county and state
  • Housing resources, including information on emergency housing
  • Financial wellness, including information about emergency loans and grants.
• CARE at SARC: “UC San Diego’s confidential* advocacy and education office for sexual violence and gender-based violence.” Please visit their website for more information about:
  • Scheduling an appointment
  • Making a report
  • Support groups and workshops. 
• The Office for Students with Disabilities serves students with documented disabilities and can assist with providing accommodations to students in classrooms and labs. Their website also has information about:
  • How to submit a request for accommodations
  • Types of accommodations available
  • Workshops and lectures  
• Student Legal Services provides a number of different services, including:
  • Counseling for individuals and groups
  • Attorney referrals
  • Educational workshops and lectures 
• The Writing Hub, a unit within the Teaching + Learning Commons, offers writing support to graduate students, including:
  • Writing consultations
  • Writing retreats and workshops
  • Dissertation writing resources   
• There a number of different resource centers on campus that serve UC San Diego’s diverse student population: 
  • APIMEDA Programs and Services
  • Black Resource Center
  • Cross Cultural Center
  • First Gen Initiative
  • Intertribal Resource Center
  • LBGT Resource Center
  • Raza Resource Centro
  • Undocumented Student Services
  • Women's Center

 

Student Organizations and Life

 

Below please find information about student organizations and additional student life-related opportunities. 

• Student organizations: With over 600 student orgs on campus, there are plenty of opportunities to get involved. For a comprehensive list of student orgs, please visit the website for the Center for Student Involvement (CSI). A few student orgs of note:
  • Bioengineering Graduate Society (BEGS)
  • Gender Minorities in Bioengineering (GMBE)
  • Graduate & Professional Student Association (GPSA)
• ArtPower: provides performing and media arts at UCSD, including music, dance, and special events. Their website includes information about:
  • Upcoming events and performances
  • Purchasing individual tickets or season passes
  • Special event pricing for studetns
• Craft Center: “a space dedicated to the exploration and celebration of creative processes.” The Center offers:
  • Crafting classes and workshops
  • Open studio access
  • Custom creative experiences
• The Center for Ethics and Spirituality is a “self-supporting campus resource assisting members of the UC San Diego community in their personal pursuits of spiritual well-being.”

 

GENERAL TOPICS

2024-25 Tentative Graduate Course Offerings

 

Below please find a list of our tentative Bioengineering course offerings for the current academic year, which should be used for planning purposes only. Courses are subject to change prior to posting to the Schedule of Classes each quarter, so please keep this in mind. The course number and title are listed with the instructor’s name listed in parentheses.

Fall 2024	Winter 2025	Spring 2025
216: Neurointegrated Biolelectronics (Cauwenberghs) 219: Data Science in Multiscale Biology (Valdez-Jasso & Schoenberg) 221: Mathematical Methods for Bioengineering (Valdez-Jasso) 230A: Biochemistry (Huang) 241A: Tissue Engineering & Regenerative Medicine: Foundations (Christman) 242: Polymer Science & Engineering (Cai) 247A: Advanced BioPhotonics (Shi) 254: Synthetic Biology (Hasty) 280A: Principles of Biomedical Imaging (Liu & McVeigh) 281: Seminar in Bioengineering (McCulloch) 282: Seminar in Faculty Research (Engler) 292: Scientific Ethics (Ross) 294A: Patient-Centered Clinical Medicine (King)	202: Bioinformatics II: Introduction to Bioinformatics Algorithms (Pevzner) 207 (261B): Medical Device Engineering Design (Friend) 207: Systems Medicine (Subramaniam) 212: Systems Biology and Bioengineering II: Large-Scale Data Analysis (Palsson) 223: Thermodynamics, Statistical Mechanics, Interfacial Phenomena in Living Systems (Kravets) 225: Business of Biotech (Bartko) 226: Foundations of Bioengineering I: Tissue and Cell Properties (Schmid-Schoenbein) 230B: Cell and Molecular Biology (Engler) 238: Molecular Biology of the Cardiovascular System (Chen & Evans) 241A: Tissue Engineering & Regenerative Medicine: Foundations (TBA) 241B: Tissue Engineering & Regenerative Medicine: Cell Microenvironment (Khojah) 247B: BioElectronics (Joseph Wang) 277: Tissue Engineering Laboratory (Khojah) 278: Magnetic Resonance Imaging (Contijoch) 280B: Comparative Biomedical Imaging (TBA) 281: Seminar in Bioengineering (Aguado) 291: Professional Issues in Bioengineering (Lal) 292: Scientific Ethics (Ross) 294B: Engineering in the Patient Healthcare System (Schmid-Schoenbein)	203: Genomics, Proteomics, and Network Biology (Bafna & Zhong) 207 (261C): Medical Device Engineering Design (Taylor) 207 (262): Biomaterials (TBA) 207: Communication Skills for Bioengineers (Kwon) 209: Continuum Mechanics Applied to Medicine and Biology (Acevedo) 213: Systems Biology and Bioengineering III: Building and Simulating Large-Scale in Silico Models (Palsson) 224: Regulatory Affairs (Prado) 227: Transport Phenomena in Living Systems (Fraley) 232: Musculoskeletal Health, Injury, and Disease (Sah) 233: Neuromuscular Physiology and Biomechanics (Shah) 234: Intro to Neurophysiology: Molecules to Systems (Silva) 235: Molecular Imaging and Quantitation in Living Cells (Bintu) 276: Numerical Analysis in Multiscale Biology (McCulloch & Amaro) 280C: Imaging Cardiovascular Disease (McVeigh) 281: Seminar in Bioengineering (Smarr) 283: Supramolecular Structure Determination Laboratory (Ghassimian) 285: Statistical Learning in Bioinformatics (Alexandrov) 292: Scientific Ethics (Ross) 294C: Clinical Experience in Bioengineering (Engler)

 

 

Advice for Students

 

The Department encourages students to seek advice on their graduate studies, graduate student life, and research from a variety of sources, including faculty, staff, and fellow students. Below you will find some helpful advice from current students and alumni who are or were once in your shoes! We thank BEGS for their assistance in gathering this advice! Note: some entries have been edited for clarity and length. Opinions expressed in quotes are those of the author of the advice and should be viewed as advice only (not policy).

On Coursework and Classes:

• “Form study groups”
• “You are not competing with your classmates, so make an effort to get to know your classmates and help each other out regardless of program (MS, PhD, etc). Everyone here is brilliant and approaches problems differently. You can all succeed together!”
• “Be careful taking a class outside of the department when you have little to none of the required prerequisite knowledge! I took an EE class that was incredibly challenging and it probably would have been wiser to audit the course, rather than take it for credit.”

On Graduate Student Life:

• “Take care of ourselves; a good physical and mental status is the foundation for any amazing research.”
• “Follow graduate school and PhD pages and accounts on social media. The difficulties of graduate school portrayed by cartoons or memes are oddly specific and widespread across the world.”
• “It is completely acceptable to take a mental health day and/or a leave of absence. Your degree is important, but your mental health and well being are essential to your success.”
• “Talk to a few focused people at every level of the department (undergrads, grads, administration, and professors that resonate with your project or personality.) As a graduate student, your success is deeply integrated into the success of your lab and the department and vice versa. Actively communicating to different types of people is key for the success of all stakeholders.”
• “Become involved with the bioengineering graduate student society. Having a community will greatly improve your experience by providing social events to network, people with shared experiences to vent with, and a great place to seek advice or mentorship from.” 
• "Stay Positive, and be firm in your beliefs regarding your research and goals. Do things that interest you to avoid burn-out." 

On Research:

• “Try to find a specific problem in the world that you're really passionate about working on.”
• “When figuring out how to solve a problem, or how to take care of yourself, forge the path that works for you. You are ultimately the primary author of your work and life, so if you're not ok, your work will not be ok. Communicate difficulties, but with a plan integrating reality with an understanding of how you tick.”
• For PhD Students: “Your PhD is a group project. At the end of your PhD, you realize you were paired up with yourself from 4-5+ years ago, and you are picking up the pieces, learning from and fixing the mistakes from when you started your PhD. Your 'partner' made a lot of mistakes. Look back and appreciate your growth.”
• “Choose a lab based on the lab environment over your potential research project. Your project may change many times due to new discoveries, but the lab environment may never change.”
• “When looking for a lab, always find someone that is willing to tell you the less-than-great things about the lab. If it's all good things, that can be a red flag since there's no perfect lab environment.”

