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BERKELEY CONNECT IN
COMPUTATIONAL BIOLOGY

The Berkeley Connect program opens up the extraordinary resources of the University to you: the extraordinary students on our campus. By joining, you will become part of a community of like-minded faculty, mentors, and students that will provide a supportive environment in which to exchange and discuss ideas and goals. Berkeley Connect will help you make the most of your time at the University as you learn more about the emerging field of Computational Biology. We are excited to get to know you.

Message from the Director

Nicholas IngoliaThe future of biological innovation will be created by a new generation of biologists who are as comfortable with computational and statistical analysis as they are with laboratory work. Berkeley Connect in Computational Biology is a mentoring program that accepts students from the biological or mathematical/computational sciences with a serious interest in computational biology.

Students joining the program will:

  • Become part of a community of active and engaged students with a serious interest in both computation and biology.
  • Become exposed to research, and get to meet researchers, in computational biology.
  • Receive mentoring and advice in how to structure an educational program combining computation and biology at UC Berkeley.
  • Get the opportunity to participate in special events and to join field trips to companies in the Bay Area that employ computational biologists.

Berkeley Connect in Computational Biology is offered in the Fall semester only.

Nicholas Ingolia
Faculty Director, Berkeley Connect in Computational Biology

Program Description

Berkeley Connect links undergraduate students with experienced mentors in Computational Biology. These mentors lead small groups (not more than 20) students in regular meetings; they also meet with students one-on-one to provide guidance and advice. The core of the Berkeley Connect program is a one-credit, pass-fail course that is designed to create a community of students with similar intellectual interests.There is no homework associated with Berkeley Connect: no exams, no papers, no quizzes. Instead, small group meetings focus on sharing ideas and learning new skills related to Computational Biology as a way to foster friendships and provide a supportive intellectual community for Berkeley undergraduates.There is not currently an undergraduate degree program in Computational Biology at UC Berkeley. Berkeley Connect in Computational Biology is designed for students with an intended or declared major in the biological or mathematical/computational sciences who have a serious interest in the interdisciplinary field of computational biology.

Every semester, Berkeley Connect sponsors a wide range of activities and events for participating studentsThey include:

  • small-group meetings led by your mentor;
  • one-on-one meetings with your mentor;
  • special events, including informal lectures by professors and guest speakers, and panels on career options, graduate school admissions, and other topics;
  • and visits to Berkeley resources.

At the heart of Berkeley Connect is the relationship between you and your mentor. The Berkeley Connect mentors are advanced graduate students or recent PhDs in Computational Biology, who are chosen both for their demonstrated commitment to undergraduates and for their scholarly achievement. They are dedicated to providing the kind of close-knit community and one-on-one attention that can be hard to find at a large university.

When you sign up for Berkeley Connect, you will join one of the small groups of participants in Computational Biology. Your small group will be led by your mentor, and will meet every other week during the semester for an hour-long dinner discussion sessions. Discussions will focus on key intellectual issues within Social Welfare as well as key skills you need to succeed in the major. Above all, the small groups will focus on building connections among students, so that each group becomes a supportive community for all participants.

You will also meet with your mentor one-on-one at least twice during the semester, once to get acquainted, and a second time just before Tele-Bears, to discuss your plans for completing your major. Your mentor also has office hours every other week, during which you are free to show up and ask questions, talk over your day or your week, discuss what you are learning in class, or just have an informal conversation.

Faculty

Nicholas IngoliaNicholas Ingolia is an Assistant Professor of Molecular and Cell biology and a core member of the Center for Computational Biology at UC Berkeley. His research focuses on the regulation of translation in order to understand how and why some mRNAs are translated better than others and some mRNAs show marked shifts in translation under different conditions. His lab develops and applies global and high-throughput experimental approaches to understand translational regulation and relies heavily on computational and statistical analysis of data from these experiments. Most notably, he developed the ribosome profiling technique for profiling translation by deep sequencing, and his lab continues to refine this methodology as well as applying it to a broad range of questions, ranging from the basic molecular mechanisms underlying translational control through its impact on human health and disease. You can learn more about the Ingolia lab here.

Berkeley Connect Mentors

Amanda MokAmanda Mok is a second-year graduate student in Computational Biology. She is interested in uncovering the genetic and epigenetic factors that influence human health. Before starting the PhD program, Amanda studied Biological Engineering and Music at MIT, and Epidemiology/Biostatistics at the UC Berkeley School of Public Health. Outside the lab, she performs regularly on piano and violin with various classical music ensembles in the Bay Area. She is very excited to be a Berkeley Connect Fellow and to help expose UC Berkeley undergraduates to the field of computational biology!

