This workshop will introduce the basic Linux concepts that used for running programs, writing scripts and programs. Taught in a hands-on format, this workshop will introduce how to use command line, either on a local Linux workstation or through remote access with SSH. Scripting and programming languages will be briefly introduced and compiling and running programs will be discussed. The concept of shell (bash and csh), Python, and C will be introduced.

This workshop is aimed at students and researchers who want to learn how to download and compile software from scratch. It will introduce the concept of compiling advanced software packages with “make” and different Linux compilers (GNU, Intel or PGI). Compiling software for GPUs with CUDA will also be covered. The concepts of required packages, libraries and include files will be covered. Some practical tricks and good practices will also be covered. For users of HPCC, a discussion about using a queuing system such as SLURM will also be discussed.

Most life science disciplines need common Bioinformatics tools to answer different questions. To this end, this workshop is designed for students or researchers that are just starting on their career in life sciences. We are going to start with the most basic and most popular tool in Bioinformatics; BLAST (Basic Local Alignment Search Tool). We are going to briefly cover the basics of sequence alignment and delve into the command line aspects. The focus will be on creating specialized databases for your own research. We also will leverage some of the skills we learned in the Linux workshops.