On Faculty Advisors and Committees:

• “Find a research mentor - it can be in your lab or another lab, preferably someone in the lab 80%+ of their time. Faculty advisors may not be in the lab as frequently as your research mentor, and there is going to be a disconnect. You will have an inherently different research experience/journey from your faculty advisor, so manage expectations.”
• “This takes time and experience, but learn to say 'no' [in a professional way]  to your advisor. Some experiments or analyses can be a waste of time, and sometimes you have too much on your plate. Saying 'no' is a sign of growth, understanding the science, and understanding what you can handle.”
• “Involve your committee members early and often, they really help with project management, understanding expectations, and having a professor that is not your PI to give you academic and mental health advice.”
• “Talk with your advisor about classes (both taking and serving as a teaching assistant) that will be most relevant to your research and interests.”
• “Please communicate regularly with your dissertation committee. Your committee can help if you have disagreements with your advisor.”
• “Do your best to find fellow graduate students and faculty members who will advocate for you and support you, even if they're not connected to your lab. Outside perspectives can be refreshing and, honestly, they can help you find new opportunities or pivot in new directions if you want to do something different after graduating. While it may seem scary, sometimes just asking a faculty member or admin for something really is the best approach. The worst they can do is say no (or never respond, of course).”

 

Computing

 

Every Engineering student enrolled at UC San Diego is assigned an SSO and AD passwords. These will allow you access to academic, course, financial and computing resources. This includes access to any computer in the campus computer labs, classroom labs or open computers in the libraries. In addition, the campus has obtained certain licenses for specific engineering oriented software. Information about software licenses can be found on Blink. Please note that not all popular titles are available. 

The Bioengineering Department also has a joint use instructional classroom/open lab (PFBH room 161) consisting of 28 computers that run both Windows and Linux. This facility is primarily used for instruction of Bioengineering computer intensive courses and to provide access to specialized software required for certain Bioengineering courses. It is only available for use during normal open hours for Powell-Focht Bioengineering Hall.

 

Degree Aim Changes in BENG

 

As outlined on our Degree Programs page, the below diagram illustrates which degree aim changes are allowed within the graduate programs in the Shu Chien-Gene Lay Department of Bioengineering. The arrows show the direction of the allowed degree aim change. For example, an arrow points from “PhD” to “MS Plan II- Comp Exam” but does not point in the other direction, indicating that PhDs may switch to the MS Plan II, but the MS Plan II cannot switch to the PhD. 

Please note that by accepting admission to one of these programs, the student acknowledges that they may not request an exception to switch their degree aim outside of the degree aims changes that are allowed per the diagram below.

 

For questions about the specific petition process for each degree aim change, please speak with the Bioengineering Student Affairs Office.

 

Department Conflict Resolution Policy

 

General Information 

This is the official Department of Bioengineering Conflict Resolution Policy and is meant as a resource guide for Bioengineering students and faculty when navigating potential conflicts. Conflict may look different in each lab and/or in each specific situation, so please keep this in mind when reviewing this policy and applying it to your specific situation. 

Students should feel that they can go to the Bioengineering Student Affairs Office to discuss any concern. The Student Affairs staff receive specific training on dealing with student concerns and must follow the Family Educational Rights and Privacy Act (FERPA), which includes keeping conversations confidential to the extent possible without promising confidentiality when discussions intersect with other laws. It is important to note that the Department cannot guarantee confidentiality in certain circumstances, such conflict related to harassment or discrimination, as staff and faculty are considered mandated reporters by law, including CANRA, Title IX, and the Clery Act. Therefore, we provide confidentiality when able and work with students when we are not in order to get the information reported to the appropriate offices. 

If you or your faculty advisor have any questions about this policy, please contact the Bioengineering Graduate Studies Committee (GSC) Chair and the Bioengineering Student Affairs Office, either the Coordinator of Graduate Affairs or the MS/MEng Coordinator.

Common Sources of Conflict and Tips to Avoid Conflict

Research Performance or Progress 

• In general, your PI has goals for both your development as well as projects that need to be finished within specific timeframes or deadlines that may be perceived as not possible by the student. 
• We recommend you be open and honest with your understanding of those goals and communicate with your PI what you need in order to accomplish these goals. 
• Experiments can fail often and for a variety of reasons. A common source of conflict in these scenarios is differing approaches between you and the PI on how these experimental problems are resolved. 
  • Use your research rotation or trial period to learn about your PI’s preferences for how students think through and present problems. Speak with others in the lab for different communication techniques that have worked for them.
• For instances in which a faculty member assigns an “unsatisfactory” grade for research credit (BENG 299) and the reasoning for this grade is not clear to the student, we recommend speaking with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/or Department Chair to mediate concerns about research progress
  • To help avoid this issue, we recommend having a consistent record of your research progress, and presenting this regularly to your PI either via email or in one-on-one meetings. After meetings, send an email with a summary of the discussion

Thesis Project Time Management

• More often than not, you will not be spending all of your time working solely on your thesis project. You may be working on a few projects and/or assisting with grant writing. 
  • We recommend you work with your PI to understand the work requirements for graduate students in the lab and find a balance that works for you. Your research rotation or trial period in a lab would be a good opportunity to gain this understanding.

Vacation and Personal Time

• Make sure to ask your PI about their vacation policy during your research rotation or trial period as this can vary by PI. Biological experiments may require that you are present during holidays, weekends, etc. Do not assume you will always have federal, state, or other holidays off if specific projects require you to come into the lab to attend to them. 
• In regard to work versus personal time, some PIs may expect a typical “9-5” work day, while others may not. Additionally, some PIs may expect you to respond to emails in the evenings, while others may not. 
  • We recommend clarifying during your research rotation or trial period work schedule expectations. 
  • In general, it is a good idea to provide at least several weeks notice when taking time off. Unexpected absences, especially at critical time(s) in your training, may become a source of friction with your PI. 
• In general, if you are assisting in grant or manuscript writing, then it is critical to figure out how to best work on your PIs timeline as they may operate on different schedules and may need you to conform to their schedule to get the submission done.

Communication Strategies

When communicating concerns about conflict, keep in mind some of these communication strategies during the discussion. These strategies work for meetings and written communication. 

• Consider the priorities and scheduling/time constraints of the other person 
• Make sure to define the purpose of the meeting or email, and think about “Where is the relationship now and where do you want it to be at the end of the conversation?”
• Use "I Statements" to help guide your conversation. 
• Be cautious using objective statements that may invalidate another’s point of view and discourage the other person from sharing their view.
• Use Active Listening Skills to focus on what the other person is saying, avoid interruptions, and pause before responding.
• Stop the conversation if it has escalated to the point where neither party is listening and recommend resuming the conversation at another time. An example of this would be: “I need to think about what you said. Can we resume this conversation another time?”

Conflict Among Lab Members

If conflict arises between you and another lab member:

• Take a step back and consider the personality differences between you and whomever you have the conflict with
• Think about a communication medium that you are most comfortable with for discussing this conflict. The goal would be to find a method where both parties can listen, think, and respond clearly and respectfully. 
  • For example, you may be an introverted person while the other lab member is an extroverted person. A direct face-to-face discussion may not be desirable if you need more time or space to discuss the conflict. An email or another medium that allows slower but uninterrupted and thoughtful exchange may be better. 
  • Follow the general communication strategies above.

If communication breaks down, let your PI know about the conflict. When discussing the conflict with your PI, clearly define what relationship you want to have with the other person and ask if your PI can help you. Avoid an accusatory tone and follow the general communication strategies above. It is normal to not get along with everyone in the lab, but you need to have at least a working relationship with people who you depend on. 

If the conflict continues even after speaking to your PI, ask for outside help. We recommend speaking with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/ or Department Chair to help mediate these conflicts. 

Conflict Between Student and PI

Your progress in the program is highly dependent on a strong positive relationship with your PI as you need their support to finish your M.S. thesis or Ph.D. dissertation. Keep in mind PIs do not receive formal training on managing people in communication or conflict resolution, so using the previously recommended communication strategies can help avoid most conflicts.

Sometimes difficult conversations with your PI need to happen multiple times. We recommend keeping a record of your interactions as a way to observe patterns, note changes, and recall specifics from each interaction. 

