Intro to BASH and the command-line shell

The Hacker Within

In this session, we will attempt to teach Bash (i.e. the Unix shell, the thing that you have on your Mac that opens when you click Terminal) from an introductory to an intermediate/advanced level. Windows users: some versions of Windows 10 have a Linux subsystem, but you can also install Cygwin to follow along.

We’ll start from basics of the shell and attempt to get all the way to some advanced stuff (I’m being vague on purpose; we’ll stop and answer questions so that might determine our endpoint).

Invite your friends, especially those who are scared of command line interfaces but still want to know things! We’ll be in BIDS / 190 Doe Library starting at 5pm on Wednesday. As always, we’re a come when you can / leave when you need to sort of group, but we hope to see you there.

Full details about this session of The Hacker Within are posted here: http://www.thehackerwithin.org/berkeley/posts/2018-01-31-bash-shell.html.

The Hacker Within is a weekly peer learning group for sharing skills and best practices in scientific computation and data science. In these friendly sessions, peers at all levels of experience share topics useful in scientific software development workflows. For more information, sign up for the THW mailing list or contact the organizers directly at thw-admin@berkeley.edu.

Speaker(s)

Diya Das

Alumni - BIDS Data Science Fellow

Diya Das completed her BIDS Data Science Fellowship in May 2019 and is now an Informatics Analyst II in Development Sciences Informatics at Genentech. At UC Berkeley, she was a postdoctoral researcher in the lab of John Ngai, where she studied regeneration in the olfactory epithelium, the tissue responsible for our sense of smell. She analyzed how olfactory stem cells contribute to both steady-state differentiation and injury-induced regeneration using single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq) and other genomics techniques. Her first co-authored paper, a collaboration between biologists, computer scientists, and statisticians, demonstrated the paths by which adult stem cells choose between neuronal and non-neuronal fates. Her second co-authored paper addressed how these stem cells mediate tissue regeneration after severe chemical injury. She's also contributed to methods papers for the analysis of scRNA-seq data (available here and here). 

Diya also facilitated opportunities for fellow researchers to develop their data science skills by coordinating the BIDS Software/Data Carpentry workshops (she was a Software Carpentry instructor and lesson maintainer), and organizing The Hacker Within, a weekly meeting for demonstration of scientific computing tools. She also led the Career Paths & Alternative Metrics Working Group (chaired by BIDS Senior Fellow Henry Brady), which addresses the career paths available to data scientists within academia.

Diya was formerly the Co-Director and Development Lead of Beyond Academia, a grad student and postdoc-run group whose mission is to encourage career exploration and help their peers nurture skills necessary to be competitive in their future careers. She was also an organizer of the 2017 CDIPS Data Science Workshop, which helped grad students and postdocs explore data science careers via mentored team projects, lectures, skills-based workshops, and company visits. 

David DeTomaso

PhD Student, Computational Biology
University of California, Berkeley