command-line-teaching by smangul1

Catalogue of resources providing first-time learners with basic knowledge of command line

Researchers in the life sciences and medical sciences increasingly rely on applications that lack a graphical interface and require typing commands through a terminal rather than using a mouse and graphical interface (GUI). Scientists who are not trained in computer science face an enormous challenge in analyzing high-throughput data.

We have prepared online catalogue of resources and published papers providing first-time learners with basic knowledge of command line. The catalogue was prepared for our study “Addressing the digital divide in contemporary biology: Lessons from teaching UNIX” http://dx.doi.org/10.1016/j.tibtech.2017.06.007

Online resorces

Carpentry, http://swcarpentry.github.io/shell-novice/
Unix & Perl Primer for Biologists, http://korflab.ucdavis.edu/unix_and_perl/
Introduction to Computational Modelling for the Biosciences, https://flxlexblog.wordpress.com/category/teaching/
What to Teach Biologists about Computing, http://spartanideas.msu.edu/2013/07/11/what-to-teach-biologists-about-computing-the-morning-after/
Command Line Coding , http://stem.planteome.org/node/28
Teaching computational biology is as easy as Pi, https://blogs.biomedcentral.com/bmcseriesblog/2013/08/12/teaching-computational-biology-is-as-easy-as-pi/

Courses

Introduction to Unix for life scientists (Event Ended), https://www.eventbrite.com.au/e/introduction-to-unix-02-06-16-registration-25367516926
Gentle hands-on introduction to Python programming, http://www.vib.be/en/training/research-training/courses/Pages/Gentle-hands-on-introduction-to-python-programming.aspx
UNIX command line and scripting, http://mygoblet.org/training-portal/materials/unix-command-line-and-scripting

Published paper

Eglen, Stephen J. “A quick guide to teaching R programming to computational biology students.” PLoS Comput Biol 5.8 (2009): e1000482.
Watson-Haigh, Nathan S., et al. “Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.” Briefings in bioinformatics 14.5 (2013): 563-574.
Via, Allegra, et al. “Ten simple rules for developing a short bioinformatics training course.” PLoS Comput Biol 7.10 (2011): e1002245.

We are working to improve the catalogue. New resourse or paper can be added by Issues iterface using this link (use New Issue button): https://github.com/smangul1/command-line-teaching/issues