​If you are concerned about raising sensitive issues, such as negative results or concerns about your PI’s behavior, directly with your PI due to concerns about anger and/or retaliation, we highly recommend addressing the situation as soon as possible through a third party. We suggest first talking through specific negative interactions that have led to this feeling with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/or Department Chair or any other PI who you have a close relationship with.

In situations where you have been yelled at, degraded, harassed, or discriminated by your PI, we highly recommend you speak with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/ or Department Chair. The Office for the Prevention of Harassment & Discrimination (OPHD) or Office of the Ombuds can also be a resource for situations of this nature. 

Changing Labs

For Ph.D. students, a Ph.D. degree is a long process and you should feel like the time you invest into that process is worth it. For masters students, due to time constraints, you want to keep in mind what will serve you best in your limited time in the program. If you feel like the lab you have chosen will not be able to assist you in obtaining your degree or to train you for a career that you would like to have after you graduate, you have a good reason to look into changing labs.

A limited number of students change labs every year for a variety of reasons, so PIs should understand that there is the possibility of students looking to change labs. If you are considering changing labs after your research rotation or trial period, you should know that many people have successfully done this before you. For Ph.D. students it is important to recognize that these changes must occur before the Senate Exam; lab changes after the Senate Exam are not possible.

We highly recommend discussing lab changes with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/or Department Chair. Speaking to department personnel does not commit you to leaving your lab but can be a good first step in deciding whether or not to change labs. Conversations are often very productive and can result in differences being resolved. There are three main choices that you will be given when you discuss the issue with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/ or Department Chair:

1. Stay in your current lab and work out the conflict with assistance from the Department
2. Stay in the program, but work on leaving the your current lab and finding a new lab
3. Leave the program and work toward an MS Plan I- Thesis (using existing data from your research) or MS Plan II- Comprehensive Exam instead of the previous Ph.D. Note, for Ph.D. students who have already passed the Senate Exam, changing labs is no longer possible and you should plan to work toward the MS Plan II.

We recommend talking through each scenario with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/or Department Chair and thinking about your options carefully. This can be a difficult discussion to have when you are confused about the next step and looking for validation. Understand that they will not tell you what you should do, but will provide realistic options for where you are at in your program. 

Once you have decided that the best move for your training, career and wellbeing is to change labs, you will need to discuss changing labs with your PI. This discussion can occur one-on-one but is often more comfortable for both student and PI when third parties are present, e.g., Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/or Department Chair. Below you will find some tips on what to do before telling your PI you are leaving the lab.

Before you officially leave the lab but you have decided to leave, consider what you will need to get done:

1. Prepare a plan and a timeline for how to expected to wrap up projects and transition off of other projects or tasks
2. Reach out to other faculty to discuss research rotations. Be prepared to talk about why you are leaving the lab.
3. For Ph.D. students, speak with your current PI, the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/or Department Chair about funding options during this transition period.
   • If the department is assisting with support, you may have to TA courses even if you have completed your TA requirement. 

When trying to identify a new lab in which to complete your research, consider:

• Researching your research interests
• Reading through recent publications from the lab(s) you are interested in
• Newer and affiliate faculty who may have a higher likelihood of openings in their labs
• Contacting the PI with an introduction to who you are, why you are interested in their lab, and ask if they are open to taking a transitioning student
• Speaking with the PI about funding 

Prepare the conversation with your PI. We highly recommend talking it through with the Bioengineering Student Affairs Office, GSC Chair, Department Vice Chair, and/ or Department Chair. In the past, the GSC Chair and Department Vice Chair have assisted in writing the email to your PI to signal your intention to leave the lab. This is an opportunity to make sure nothing is misunderstood and that you are supported by the department. Be clear and be confident in your decision during your discussion

Additional Resources
Below please find a list of additional conflict resolution resources:

• Division of Graduate Education & Postdoctoral Affairs page on Conflict Resolution
• Article about How to Handle Conflicts in Grad School
• The Office for the Prevention of Harassment & Discrimination (OPHD) “educates the UCSD community about issues of bias, harassment, and discrimination, and assists with the prevention and resolution of these issues.”  
• The Office of the Ombuds “provides a confidential, safe space for UCSD community members to talk about concerns and problem-solve issues arising from interpersonal and group conflict.”
• The Dean’s Office can also provide assistance via their Guaranteed Transitional Support Program. Students should contact Dr. Darren Lipomi, the Associate Dean of Students for the Jacobs School of Engineering.

Acknowledgment
This policy was developed in collaboration with department faculty leadership, the Graduate Studies Committee, BE Diversity Council, Bioengineering Student Affairs, and BEGS. The finalized text was adapted from documents developed and written by BEGS, the BE Diversity Council, Bioengineering Student Affairs, the Jacobs School of Engineering, and the Division of Graduate Education & Postdoctoral Affairs (GEPA).

 

EASy Requests

 

The Enrollment Authorization System (EASy) is a campus system used to streamline requests for: 

• Requesting pre-authorization for a course(s) which the student may not have met the prerequisites or restrictions
• Requesting instructor approval for a course
• Dropping courses and research/ rotation units after Week 2
• Changing units after Week 2
• Changing grading options after Week 2

EASy does not automatically enroll students in courses. Students must still enroll via WebReg if “cleared” for a course via EASy. 

Adding Courses

Students can add courses via WebReg through the Friday of Week 2 of each quarter. After Friday, any "Late Add" requests must be submitted via EASy. The Department will only consider these types of requests for research and rotation units.

Please note that EASy requests submitted by graduate students from outside of BENG for required/ core BENG courses will not be considered until week 0/1 of the quarter in order to ensure that BENG grad students are able to enroll in their required coursework. If there is still space in these courses come week 0/1, then graduate students from outside of BENG may submit an EASy request at that time. It will be routed to the instructor for their review. The request is not guaranteed to be approved.

Dropping Courses

Students can drop courses via WebReg through the Friday of Week 2 of each quarter. After Week 2, all graduate students must submit an EASy request to request to drop any course. This extra step to drop a course is required due to strict policies around funding and full time status at the graduate level.

Please note that for drops submitted via EASy, the drop deadlines listed on the Enrollment & Registration Calendar each year are the dates by which the student must submit the EASy request. These dates are NOT by which the EASy request must be processed. As long as the student submits the drop request by the appropriate drop deadline date then it will be honored even if the request is processed by the Department or Registrars’ Office after the drop deadline date.

 

Survival Skills

 

Increasing attention has been paid to identifying the core skills needed in order to be a successful graduate student and scientist in the highly competitive environment that today’s research students and junior scientists face. Some important skills that have been identified include:

• Study, work, and teaching skills
• General technical writing and presentation skills
• How to write a scientific paper and respond to reviews
• Writing grant applications and getting financial support
• Making posters and slide presentations
• Answering questions and communication with public
• Identifying an advisor and a research project
• Searching for literature and using the library effectively
• Accurate data recording
• The appropriate use of statistical analysis
• Obtaining permission to use animal and human subjects
• Social responsibility of research
• Management of time and stress
• Relationships with faculty, students, and staff, including handling problems in the workplace
• Preparing for life after graduate school, including preparing a CV, career management, and negotiations

 

This list is not exhaustive but it gives you an idea of the many new skills that you will need to develop as a successful graduate student. It is also easy to see that many of these matters include considerations of scientific and professional ethics which are discussed in other sections of this handbook.

While most of these skills are acquired informally in the process of obtaining a graduate degree, there are many advocates, especially students themselves, of some optional formal training in these areas. At present UC San Diego does not have a program or course that covers all these areas, but some courses cover some of them. Several departments offer courses in “Science Communication,” “Research Survival Skills,” and other such topics. Please reference the UC San Diego General Catalog and the Schedule of Classes to find more information about these course offerings.

 

Waiving or Transferring Courses

 

Below please find information about petitioning to waive or transfer courses based on degree aim. Note that the below is general information and guidance and does not guarantee any petition will be approved. Students are responsible for completing all course requirements for their respective degree aim unless a petition to waive or transfer credit is explicitly approved by the Graduate Studies Committee (GSC).

Masters Programs
Masters degrees are considered “unit-based” degrees, which among other things, means that students are expected to meet the unit requirements for their degree aim by completing the required coursework for their respective degree aim. The overall unit requirement for each degree aim cannot be waived or altered. For example, an MS Plan I-Thesis student must complete 52 units of coursework in order to complete the course requirement for the degree, broken down as: 24 units of core courses, 12 units of electives, 12 units of BENG 299 research, and 4 units of seminars. If these 52 units are not completed, then the student does not qualify to receive the degree. 

