Serghei Mangul and Lana Martin, together with Alexander Hoffmann, Matteo Pellegrini, and Eleazar Eskin, recently published a paper describing a workshop model for training scientists, who have no computer science background, to use UNIX. Our paper is available online as a preprint and will appear in an upcoming “Scientific Life” section of Trends in Biotechnology.
Scientists who are not trained in computer science face an enormous challenge analyzing high-throughput data. Serghei developed a series of workshops in response to growing demand for life and medical science researchers to analyze their own data using the command line.
Administered by UCLA’s Institute for Quantitative and Computational Biosciences (QCBio), these workshops are designed to help life and medical science researchers use applications that lack a graphical interface. Our paper presents a training model for these workshops—a flexible approach that can be implemented at any institution to teach use of command-line tools when the learner has little to no prior knowledge of UNIX.
QCBio currently offers similar workshops to the UCLA community. In tandem with this publication, we created an online catalogue of resources and papers aimed to provide first-time learners with basic knowledge of command line: https://smangul1.github.io/command-line-teaching/.
We encourage fellow instructors of Bioinformatics, as well as scientists who are new learners of the command line, to read our paper and share their thoughts! Email us at: lana [dot] martin [at] ucla [dot] edu.
The full citation of our paper:
Mangul, Serghei, Martin, Lana S., Hoffmann, Alexander, Pellegrini, Matteo, and Eskin, Eleazar. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends in Biotechnology; doi: 10.1016/j.tibtech.2017.06.007.
Advance preprint copies of our paper may be downloaded here: http://www.cell.com/trends/biotechnology/fulltext/S0167-7799(17)30156-7
On Wednesday, June 7, faculty, staff, and undergraduates began a new tradition for the UCLA Bioinformatics Minor Program. Prof. Eleazar Eskin, chair of the Minor Program, hosted the first annual Bioinformatics Minor End-of-Year Celebration to recognize and celebrate undergraduates who completed the requirements for the Minor.
This year’s celebration took place in the Hacienda Room at the Faculty Center. In attendance were faculty and staff from the Schools of Medicine, Engineering, and Life Sciences, and from the Office of Academic and Student Affairs. The reception kicked off with a poster session presenting research completed during the Minor program. As a founding faculty member of the Minor, Prof. Eskin shared a few remarks on the small-scale origins—and upward-scaling trajectory—of the Minor Program. Since 2012, the Minor has succeeded at providing non-computational students with a solid foundation in, and familiarity with, active research problems at the interface of computer science, biology, and mathematics.
Greg Darnell, a UCLA alumnus who completed the Bioinformatics Minor in 2013 and is now a PhD student in Bioinformatics at Princeton, delivered a keynote speech. Mr. Darnell emphasized the extent to which the field of Bioinformatics has changed since he began coursework and research as an undergraduate at UCLA in the early 2010s. Recent “big data” explosions in the Biosciences have created exciting challenges and opportunities for emerging scholars—such as the graduates honored at this reception.
Twenty students were awarded certificates of recognition for their intellectual curiosity, creativity and dedication to interdisciplinary studies. These students join a unique and exemplary group of Bioinformatics Minor graduates who have made their mark in one of UCLA’s most challenging and unique academic programs, spanning Engineering, Biology, and Medicine.
In addition, Prof. Eskin presented three cash research awards to students, Brandon Jew, Ruth Johnson, and Michael Thompson, who demonstrated exceptional talent in their Bioinformatics research projects. Faculty and staff associated with the UCLA Bioinformatics Minor Program are excited to continue this new tradition, including the awarding of certificates and research awards, in future Spring quarters.
Congratulations to the 2016-17 graduates and graduating seniors in the Bioinformatics Minor! In addition to this year’s graduates, a certificate of recognition was also presented to past graduates Leah Briscoe (‘16), Alec Chiu (’16), and Greg Darnell (‘13). Go Bruins!
2016-17 Bioinformatics Minor Graduates:
Christian Garrison St Pierre
Anthony Bohr Zhu
See other blog posts on undergraduate training at UCLA:
This month, the editors of The American Journal of Human Genetics interviewed Eleazar Eskin and Farhad Hormozdiari on their recent paper, “Widespread Allelic Heterogeneity in Complex Traits.” Read the full interview here: