Introduction to Shell Scripting

Join today
  • Instructor:  Ross Dickson
  • Level: Beginner
  • Duration: 1.5 hours
  • Helpers: Serguei Vassiliev
  • Date:  January 30, 2025 | 10:00 - 11:30 am (Atlantic)
  • Prerequisite: Intro to Linux or similar experience
Empty space, drag to resize
COURSE DESCRIPTION

This workshop is designed for either new HPC users who are familiar with working in a Linux environment, but have not had experience with shell scripting, or for experienced users seeking to get more out of shell scripting.

Shell scripting helps you save time, automate file management tasks, and better use the power of Linux. This session teaches you how to name, locate and set permissions for executable files, taking input and producing output. You will learn about job scripts, shell variables and looping commands.This session will be delivered online.
 
In order to get the most from the session, participants are strongly encouraged to have a Digital Research Alliance of Canada/ACENET account and to follow along with the exercises. To register contact your supervising professor, ask for their CCRI, then visit https://ccdb.alliancecan.ca/account_application. If your professor is not registered with the Alliance, please have them register, then follow up with you. In addition to an Alliance account, you will want a computer with Windows, MacOS X, or a Unix-based operating system (not a ChromeBook), and a stable internet connection. A registered account is not mandatory, just recommended to get the most out of our lessons. You can attend the first session to see how ACENET can assist in accelerating your computational research before you decide to obtain an account, if you wish.

SETUP REQUIREMENTS
  • You will want a computer with Windows, MacOS X, or a Unix-based operating system (not a ChromeBook), and a stable internet connection. A registered alliance account is not mandatory, just recommended to get the most out of our lessons. You can attend the first session to see how ACENET can assist in accelerating your computational research before you decide to obtain an account, if you wish.
  • For Windows users, download MobaXterm.

Meet your teaching team

Ross Dickson

Instructor

Lead Research Consultant

Ph.D. Computational Chemistry, Queen’s University

ITIL Foundation Certificate

Based at Dalhousie University, Ross joined ACENET in 2007 as a Research Consultant. His responsibilities span education, documentation, and client support, and he manages job scheduling policies on ACENET’s high-performance computing clusters. He has worked with users across many disciplines including chemistry, physics, biology, oceanography, neuroscience, several engineering disciplines, philosophy, and management studies. Following his doctoral and postdoctoral studies in computational chemistry, Ross worked in software development for Hypercube Inc., makers of HyperChem for Windows, and for Molecular Mining Corporation where he helped specify some of the earliest software for analyzing high-throughput gene expression data.

Sarah Clarke

Host

Digital Training Specialist
MSc Computational Chemistry, Dalhousie University

Sarah, based in Nova Scotia, joined ACENET in 2023. She has a range of teaching experience and held regular teaching assistant positions. Passionate about scientific literacy, Sarah has developed teaching materials and taught programming and robotics to youth in St. John's. She has also led professional development workshops for teachers, focusing on digital skills. For her MSc in Computational Chemistry research, she focused on interfacing crystal structure prediction methods.

Serguei Vassiliev

Helper

Research Consultant

Ph.D. Biophysics,  University of New Brunswick

Serguei joined ACENET in 2019 as a Research Consultant at UNB. His background is in experimental and computational biophysics. After doctoral and postdoctoral studies in biophysics of photosynthesis, Serguei was Alexander von Humboldt Research Fellowship recipient at the Technical University of Berlin where he studied energy conversion in natural and artificial photosynthetic systems using ultrafast laser spectroscopy. More recently he was working as a research associate at Brock University with Dr. Douglas Bruce, where he was engaged in inter-disciplinary research of photosynthesis, integrating biology, computational chemistry, physics and data science. Working at Brock University, Serguei developed specialized programs for global and target analysis of time-resolved spectroscopic data, and analysis of molecular dynamics trajectories. Serguei’s research interests include molecular modelling, simulations of water and oxygen transport in proteins, and computation of the properties of cofactors in protein complexes.