Per university policy outlined on the GEPA website, masters students may petition the GSC to “transfer” graduate-level credit from another institution so long as that credit was not “used to fulfill the requirements of any other degree or certificate, and must have been completed with a B- or better grade and must have been taken prior to enrollment as a graduate student at UC San Diego.” Additionally, per policy, the student must provide “proof that the course work to be transferred was not used to satisfy requirements for any other degree or certificate program.” 

Petitions will only be considered by the GSC for courses the student believes are graduate-level equivalents to UC San Diego Bioengineering courses. Keep in mind petitions are not guaranteed to be approved. Note that if a petition is approved, the student must still make up the missing units in order to satisfy the unit requirement for the degree. For example, if an MS Plan I-Thesis student successfully petitions two core courses, they must take two additional courses to replace the units for these courses in order to meet the 52 unit requirement for the MS Plan I-Thesis degree.

In order to petition, please reach out to the Bioengineering MS/MEng Coordinator to request more information on the process. 

PhD Program
PhD programs are considered “research-based” degrees, which among other things, means that students are expected to meet the research requirements of the degree. Additionally, departments can also establish other requirements for the degree, including coursework, teaching, and seminars.

In addition to completing research toward a dissertation, the Bioengineering Department requires PhD students to complete:

• 6 core courses
• 4 elective courses
• 4 seminars
• 3 Graduate Instructional Apprenticeship
• 1 ethics course

PhD students may petition the GSC to “waive” some of the above mentioned coursework based on previously completed graduate-level coursework at UC San Diego or another institution. Petitions will only be considered by the GSC for courses the student believes are graduate-level equivalents to UC San Diego Bioengineering courses. Keep in mind petitions are not guaranteed to be approved. Note: if the student already has a masters degree, this does not automatically waive course nor guarantee any courses will be waived for the PhD degree. If the petition is not approved, the student would still be required to complete all of the above mentioned coursework. 

In order to petition, please reach out to the Bioengineering Coordinator of Graduate Affairs to request more information on the process.

 

 

RESEARCH TOPICS

Animal Use

 

The use of experimental animals is an essential component in the research of many Bioengineering graduate students. UC San Diego has excellent animal care facilities and professional veterinary staff. UC San Diego’s animal care and use program, including its facilities, is regularly inspected by the USDA and is fully accredited by AAALAC, International.

All research and teaching at UC San Diego involving live vertebrate animals must be conducted under an Animal Use Protocol approved by the UC San Diego Institutional Animal Care and Use Committee (IACUC), which consists of veterinarians, scientists and lay people. The committee adheres to the Public Health Service (PHS) Policy on Humane Care and Use of Laboratory Animals, which is enforced by the Office of Laboratory Animal Welfare (OLAW) of the National Institutes of Health (NIH), as well as the Animal Welfare Act and Animal Welfare Regulations enforced by the USDA. Any changes to the procedures described in the protocol must be approved in advance by the IACUC.

Students and personnel who participate in any capacity in animal research at UCSD must first register with the IACUC, be listed on an approved Animal Use Protocol, and submit a Personnel Qualifications (PQ) Form. Their qualifications must be approved by the IACUC Office before working with animals. Each person must also complete the “Orientation to Animal Research at UCSD” class and be adequately trained in each species and each procedure that they will perform. Personnel must also enroll in the Occupational Health and Safety Program (OHSP). Once they have been added to an Animal Use Protocol, they will have access to the current protocol online.

If you have any health, training or ethical concerns regarding the use of animals in your research do not hesitate to discuss them with a faculty member.

For more information, please visit IACUC or contact the IACUC office at 534-6069 or iacuc@ucsd.edu.

 

BENG 298L vs. BENG 299

 

The department offers two different types of research credit: BENG 298L (Laboratory Research Rotation) and BENG 299 (Graduate Research). Below please find their official course descriptions from the UC San Diego General Catalog.  

• BENG 298L. Laboratory Research Rotation (4) 
  • Laboratory research rotation for first-year BENG PhD students. Students will write a final paper. (S/U grades only.) Prerequisites: PhD student in bioengineering. (F,W,S)
• BENG 299. Graduate Research (1–12)
  • Independent work by graduate students engaged in research and writing theses. (S/U grades only.) Prerequisites: consent of instructor. (F,W,S)

“BENG 298L” is the class code for PhD students to receive academic credit for rotation research they conduct in a lab. Sections of BENG 298L are not automatically added to the Schedule of Classes or WebReg, so students must submit a “Special Studies” request via EASy for BENG 298L and select the faculty member from the drop down menu. The EASy request will route for review/ approvals and the student will then need to enroll via WebReg once the EASy request is fully processed. 

Some MS Plan I - Thesis students express interest in "rotating" in a lab before committing to see if the lab is a good fit. The department prefers to think of this as a “trial run” or as the student “testing out the lab.” The department prefers not to use "rotating"/ "rotation" in these situations as these are official terms used in the PhD program to denote BENG 298L research rotations and do not apply to the MS program. MS Plan I- Thesis students are not required to complete rotations, and should not enroll in BENG 298L. If an MS Plan I- Thesis student wants to test out a lab, they should enroll in BENG 299 under that faculty member.

"BENG 299" is the class code for MS Plan I- Thesis students and PhD students to receive academic credit for research they conduct in a lab. Students should enroll in a section of BENG 299 units under the faculty member of the lab in which they are conducting their research. In order to enroll in BENG 299 the student must first secure a spot in a lab. This means that the student needs to contact the faculty member, have a discussion, and come to a mutual agreement for the student to work in the lab. Students should NOT enroll in research units unless they have the faculty member’s permission to enroll. 

Sections of BENG 299 are generally available every quarter for Bioengineering faculty and faculty affiliates. If a student is attempting to work with a faculty member outside of Bioengineering for which a section of BENG 299 has not already been set up, the student should submit a “Special Studies” request via EASy for BENG 299 and select the faculty member from the drop down menu. The EASy request will route for review/ approvals and the student will then need to enroll via WebReg once the EASy request is fully processed.

BENG 298L Syllabus

BENG 299 Syllabus

 

Health and Safety

 

Laboratory research can involve significant exposure to significant hazards to your personal health and safety. It is important to receive thorough safety training before you begin working in a laboratory. State and Federal regulations as well as University policy require that your safety training be documented and that evidence of your training be available for inspection. The safety officer for the Bioengineering Department is Douglas Gurevitch, Research & Development Engineer.

Every laboratory has a safety contact person, a copy of the UC San Diego Laboratory Safety Guide, a First Aid kit and a fire extinguisher. Each lab or Principal Investigator also maintains lab-specific safety information including a laboratory "Chemical Hygiene Plan", a laboratory "Biological Use Authorization, a laboratory "Radiological Use Authorization", and a file that records the training of all students and personnel.

Extensive safety and injury prevention material is available from the Office of Environmental Health and Safety (EH&S) on campus (534-3660). Much of this information is also available on-line via the Blink safety webpage.

EH&S offers regular classes on general safety through its Injury and Illness Prevention Program. These classes are very useful and cover basic topics including safety orientation, hazard communication, safe computer use, earthquake preparedness, fire, and preventing back injuries.

Additional specialized training will be needed by many students on topics such as:

Radiation safety — all students using radioisotopes must be registered with EH&S and trained Biosafety — all students intending to work on tissue culture at Biosafety Level 2 or above must be trained

• Consult your lab safety contact person, EH&S or the department safety officer for more information.
• Chemical carcinogens — your principal investigator is responsible for notifying you if you may be exposed to known carcinogens
• Protective equipment — must be worn when handling dangerous materials or using hazardous equipment

 

 

Research Ethics

 

As scientists are exposed to closer public scrutiny and demands for greater accountability, the importance of formal training in the many complex ethical issues that surround scientific research is growing. In particular, Ph.D. students in the Bioengineering Department should be aware that the National Institutes of Health requires some training and discussion in ethical issues as a condition of financial support.

At present ethical topics are discussed in the department in several ways, including:

• In the required Ph.D. course BENG 292: Scientific Ethics
• Seminars during our regular Departmental Seminar series by scientists, officials and others experienced in scientific ethics
• Group discussions, frequently during regular lab meetings
• As a component of regularly scheduled courses.