Amanda Mok, a.mok@berkeley.edu

Office Hours: Tuesday 2-3:30pm, event weeks only (otherwise, please email) in 467 Evans


Syllabus

Attendance Policy: All events are mandatory unless stated otherwise, so please plan to attend every event. If you have conflicts, please let your mentor know ASAP.

Grades: This course is Pass/Not Pass. To pass, you must complete the following items:

  1. Attend small group
  2. Attend two 1:1 meetings with your mentor.
  3. Attend special events (unless you have a legitimate excuse, such as class, practice, work, etc.)
  4. Complete the end-of-semester survey.

Events: Most events will be held Wednesday 5-6:30pm, and small group meetings are Wednesdays 5-6pm (CMPBIO 198BC) or 6-7pm (CMPBIO 98BC). Speakers and panelists are volunteering their time to answer questions and tell you about their experiences. Please be respectful and attentive. This is a rare opportunity to ask lots of questions about their past and current experiences in computational biology. There will also be two field trips – two lab visits on campus and one SF trip – but if you cannot make either of the available options, please let your mentor know.

Food: All events held in HMB 310 will also provide dinner. Your mentor will have to clear all traces of food from the classroom, so please make sure to clean up after yourself to lighten up the cleaning load. Let your mentor know by email if you have any food allergies or restrictions.

1:1 Meetings: There will be two required 1:1 meetings with your mentor – one early on to meet your mentor, and another mid-semester to discuss future courses/plans/etc. A sign-up sheet will be posted on bCourses once ready. This is a great opportunity to get to know your mentor, and for them to get to know you!

DSP Policy: Please contact your mentor by email ASAP to discuss and arrange options if needed.

Safety: We generally meet in the evening, and as the semester advances, it may be dark as you leave class. Get a BearWALK escort to walk you home (in service from dusk to 4am) through BearWALK.berkeley.edu or by calling (510) 642-9255; or take a Night Safety Shuttle. Try not to walk alone, and pay attention to your surroundings!

Schedule of Events (subject to change – see bCourses for announcements!)

Date Details Time
Wed Aug 23 Welcome Event 5pm to 6:30pm
Wed Aug 30 What is computational biology? CMPBIO 198BC

CMPBIO 98BC

 

5pm to 6pm 6pm to 7pm

Sept 5-7 1:1 Meetings
Wed Sept 13 Campus Lab Visit: Genomics Sequencing Lab 5pm to 6:30pm
Wed Sept 20 Getting Involved in Research CMPBIO 198BC

CMPBIO 98BC

 

5pm to 6pm 6pm to 7pm

Wed Sept 27 Graduate Student Panel 5pm to 6:30pm
Wed Oct 4 Challenges in Computational Biology CMPBIO 198BC

CMPBIO 98BC

 

5pm to 6pm 6pm to 7pm

Wed Oct 11 UCSC Genome Browser Tutorial CMPBIO 198BC

CMPBIO 98BC

 

5pm to 6pm 6pm to 7pm

Wed Oct 18 Student Advisor Panel 5pm to 6:30pm
Wed Oct 25 Industry Field Trip TBA
Oct 31 – Nov 3 1:1 Meetings
Wed Nov 8 Career Panel 5pm to 6:30pm
Wed Nov 15 Career Goals Discussion CMPBIO 198BC CMPBIO 98BC  

5pm to 6pm 6pm to 7pm

Wed Nov 22 THANKSGIVING BREAK
Wed Nov 29 Future of Computational Biology Faculty Talk 5pm to 6:30pm
Wed Dec 6 RRR Week – Study Break (optional) 5pm to 6:30pm

Schedule

To find sections in the upcoming semester, search the Schedule of Classes for Computational Biology 98BC (for first-year and sophomores) or 198BC (for juniors and seniors).

To help you meet other students who share your experiences and perspectives, Berkeley Connect sections are designated as lower division (first-year students and sophomores), new junior transfers, and upper division (juniors and seniors), but you can enroll in any section that fits your schedule and credit requirements.

To get on the Berkeley Connect in Computational Biology mailing list, please fill out this interest form.

How to Sign Up

To participate in Berkeley Connect in Computational Biology, you enroll in a section of Computational Biology 98BC or 198BC (one unit, taken on a Pass/Not Pass basis).The Berkeley Connect in Computational Biology pilot program is designed to serve students in biological or mathematical/computational science majors who have indicated their interest in this particular area of study. If you are interested in this field and would like to be added to our mailing list, please fill out this interest form.

Contact Us

Please see our FAQs.  If you have additional questions about Berkeley Connect in Computational Biology, please contact:  Nir Yosef, Faculty Director, Berkeley Connect in Computational Biology, niryosef@berkeley.edu.

Xuan Quach, Administrative Director, Center for Computational Biology,  xuquach@berkeley.edu

You can also contact the central Berkeley Connect office  at berkeleyconnect@berkeley.edu or (510)664-4182.

Links & Resources