Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX

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:

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:

About Lana Martin

i write and teach.