Other departments at UC San Diego also have regular offerings of workshops and seminars on ethical issues, including topics such as scientific misconduct, government regulation, use of genetic information, whistle blowing, animal and human subject trials, and other subjects related to authorship and plagiarism.

Additional Resources:

• The Research Ethics Program at UC San Diego’s Ethics Office offers a number of resources, workshops, and information about ethical research conduct
• The Institute for Practical Ethics offers working group for different research areas to discuss ethical research conduct  
• The National Academies of Sciences, Engineering, and Medicine offer a book on responsible conduct in research called On Being a Scientist: A Guide to Responsible Conduct in Research: Third Edition. The hypothetical case studies it contains are an excellent starting point for discussion of important and frequently complex topics such as assigning credit and priorities, determining authorship, the integrity of scientific data, recognizing and responding to ethical violations, ethics and grant writing.

 

Research Facilities

 

Biotechnology  -  PFBH rooms 021, 035, 345

Information Technology  -  OEC, Jacobs Hall Suite 4100

Functional MRI  -  W.M. Keck Building, UC San Diego Medical School

Cell Engineering Research Center (CERC)  -  Jacobs Hall labs 5307, 5311, 5313,5315, 5319

 

Research Projects

 

Research is an integral component of graduate studies in the Ph.D. and M.S. Plan I- Thesis degree programs. Thesis students are not expected to have identified a research project and research advisor at the start of their graduate studies. The department therefore assigns an initial academic advisor to each graduate student. The department tries to match the interests of the student with those of the assigned faculty advisor, and hence it is common that the academic advisor becomes the research advisor and thesis committee chair. However, there is no obligation.

Choosing a Research Project

Research students are encouraged to consider their research project early and carefully. To help with this decision, there are several things new students can do:

• Attend weekly departmental seminars. They include presentations by Bioengineering and affiliated faculty, and reflect the diverse bioengineering research activities and interests here. 
• Meet with faculty members to discuss your research interests and find out more about their research activities, and inquire about attending research group meetings. Most of the faculty extend an open invitation to new students to join in on these regular meetings. We recommend starting this process during Fall quarter.
• Plan on enrolling in Graduate Research (BENG 299) for at least two quarters during your first academic year with explicit permission from the faculty member. 
  • Laboratory rotations (BENG 298L) help Ph.D. students to familiarize themselves with the research area, environment, and personnel involved. They also provide the prospective research advisor(s) with an opportunity to evaluate the potential and suitability of the student for doctoral research in general and for participation in his or her laboratory. 
  • Faculty advisors will be happy to discuss the student's research interests in detail to assist the student to identify the research lab and environment best suited to the student's interests, background and academic objectives.

 

MASTERS TOPICS

MS Comprehensive Exam Process

 

Outlined below is the administrative process to follow when preparing for your MS Comprehensive Exam (“Comp Exam”).

1)  Notify the Bioengineering MS/MEng Coordinator via email about your intent to take the Comp Exam BEFORE the end of Week 2 of the quarter in which you plan to take the Comp Exam. Ideally, you would notify the Coordinator the quarter before you plan to take the Comp Exam.
2)  The Bioengineering MS/MEng Coordinator will review your academic record to determine if you are eligible to take the Comp Exam that quarter. 

• If eligible, the Coordinator will process paperwork to advance you to candidacy. You must be advanced to candidacy in order to be eligible to sit for the Comp Exam.
• If not eligible, the Coordinator will work with you to determine when you would be eligible to take the Comp Exam.

3)  The Bioengineering MS/MEng Coordinator will work with the Graduate Studies Committee to assemble a Comp Exam Committee and schedule date(s) to hold the Comp Exam for that quarter based on the number of students eligible to take the Comp Exam.
4)  Once date(s) and times for the Comp Exam have been finalized, the Bioengineering MS/MEng Coordinator will reach out to eligible students to schedule their Comp Exams. 

• This will be done via email and students will be expected to respond to the email promptly with their preferred date(s) and times in preference order.
• The Coordinator will respond back confirming the finalized day and time for the student’s Comp Exam.

5)  On the day of your Comp Exam, the Bioengineering MS/MEng Coordinator will prepare the Final Report Form for your exam via DocuSign, and route it to the committee. 

• The committee will sign the Report Form via DocuSign if you successfully pass the Comp Exam. 
• You will receive a notice from the Coordinator of your Comp Exam results.
• DocuSign will then route the Report Form to our Department Chair for signature before routing to the Division of Graduate Education & Postdoctoral Affairs (GEPA) and the Registrar’s Office for processing. 

6)  You will receive an official notice from the Dean of the GEPA of your degree conferral. Congratulations, you have been awarded your MS!

• The degree conferral date listed will be the last day of the quarter. 
• The degree usually takes 1-3 months to process and post to your Academic History and official transcript after the quarter has ended. 
• After the degree has been processed, your diploma is mailed to you to the permanent address listed on your TritonLink account. Please make sure your permanent address is up-to-date in TritonLink. You should expect the diploma to arrive in the mail 3-6 months after the quarter has ended. 

 

 

How to Constitute and Reconstitute an M.S. Thesis Committee

 

Outlined below is the process to constitute, or set up, an MS Plan I Thesis Committee and how to request a reconstitution if changes need to be made to a previously constituted committee.

Initial Committee Constitution

1)  Meet with your research advisor to discuss who should be appointed to your committee

• A masters committee has three members, with the option to add an additional “fourth member” as appropriate.   
  • The University requires that at least two members of your committee are Bioengineering faculty. 
  • If your faculty advisor is outside of Bioengineering, the Department requires you to have a Bioengineering faculty member serve as a co-chair on the committee. 
• The Division of Graduate Education & Postdoctoral Affairs (GEPA) has a Master's & Doctoral Committee Membership Table that provides guidance on who can serve on a committee.

2)  Once you have discussed your committee with your research advisor, email your finalized list to the MS/ MEng Coordinator. 

• In the email please include the following information for EACH committee member:
  • First and last name
  • Academic rank (e.g. “Associate Professor”)
  • Home department 
• Committee status (e.g. Chair, Co-Chair, or regular committee member)
• Please provide this list at least four weeks before your MS Thesis Defense to allow time for it to get processed.

3)  The MS/MEng Coordinator will electronically route your committee request to the Department Chair and to the Dean of the GEPA for review. 

• You cannot defend your MS Thesis until the Graduate Dean approves your committee. If you have not received an email from the Dean approving your committee by one week before your defense, please contact the MS/MEng Coordinator.

4)  You will get an email notice from the Dean when your committee is approved. Congratulations, your committee has been constituted!

Reconstituting an Established Committee

If you need to make changes to a committee that has already been constituted, you will need to make a request to reconstitute the committee. Typically a reconstitution is needed to add or remove faculty on the committee, make changes to committee member status (i.e. chair/ co-chair versus regular member), to be in compliance with Conflict of Interest (COI) concerns, and update faculty titles.  

1)  Meet with your research advisor to discuss what changes need to be made to your committee.

• Keep in mind, the GEPA has a Master's & Doctoral Committee Membership Table that provides guidance on who can serve on a committee.

2)  Once you have discussed the changes to be made to your committee with your research advisor, email your updated list to the MS/ MEng Coordinator. 

• In the email please include the following information for EACH committee member:
  • First and last name
  • Academic rank (e.g. “Associate Professor”)
  • Home department 
  • Committee status (e.g. Chair, Co-Chair, or regular committee member)
• In the email you must also provide a justification or explanation for EACH change being made to the committee. This is required in order to submit the reconstitution request.

3)  The MS/MEng Coordinator will electronically route your committee request to your Committee Chair, the Department Chair, and to the Dean of the GEPA for review. 

• You cannot defend your MS Thesis until the Graduate Dean approves the committee reconstitution request. 

4)  You will get an email notice from the Dean when your committee reconstitution request is approved. Congratulations, your committee has been reconstituted!  

 

M.S. to Ph.D. Petition Process 

 

Outlined below is information related to the M.S. to Ph.D. petition process. As noted on the Degree Programs page, this process is open only to students in the M.S. Plan I- Thesis degree program. 

