UCLA Bioinformatics: The Philosophy of the Undergraduate Program

Bioinformatics is an important interdisciplinary research area with tremendous opportunities in graduate training and industry employment.  Yet, few academic institutions offer undergraduate programs designed to prepare students for opportunities in Bioinformatics.

The UCLA Undergraduate Bioinformatics Minor is an academic program established in Fall 2012 at UCLA.  Undergraduates in any Major can obtain a Bioinformatics Minor by completing an additional 8 courses. Since Fall 2012, approximately 80 students have joined the Minor program. These students represent Majors in over a dozen UCLA departments, including: Computer Science; Chemistry; Molecular, Cell, & Developmental Biology; Microbiology, Immunology, and Molecular Genetics; Ecology and Evolutionary Biology; and Computational and Systems Biology.

Over 45 faculty specializing in computational and experimental biology are associated with the Bioinformatics Minor, spanning the fields of biology, mathematics, engineering, and medicine. Course offerings from more than 12 unique departments allow the Minor program to encompass the breadth of the growing Bioinformatics field.

Here we describe the principles and philosophy that guided the design of our Minor.

  1. Our Core Bioinformatics Courses Teach Interdisciplinary Computation. The foundation of our program is the cluster of three integrated core courses in Bioinformatics. These courses are truly interdisciplinary; they satisfy elective requirements in multiple departments and recruit students from different Majors to the Minor program. These core courses build upon the philosophy that students must first learn fundamental concepts in computation in order to later explore problems in Bioinformatics.  These courses offer basic skills and appeal to many students beyond those interested in Bioinformatics.
  1. Rigorous Background in Computation. To be successful in Bioinformatics, students must have a solid background in both computation and Biology. Our core courses require as prerequisites a substantial background in computation and statistics. To enter the Minor, we require that students have completed one year of programming and one upper division Statistics course.  To complete the Minor, our students take Linear Algebra and one upper division course on Algorithms taught by the Computer Science or Math Department.  Our students also take a Molecular Biology course taught by the Life Sciences Department. We believe that it is important for faculty in Computer Science and Program in Computing to teach programming, and for faculty in the Life Sciences to teach Biology. Further, it is important for students to take the same programming classes as do their peers in Engineering majors, and for students to take the same Biology classes alongside their peers in Life Sciences.
  1. The Bioinformatics Minor Builds upon the Students’ Major. Every student graduating from UCLA with a Bioinformatics Minor also completes an academic Major program. While we do adjust the Minor curriculum to help students efficiently complete both their Major and Minor requirements within 4 years, each of our graduates has exactly the same amount of training in their Major as fellow Majors who are not in the Minor.  This avoids a common pitfall in interdisciplinary education: students only receive a superficial background in each academic area.
  1. Bioinformatics is a Research Oriented Field. Our Minor is closely integrated with our undergraduate research program, which places students in the labs of Bioinformatics faculty. Most of the Bioinformatics Minors at UCLA are working in a research lab.  Undergraduates are strongly encouraged to engage in research. The Minor allows for a substantial amount of research credits, an allowance that helps students complete their Major and Minor requirements in four years.  In addition, many of our undergraduates participate in the Bruins-in-Genomics Summer (B.I.G. Summer) program or similar undergraduate education experience summer programs.
  1. Bioinformatics is an Increasingly Diverse Field. The core courses in Bioinformatics are designed to be interesting and accessible to students from a wide variety of educational backgrounds. Each course typically has enrollment approaching 100. Far more students who are not in the Bioinformatics Minor take these courses as electives to fulfill their Major requirements. Student enthusiasm is high for these accessible interdisciplinary courses that combine computational sciences and Biology. We find that this approach boosts broader undergraduate engagement in the field and encourages students from traditionally underrepresented groups to pursue research, graduate school, or careers in STEM fields.
  1. Let Excitement Foster Program Growth. Bioinformatics is an exciting area, and specialized training is critical for the next generation of biomedical researchers. However, undergraduate Bioinformatics programs, when offered by a college or university, are typically quite small.  Such programs are often limited in size and engagement as students are unaware of the field or become aware of Bioinformatics late in their college career. We strategized the Bioinformatics Minor program at UCLA specifically to attract students at any stage of their college career and to maximize curricular flexibility so students can easily complete Minor requirements. Many students are attracted to the Minor when they enroll in Bioinformatics core courses to fulfill elective requirements for their Major; some develop a keen interest in the field and then join the Minor. Even students who are unable to complete all Minor requirements benefit from our program; they complete key coursework and join a research lab, gaining knowledge and experience crucial for gaining employment or admission to graduate school.

Our current goal for the Bioinformatics Minor is to graduate 50 students per year.  We hope that 10 to 20 of them will enter graduate studies in Bioinformatics.  We are not there yet, but are growing. This year, around 10 graduates applied to Ph.D. programs in Bioinformatics.  Many of our students recently began or are applying to Ph.D. programs in Bioinformatics and related areas.  We expect that they will do very well in the admissions process and have great backgrounds for starting Ph.D. study in Bioinformatics.


