B.I.G. Summer in ZarLab

This summer, six young adults engaged in a unique eight-week learning experience with ZarLab, learning practical skills in genomics and bioinformatics while conducting research on large-scale human genetic datasets. These four undergraduate students participated in the Bruins-In-Genomics (B.I.G.) Summer Program, an intensive laboratory and seminar program aimed at providing real-world experience for students who are interested in pursuing interdisciplinary graduate education in the quantitative and biological sciences. In addition, two Los Angeles-area high school students participated in laboratory activities as volunteer researchers.

Eleazar Eskin, co-organizer of the summer program, and Serghei Mangul, post-doctoral scholar, hosted the young scholars in ZarLab, a UCLA computational genetics group affiliated with both the Computer Science Department and the Human Genetics Department. Mangul supervised a group of students who collaborated on a project aimed at developing computational methods for the study of the human immune system and microbiome. Working with data from one of the largest sequencing projects in the world, the Genotype-Tissue Expression (GTEx) study, the students analyzed more than 8,000 samples obtained from 544 individuals and representing 53 different tissue types. In doing so, they gained familiarization with current approaches to studying how changes in our genes contribute to common human diseases.

During a poster session on August 12, 2016, the B.I.G. participants presented the results of their work on GTEx:

  • Jeremy Rotman: “Studying the microbiome by analyzing the coverage of sequencing reads mapped to viruses, eukaryotes, and bacteria”
  • Benjamin Statz: “An improved method for analysis of variable domain of B and T cell receptors”
  • William Van Der Wey: “Functional profiling of microbial communities across multiple human tissues”
  • Kevin Wesel: “Profiling repeat elements across multiple human tissues”

In addition to mentoring B.I.G. Program students in ZarLab, Mangul developed and presented a three-part series of workshops introducing students to UNIX earlier during the program.

Eskin and Mangul also hosted a B.I.G. Program student, Samantha Jenson, who collaborated with Jonathan Flint, a world-renowned authority on the genetics of depression and co-director of UCLA’s Depression Grand Challenge. This year, Eskin facilitated a Neurogenetics working group and weekly neurogenetics seminar series for the B.I.G. Program. Participants in this group gained first-hand experience in the process of developing methods for mapping the underlying genetic causes of Major Depression Disorder. Jenson presented her work on “Structural variant discovery in Major Depression Disorder” during the August 12th poster session.

The annual B.I.G. Program is a collaboration between multiple labs and includes next generation sequencing analysis workshops, weekly science talks by researchers, a weekly student journal club, professional development seminars, social activities, concluding poster sessions, and an optional GRE test prep course. Participants also benefited from relevant workshops and research talks presented during the UCLA Computational Genomics Summer Institute (CGSI).

Congratulations to Benjamin, Jeremy, Kevin, Samantha, and William on their acceptance to and success in the B.I.G. Summer Program!

This slideshow requires JavaScript.

We thank the following generous institutions that made this year’s B.I.G. Summer Program a big success:

  • National Institutes of Health grant MH109172
  • UCOP for a UC-HBCU partnership Program in Genomics and Systems
  • NIH NIBIB for NGS Data Analysis Skills for the Biosciences Pipeline  R25EB022364
  • NIH NIMH for Undergraduate Research Experience in Neuropsychiatric Genomics R25MH109172-01

Learn more about the B.I.G. Program:
UCLA Newsroom: UCLA hosts summer program for future biosciences leaders
http://newsroom.ucla.edu/releases/ucla-hosts-summer-program-for-future-biosciences-leaders

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.

Capture

“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:
qcb.ucla.edu/collaboratory/workshops/collaboratory-workshop-1/

Introduction to UNIX 1/3
https://www.youtube.com/watch?v=liC5uM8czyo

Introduction to UNIX 2/3
https://www.youtube.com/watch?v=ArbOG6YpakU

Introduction to UNIX 3/3
https://www.youtube.com/watch?v=PHmfgIuOMFQ

 

UCLA Computational Genomics Summer Institute

ipam-logoDear Colleagues,

I am happy to announce the UCLA Computational Genomics Summer Institute, which is a new National Institutes of Health funded program at UCLA jointly hosted with the Institute of Pure and Applied Mathematics (IPAM). The program will take place each summer for one month. The dates for 2016 are July 18th – August 12th.

The program focuses on providing training in methodology development for genomics. We hope that it will be of interest to researchers at all levels. Our program builds upon a successful program hosted by IPAM in 2011 on “Mathematical and Computational Approaches in High Throughput Biology.” IPAM is a national math institute funded by the National Science Foundation.

The program consists of two parts. The first part (July 18th – July 22nd) is the Short Program which is in the format of a short course consisting of lectures from leading researchers in computational genomics. The short program is appropriate for researchers at all levels including both researchers actively involved in methodology development as well as other researchers who want to incorporate a methodology development aspect to their research program.

The second part (July 21st – August 12th) is the Long Program which is a continuation of the Short Program. The program is in the style of a typical long program hosted at IPAM where participants have opportunity to interact and collaborate with each other as well as the leading researchers who will serve as program faculty. The program is targeted toward senior trainees such as senior students or post-docs through established researchers.

Researchers at all levels — students, post-docs, staff researchers, as well as junior and senior faculty — are encouraged to participate in the program. Funding is available to support faculty and participant costs during the program. Because space is limited in the program, we are requiring interested participants and potential program faculty to apply as soon as possible.

Application materials are available on the program website (http://computationalgenomics.bioinformatics.ucla.edu). For questions about the program, interested individuals should email uclacgsi@gmail.com.

Sincerely,
The UCLA CGSI Organizing Committee
Eleazar Eskin, UCLA, CGSI Director
Russel Caflisch, UCLA. IPAM Director
Eran Halperin, Tel Aviv University
John Novembre, University of Chicago
Ben Raphael, Brown University