Petition Requirements

1) Must be a Bioengineering M.S. Plan I- Thesis student
2) Have completed or have in-progress all 6 core courses:

• Engineering Physics: BENG 226, BENG 227, third engineering physic core elective
• Life Sciences: BENG 230A, BENG 230B, third life science core elective

3) Have an overall GPA of 3.40 or higher 
4) Have a faculty advisor willing to take you on as a Ph.D. student

• They can be a Bioengineering faculty member or a non-Bioengineering faculty member. If non-Bioengineering, you must also secure a Bioengineering faculty member to serve as a co-advisor.

5) Have a funding commitment from the faculty advisor to fund you for the duration of your program

• The Bioengineering Ph.D. program is considered a “fully-funded” program with a guarantee of funding so long as the student maintains their eligibility. This means the faculty advisor must commit to:
  • Funding coming from the faculty advisor and/ or external student award (e.g. NSF, F31, AHA, etc.) at the appropriate support level.
  • No funding coming from Bioengineering or non-Bioengineering TAships as Ph.D. students in Bioengineering complete GIAships “for credit” only.
  • Continuing to fund the student as long as the student maintains eligibility. See our Financial Support page for more information about eligibility requirements. 
• The Department reserves the right to contact the faculty advisor’s fund manager to ensure there is funding readily available to cover the funding commitment. 

Petition Process and Timeline

1) At the start of each petition period, the Bioengineering Coordinator of Graduate Affairs will email all M.S. Plan I- Thesis students to announce the petition period and provide information on how to request a petition packet. Petition periods are listed below. 

Quarter	Packet Available	Packet Due	Qualifying Exam	Official Transition Quarter
Spring of the First Year	April	May	Summer between First and Second Year	Fall of the Second Year
Fall of the Second Year	October	November	December	Winter of the Second Year
Winter of the Second Year	January	February	March	Spring of the Second Year
Spring of the Second Year	April	May	Summer between Second and Third Year	Fall of the Third Year

2) M.S. Plan I- Thesis students who wish to pursue a doctorate must request a petition packet from the Bioengineering Coordinator of Graduate Affairs after the petition period is announced. 

• The petition packet includes two pages of instructions and a blank Funding Statement that will need to be completed by the faculty advisor and co-advisor, if applicable.  

3) M.S. to Ph.D. petitioners must submit their petition packet for a change in status to the Bioengineering Coordinator of Graduate Affairs by the deadline for review by the Graduate Studies Committee during the petition period. 

• A complete petition packet includes: 
  • A Statement of Purpose from the student
  • A copy of the student’s transcripts
  • The completed and signed Funding Statement
  • A Letter of Recommendation from the faculty advisor who is taking on the student
  • If the student will have a co-advisor, a Letter of Recommendation is required from that faculty member as well

4) The Graduate Studies Committee will review all complete petition packets submitted each petition period. 

• If “approved,” the committee recommends that the student be given the opportunity to take the Ph.D. Departmental Qualifying Examination. 
• If “denied,” the student is welcome to finish out the M.S. Plan I- Thesis degree 

5) If approved to sit for the Qualifying Exam, the student will be given the information for the Exam for that quarter.

• At the time of that exam, an assessment will be made on admission to the Ph.D. program. 

6) If the student passes the Qualifying Exam, a change of status from the M.S. Plan I to the Ph.D. program will be processed for the Official Transition Quarter.

 

MS Thesis Defense Process

 

Outlined below is the administrative process to follow when preparing for your MS Thesis Defense.

1)  Discuss your defense with your faculty advisor and MS committee so you know what is expected of you, including what written materials you will need to prepare and what deadlines they may have for you. 

• Work with your faculty advisor and MS committee directly to schedule your defense. Students frequently use Doodle or when2meet to determine a suitable day and time. 

2)   Notify the Bioengineering MS/MEng Coordinator via email about your intent to hold your defense.

• You can reserve PFBH conferences 291, 391 or the Zweifach Library (489) by emailing be-reservations@eng.ucsd.edu. if interested in holding your exam in PFBH.
• As soon as you have set the date, time, and location of your defense, you should notify the MS/MEng Coordinator at least two weeks in advance of your defense. This allows time for the office to get your academic file ready.
• Make sure you have notified all of your committee members of the date, time, and location of your defense.

3)  Before your defense date, you will need to schedule a “Preliminary Appointment” with the Division of Graduate Education & Postdoctoral Affairs (GEPA) to review required paperwork and information. Appointments can be scheduled via the GEPA's Calendar. 

• Helpful information about this process and the preliminary appointment can be found on the GEPA'S Dissertation & Thesis Submission page.
• Make sure to review the “Preparation and Submission Manual for Doctoral Dissertations and Master's Theses” provided at the link above.
• You may also want to schedule a “Final Appointment” at this time for after your defense. You may use the same calendar as above to do this.

4)  On the day of your defense, the Bioengineering Student Affairs Office will prepare the Masters Final Report Form for your defense via DocuSign, and route it to you and your committee. 
You and your committee members will receive an email notification describing the DocuSign process on the day of your defense. 

• Your committee will sign the Final Report Form via DocuSign after you successfully complete your defense. 
• DocuSign will then route the Final Report Form to our Department Chair for signature before routing to the GEPA and the Registrar’s Office for processing. 

5)  After your defense you will prepare all of your final paperwork to submit in time for your Final Appointment with the GEPA. 

• Keep in mind the deadline to submit all final paperwork to the GEPA in time to receive your degree that same quarter is always the last day of that quarter. For example, if you wanted to receive your degree in Spring, you would need to have your defense and submit all final paperwork to the GEPA before the last day of Spring quarter. 

6)  You will receive an official notice from the Dean of the GEPA of your degree conferral. Congratulations, you have been awarded your MS!

• The degree conferral date listed will be the last day of the quarter. 
• The degree usually takes 1-3 months to process and post to your Academic History and official transcript after the quarter has ended. 
• After the degree has been processed, your diploma is mailed to you to the permanent address listed on your TritonLink account. Please make sure your permanent address is up-to-date in TritonLInk. You should expect the diploma to arrive in the mail 3-6 months after the quarter has ended. 

 

Ph.D. TOPICS

PhD Time Limits

 

The PhD program has three time limits that students should be aware of during their graduate studies. These time limits are:

1)  Pre-Candidacy Time Limit (PCTL) -- limited to 3 years

• This time limit indicates the last quarter by which the student must “advance to candidacy” or take the Senate Exam.
• A hold will be placed on the student’s account in the last quarter until the student takes the Senate Exam.

2)  Support Time Limit (SUTL) -- limited to 6 years

• This time limit indicates the last quarter in which a student is guaranteed support in the program. After this, a faculty advisor is not required to continue to support a student.

3)  Total Registered Time Limit (TRTL) -- limited to 7 years

• This time limit indicates the last quarter in which a student can continue to be registered as a graduate student.
• A hold will be placed on the student’s account in the last quarter preventing further enrollment at the university. 

There is also a fourth “time limit” that is more so for the student’s information, and does not prevent further enrollment. This time limit is called the “Graduate Normative Time Limit” (GNOTL), and informs the student of the normative, or average, time-to-degree. Currently the normative time-to-degree for the Bioengineering PhD program is 5 years. 

 

The Departmental Qualifying Exam Process

 

Outlined below is the administrative process to follow when preparing to take the Departmental Qualifying Examination (“Qual Exam”). This exact process is specific to PhD students, but MS Plan I- Thesis students planning to petition to transition to the PhD program may find the information about the format and requirements useful. 

Overall Goal
In the mandatory and elective courses of the graduate program, the student is expected to have developed a fundamental understanding of engineering and life sciences required for research in bio/biomedical engineering. The next step in developing a research career is to be critically able to formulate a research problem with the appropriate technological underpinnings and analytical strategies, while being familiar with prior research on the topic reported in scientific literature. The Qualifying Examination is intended to assess the student’s preparedness towards this next step. 

The written portion of the proposal is expected to provide:

• the overarching objective of the research problem, followed by specific aims
• background and significance that motivates the problem(s)
• innovative components of the proposal
• research design outlining the methods, analytics, and the potential limitations. 

In the oral examination, the student is expected to demonstrate an understanding of the fundamental concepts associated with the research problem and design, details of the technological (engineering and quantitative) approaches that will be involved, and the ability to analyze the research design issues with technical clarity. The Qualifying Examination is intended to test the preparedness of the student to go beyond the curricular performance and add research thinking and orientation to the student’s arsenal going forward. It should be clarified that while this is not a substitute for the Senate Examination which is the basis for the student’s dissertation, it is meant to initiate the student into research thinking and not meant as a regurgitation of material covered in the coursework.