Read more about the Bioinformatics Minor on the official website:

Check out a list of research opportunities available for undergrads at UCLA:

Learn more about 2016 undergraduate research and B.I.G. Summer activities at ZarLab:

Applications to the 2017 B.I.G. Summer program are due January 27:

UCLA Launches CGSI with Inaugural Summer Programs

In 2015, Profs. Eleazar Eskin (UCLA), Eran Halperin (UCLA), John Novembre (The University of Chicago), and Ben Raphael (Brown University) created the Computational Genomics Summer Institute (CGSI). A collaboration with the Institute for Pure and Applied Mathematics (IPAM) led by Russ Caflisch, CGSI aims to develop a flexible program for improving education and enhancing collaboration in Bioinformatics research. In summer 2016, the inaugural program included a five-day short course (July 18-22) followed by a three-week long course (July 22 to August 12).

Over the past two decades, technological developments have substantially changed research in Bioinformatics. New methods in DNA sequencing technologies are capable of performing large-scale measurements of cellular states with a lower cost and higher efficiency of computing time. These improvements have revolutionized the potential application of genomic studies toward clinical research and development of novel diagnostic tools and treatments for human disease.

Modern genomic data collection creates an enormous need for mathematical and computational infrastructures capable of analyzing datasets that are increasingly larger in scale and resolution. This poses several unique challenges to researchers in Bioinformatics, an interdisciplinary field that cuts across traditional academic fields of math, statistics, computer science, and biology—and includes private-industry sequence technology developers. Innovation depends on seamless collaboration among scientists with different skill sets, communication styles, and institution-driven career goals. Therefore, impactful Bioinformatics research requires an original framework for doing science that bridges traditional discipline-based academic structures.

The summer 2016 courses combined formal research talks and tutorials with informal interaction and mentorship in order to facilitate exchange among international researchers. Participants in the short program attended five full days packed with lectures, tutorials, and journal clubs covering a variety of cutting-edge techniques. Senior trainees, including advanced graduate students and post-docs, underwent additional training through the long program’s residence program. The extended program enabled these scientists to interact with leading researchers through a mix of structured training programs and flexible time for collaboration with fellow participants and other program faculty.

Collaboration on a wide variety of problem types and research themes facilitated cross-disciplinary communication and networking. During both courses, CGSI participants shared technical skills in coding and data analysis relevant to genetic and epigenetic imputation, fine-mapping of complex traits, linear mixed models, and Bayesian statistics in human, canine, mouse, and bacteria datasets. Scholars at different stages of their careers explored application of these methods, among others, to emerging themes such as cancer, neuropsychiatric disorders, evolutionary adaptation, early human origins, and data privacy.

CGSI instructors and participants established mentor-mentee relationships in computational genomics labs at UCLA, including the ZarLab and Bogdan Lab, while tackling practical problems and laying groundwork for future publications. In addition, participants developed comradery and professional connections while enjoying a full schedule of social activities, including dinners at classic Los Angeles area restaurants, volleyball tournaments in Santa Monica, bike rides along the beach, morning runs around UCLA campus, and even an excursion to see a live production of “West Side Story” at the Hollywood Bowl.

CGSI organizers thank the National Institutes of Health grant GM112625, UCLA Clinical and Translational Science Institute grant UL1TR000124, and IPAM for making this unique program possible. We look forward to fostering more collaboration between mathematicians, computer scientists, biologists, and sequencing technology developers in both industry and academia with future CGSI programs.

Visit the CGSI website for an up-to-date archive of program videos, slides, papers, and more:

Enrollment in 2017 CGSI programs opens this fall with a registration deadline of February 1.

This slideshow requires JavaScript.

Video Tutorial: Serghei Mangul’s Introduction to UNIX Workshops

We present three video recordings of workshops that ZarLab postdoctoral scholar Serghei Mangul developed under the UCLA Institute for Quantitative and Computational Biosciences Collaboratory and delivered to Bruins-In-Genomics (B.I.G.) SUMMER participants. B.I.G. SUMMER is an intensive, practical experience in genomics and bioinformatics for undergraduate students who are interested in integrating quantitative and biological knowledge and considering pursuing graduate degrees in the biological, biomedical, or health sciences.

An important question for undergraduates considering careers in the biosciences is whether or not biologists need to develop robust programming skills. Biology students without backgrounds in computer science are often intimidated by applications that require inputting code or negotiating systems that lack a graphical interface, such as Unix, R, SASS, and Python.


“Becoming a programmer” may seem daunting to many students in biology, but an ability to analyze sequencing data represents a competitive advantage in today’s age of big data and next generation sequencing. By gaining familiarity with Unix, these students may find it easier to engage with other applications and programming languages commonly used in computational biology. In order to use Unix effectively, students must learn how to directly enter functional commands line-by-line into a workbench that manages multiple platforms and a unified filesystem—without the familiar aid of a graphical interface.

In this three-part series of workshops, Dr. Mangul provides just enough information for students with no computational background to get started using Unix for analytical tasks. These workshops aim to help participants learn key commands and develop fundamental skills, such as connecting, writing, and submitting basic shell scripts to a cluster.

Slides and more information about the workshop are available at the following webpage:

Introduction to UNIX 1/3

Introduction to UNIX 2/3

Introduction to UNIX 3/3