The Qualifying Exam Design
Students are evaluated on both a written and oral portion of the qualifying exam.

• The written portion of the Qualifying Exam consists of a proposal on a research topic of the student's choice. Proposals should address a well-circumscribed scientific problem in biology and/or medicine. Proposals must include quantitative engineering and/or design principles learned in core instruction. A research topic may be, but is not limited to, the student's thesis research topic. The written portion must be the student’s original, independent work and no content should be taken from existing source materials. It is advised that topics be pre-approved by the QE committee by submitting a one-page outline in advance. The proposal should include the overall objective of the proposed research project, at least two specific aims, and a research strategy based on the scientific literature. Exploratory research proposals should include one or more hypotheses; design-oriented proposals should clearly define the objectives and design requirements.
• The oral portion (45-60 minutes) of the Qualifying Exam evaluates fundamental life science and engineering principles related to the student's written proposal, the ability for independent thinking and decision making, knowledge and integration of engineering and life science concepts, and application of knowledge to interdisciplinary bioengineering problems. The students are invited to prepare an 8-minute (maximum) PowerPoint presentation as an overview of their Qualifying Exam proposal. The student will have access to a whiteboard to outline their proposal. The scope of the oral examination covers all foundational background related to the proposal. The QE committee determines the scope of the exam topics by reviewing the student’s proposal, student’s coursework, and program requirements.

Exam Committee
Qualifying exams are administered by the qualifying exam (QE) committee consisting of three bioengineering faculty members with broad expertise in areas of engineering, biological sciences, and bioengineering. The Department Chair and the Graduate Studies Committee assigns the QE committee and its Chair.

The role of the QE committee Chair is as following:

• Ensure that questions are fair and appropriate.
• Meet with the student prior to the exam to discuss philosophy and mechanics of the exam, and any other points relevant to the student and/or committee.

Exam Results
Both written and oral portions of the exam will be evaluated based on a rubric sheet that will be provided to the student at the time they receive their Official Qualifying Exam Memo. The committee will take a PASS/NO PASS vote at the conclusion of the exam before adjournment. This can be an open vote but may be a secret ballot if requested by a committee member. The final vote is binding. Committee members must each complete an evaluation with appropriate comments at the end of the exam. These forms will be delivered to the program office and can be viewed by interested students.

Exam Outcomes 
PASS (with or without recommendations/conditions) or NO PASS.

• PASS: The committee may make recommendations or conditions along with the PASS. All conditions mandated by the QE Committee must be met within one year of the Qualifying Exam date.
• NO PASS: If the exam is conducted for the first time, the student may retake the exam. The evaluation form will list recommendations or conditions the student must follow prior to the retake.

Exam Retakes

• Only one retake is permitted. Upon retake, the student must meet GPA requirements. All retakes should be scheduled as early as possible contingent on recommendations and conditions (typically within three months of the first exam).
• If a second NO PASS is obtained, the student may elect to pursue a MS or withdraw from the program.

Guidelines for Qualifying Exam Proposal
E-mail a single PDF document to the Chair of the QE committee no later than two weeks before your exam.

Format

• 11 point or larger font (Recommended fonts are Arial, Georgia, Helvetica, or Palatino Linotype)
• ½” (half inch) margins

Parts

• Biographical Sketch (3 page maximum. Template and instructions available at https://grants.nih.gov/grants/forms/biosketch.htm)
• Proposal Page 1.
• Project title
  • Project Summary: Maximum of 30 lines of text
  • Project Narrative: Maximum of 2-3 sentences
• Proposal Page 2. Specific Aims (Maximum of 1 page)
• Proposal Page 3 to 6. Research Strategy (Maximum 3-4 pages)
  • Sections must be labeled in this order and with each header: 1. Significance; 2. Innovation; 3. Approach (Research Design and Methods).
• Proposal Page 7+. Bibliography & References Cited (No page restriction). 
  • Students are expected to have detailed knowledge of referenced materials.

Suggestions to write the Qualifying Exam Proposal

• The course BENG 207: Communications Skills for Bioengineers is offered in Spring. In this course you will develop a written proposal throughout the quarter.
• Address an unsolved problem driven by a focused and testable hypothesis or a novel model or design; ask questions that prove or disprove a hypothesis rather than search for a problem or simply collect information.
• Specific Aims, including those that propose to build quantitative models, should include descriptions of the specific measurements and biological or material properties needed to test the hypothesis and how they will be obtained.
• Develop a fundamental understanding of the proposed approach, including proposed quantitative model, experimental design, measurements, and the most relevant biological and engineering constraints of the problem.
• Read and understand deeply key relevant literature (e.g., reviews, primary scientific literature, etc.) in the area.
• Engage your lab, mentors, colleagues, and collaborators in discussions about your research interest.
• Find outside experts to talk with – go prepared to ask important questions.
• Begin early to define, organize, and plan the content.
• Read equivalent example proposals to understand the expected scope and content (e.g., NIH F31 or NSF GRFP).

Rubric for Qualifying Exam
Both the written and oral portions of the exam will be evaluated based on a detailed rubric score sheet that will be provided to the student at the time they receive their Official Qualifying Exam Memo.
 

 

Obtaining an MS along the way to the Ph.D.

 

Outlined below is the process to obtain an MS Plan II degree along the way to the PhD.

Policies and Guidelines

• In order to obtain an MS Plan II you must complete 12 four-unit courses (6 core courses and 6 electives) for a letter grade. Note: four-unit courses taken in SP20, WI21, and SP21 for S/U grading may count toward the degree per grading policy released at the time in response to the pandemic.
• For elective courses taken outside of Bioengineering, you must submit a completed Elective Approval Form signed by your faculty advisor.
• We will use your Departmental Qualifying Examination to satisfy the “Comprehensive Examination” requirement for the MS Plan II degree. 
• We can file for an "MS along the way to the PhD" in Fall, Winter, and Spring quarters.
• An MS degree cannot be awarded in the same quarter you take the Senate Exam and advance to candidacy, nor in the same quarter you are awarded the PhD degree. Please plan accordingly when requesting what quarter to have the MS awarded. 

Process

1) Reach out to the Bioengineering Coordinator of Graduate Affairs to notify them of your intention to obtain an MS along the way to the PhD.

• This should be done in the quarter in which you finish the last of the course requirements or after you have completed the required courses.
• You must reach out BEFORE the end of Week 2 of the quarter in which you would like the MS to be awarded. 
  • For example, if you would like the MS to be awarded in Spring, you must reach out before the end of Week 2 of Spring to request the MS. In this example you are also welcome to reach out at the end of Winter quarter to give the Coordinator additional time to process your request. 
  • Failure to notify the Coordinator BEFORE the end of Week 2 will result in a delay of the award of the MS to the following quarter.

2) The Bioengineering Coordinator of Graduate Affairs will submit, via DocuSign, a “Master’s Application to Candidacy” Form to the Division of Graduate Education & Postdoctoral Affairs (GEPA) before the end of Week 2. 

• The GEPA typically takes 3-5 weeks to process this form, and once processed, will notify the Coordinator.

3) After the “Master’s Application to Candidacy” Form has been processed, the Coordinator will submit, via DocuSign, a “Master’s Final Report” Form for the MS Plan II degree before the end of the quarter. 

4) After the end of the quarter, the GEPA will process the Final Report Form. 

• After they have processed the form, they will forward it to the Registrars’ Office for additional processing. 
• This processing can take 1-3 months after the quarter has ended.  

5) You receive your MS degree! 

• The degree conferral date listed will be the last day of the quarter. 
• The degree usually takes 1-3 months to process, as noted above, and post to your Academic History and official transcript. 
• After the degree has been processed, your diploma is mailed to you to the permanent address listed on your TritonLink account. Please make sure your permanent address is up-to0date in TritonLink. You should expect the diploma to arrive in the mail 3-6 months after the quarter has ended.

 

How to Constitute and Reconstitute a Doctoral Committee

 

Outlined below is the process to constitute, or set up, a Doctoral Committee and how to request a reconstitution if changes need to be made to a previously constituted committee.

Initial Committee Constitution

1)  You should meet with your research advisor to discuss who should be appointed to your committee.

• A doctoral committee has four members, with the option to add an additional “fifth member” as appropriate.   
• The University requires that:
  • A minimum of four members with UC San Diego faculty appointments 
  • At least two members of your committee be from your home department (Bioengineering)
  • At least one member must have a primary appointment in a department different from the chair’s primary department
  • At least one member must be tenured or emeritus 
• More information about committee requirements can be found in the "Appointment of the Doctoral Committee" section of Division of Graduate Education & Postdoctoral Affairs (GEPA)’s website.
• The GEPA has a Master's & Doctoral Committee Membership Table that provides guidance on who can serve on a doctoral committee

2)  Once you have discussed your committee with your research advisor, email your finalized list to the Bioengineering Coordinator of Graduate Affairs. 

• In the email please include the following information for EACH committee member:
  • First and last name
  • Academic rank (e.g. “Associate Professor”)
  • Home department 
  • Committee status (e.g. Chair, Co-Chair, or regular committee member)
• Please provide this list at least three weeks before your Senate Exam to allow time for it to get processed.

3)  The Bioengineering Student Affairs Office will electronically route your committee request to the Department Chair and to the Dean of the GEPA for review. 

• You cannot take the Senate Exam until the Graduate Dean approves your committee. If you have not received an email from the Dean approving your committee by one week before your exam, please contact the Bioengineering Coordinator of Graduate Affairs. 

4)  You will get an email notice from the Dean when your committee is approved. Congratulations, your committee has been constituted!    

Reconstituting an Established Committee

If you need to make changes to a committee that has already been constituted, you will need to make a request to reconstitute the committee. Typically a reconstitution is needed to add or remove faculty on the committee, make changes to committee member status (i.e. chair/ co-chair versus regular member), to be in compliance with Conflict of Interest (COI) concerns, and update faculty titles.

1)  Meet with your research advisor to discuss what changes need to be made to your committee.

• Keep in mind, the GEPA has a Master's & Doctoral Committee Membership Table that provides guidance on who can serve on a doctoral committee.

2)  Once you have discussed the changes to be made to your committee with your research advisor, email your updated list to the Bioengineering Coordinator of Graduate Affairs. 

• In the email please include the following information for EACH committee member:
  • First and last name
  • Academic rank (e.g. “Associate Professor”)
  • Home department 
  • Committee status (e.g. Chair, Co-Chair, or regular committee member)
• In the email you must also provide a justification or explanation for EACH change being made to the committee. This is required in order to submit the reconstitution request.

3)  The Bioengineering Student Affairs Office will electronically route your committee request to your Committee Chair, the Department Chair, and to the Dean of the GEPA for review. 

4)  You will get an email notice from the Dean when your committee reconstitution request is approved. Congratulations, your committee has been reconstituted!  

 

The Senate Exam Process

 

1)  Discuss your Senate Exam with your faculty advisor so you know what is expected of you, including what written materials you will need to prepare.

2)  Notify the Bioengineering Coordinator of Graduate Affairs via email about your intent to take the Senate Exam.

• To allow adequate time, you should do this at least four weeks before the time you expect to take the Senate Exam. 

3)  Constitute, or set up, your Doctoral Committee. See the separate section “How to Constitute and Reconstitute a Doctoral Committee” in this handbook for more information.

4)  Once you have submitted your committee to the Bioengineering Student Affairs Office and as you await your committee approval, you can start scheduling your Senate Exam. 

• You can reserve PFBH conferences 291, 391 or the Zweifach Library (489) by emailing be-reservations@ucsd.edu if interested in holding your exam in PFBH.
• As soon as you have set the date, time, and location of your Senate Exam, you should notify the Coordinator of Graduate Affairs at least two weeks in advance of your Senate Exam. This allows time for the office to get your academic file ready for the exam. 
• Make sure you have notified all of your committee members of the date, time, and location of your Senate Exam.

5)  Your committee is approved, you have set the date/ time/ location of your Senate Exam – you are ready to take the Senate! The Bioengineering Student Affairs Office will prepare the Application to Candidacy (Report) Form for your Senate Exam via DocuSign, and route it to you and your committee on the day of your Senate Exam. 

• You and your committee members will receive an email notification describing the DocuSign process on the day of your Senate Exam. 
• Your committee will sign the Report Form via DocuSign after you successfully pass the Senate. 
• DocuSign will then route the Report Form to our Department Chair for signature before routing to the Division of Graduate Education & Postdoctoral Affairs (GEPA)  and the Registrar’s Office for processing. 

6)  Before the Report Form is fully processed, you will be responsible for paying a $50 Candidacy Fee. 

• This fee will be charged to your TritonLink account, so monitor your student account activity regularly so you can pay the fee as soon as it is charged.

7)  You will receive an official notice from the Dean of the GEPA of your successful advancement. Congratulations you are now in-candidacy!

 

The Dissertation Defense Process

 

Outlined below is the administrative process to follow when preparing for your PhD Dissertation Defense.

1)  Discuss your defense with your faculty advisor and doctoral committee so you know what is expected of you, including what written materials you will need to prepare and what deadlines they may have for you. 

• Work with your faculty advisor and doctoral committee directly to schedule your defense. Students frequently use Doodle or when2meet to determine a suitable day and time. 
• Keep in mind that it is GEPA policy to make (at least) a draft of your written thesis available to your thesis committee four weeks in advance. When providing thesis materials to the thesis committee, students must cc the Bioengineering Coordinator of Graduate Affairs in this communication to ensure compliance with this academic policy. Failure to provide a written draft 4 weeks in advance of an oral thesis could result in graduation delays.

2)  Notify the Bioengineering Coordinator of Graduate Affairs via email about your intent to hold your defense.

• You can make a request to reserve the Fung Auditorium on our Fung Auditorium page if interested in holding your defense in PFBH
• As soon as you have set the date, time, and location of your defense, you should notify the Coordinator of Graduate Affairs at least two weeks in advance of your defense. This allows time for the office to get your academic file ready.
• Make sure you have notified all of your committee members of the date, time, and location of your defense.

3)  Before your defense date, you will need to schedule a “Preliminary Appointment” with the Division of Grduate Education & Postdoctoral Affairs (GEPA) to review required paperwork and information. Appointments can be scheduled via the GEPA's Calendar. 

• Helpful information about this process and the preliminary appointment can be found on the GEPA’s Dissertation & Thesis Submission page.
• Make sure to review the “Preparation and Submission Manual for Doctoral Dissertations and Master's Theses” provided at the link above.
• You may also want to schedule a “Final Appointment” at this time for after your defense. You may use the same calendar as above to do this.

4)  At least a few days to a week before your defense you will need to send an email notice to be-people@ucsd.edu announcing your defense. A template for the announcement is provided below for your reference.

Email Subject Line: PhD Dissertation Defense Announcement - [Student’s Name]   Email Body: UC San Diego Department of Bioengineering Ph.D. Dissertation Defense   [Student’s Full Name]   ["dissertation title"] [date] [time]   [if via Zoom] Due to public health concerns, this defense will be open to the public via Zoom: [Zoomlink, password]   [if in-person: location, including building and room number]   Committee in Charge                                     [Committee List]                                   Abstract [abstract]

 

5)  On the day of your defense, the Bioengineering Student Affairs Office will prepare the Doctoral Final Report Form for your defense via DocuSign, and route it to you and your committee. 
You and your committee members will receive an email notification describing the DocuSign process on the day of your defense. 

• Your committee will sign the Final Report Form via DocuSign after you successfully complete your defense. 
• DocuSign will then route the Final Report Form to our Department Chair for signature before routing to the GEPA and the Registrar’s Office for processing. 

6)  After your defense you will prepare all of your final paperwork to submit in time for your Final Appointment with the GEPA. 

• Keep in mind the deadline to submit all final paperwork to the GEPA in time to receive your degree that same quarter is always the last day of that quarter. For example, if you wanted to receive your degree in Spring, you would need to have your defense and submit all final paperwork to the GEPA before the last day of Spring quarter. 

7)  You will receive an official notice from the Dean of the GEPA of your degree conferral. Congratulations, you have been awarded your PhD!

• The degree conferral date listed will be the last day of the quarter. 
• The degree usually takes 1-3 months to process and post to your Academic History and official transcript after the quarter has ended. 
• After the degree has been processed, your diploma is mailed to you to the permanent address listed on your TritonLink account. Please make sure your permanent address is up-to-date in TritonLink. You should expect the diploma to arrive in the mail 3-6 months after the quarter has ended.