Slides and Handouts from Previous Classes
Course intended for researchers that are new to Linux/Unix. Covers Unix/Linux operating system concepts, a little history, basic file system navigation, text editing, bash (shell) syntax, file transfer, and a number of useful commands and utilities. Mark Patkus, 11 Sept 2013
The default shell on many Linux systems is bash. Bash shell scripting provides a method for automating common tasks on Linux systems (such as Helix and Biowulf), including transferring and parsing files, creating qsub and swarm scripts, pipelining tasks, and monitoring jobs. Click here for a set of bash scripts for simulating a workflow. There is a summary of Linux commands available as well.
David Hoover, 18 Sep 2013
NIH Biowulf cluster: Scientific Supercomputing
Introduction to the Biowulf Linux cluster, cluster concepts, accounts, logging in, storage options, interactive vs. batch jobs, how to set up and submit a simple batch job, batch queues, available software, and job monitoring. Hardware & network configuration, types of nodes, selection of nodes using properties, system software, and application demos.
[PDF] Steven Fellini & Susan Chacko, 25 Sep 2013
Linux & the NIH Biowulf for NCI
Short course for NCI researchers covering basics of Linux/Unix and the Biouwlf cluster. Susan Chacko & Mark Patkus, 5 Dec 2013
Next-Generation Sequence Analysis on the NIH Biowulf
Sean Davis, NCI. 24 Mar 2011. Class tutorial.
Biowulf Cluster: Advanced Topics. Recent hardware upgrades,
high-performance data transfer, PBS job dependencies and job
arrays, advanced swarm features, benchmarking parallel codes, GPU
nodes, hyperthreading, optimal node selection and monitoring memory
Steven Fellini, Susan Chacko, and David Hoover. 19 Jan 2011.
Utilization of the Biowulf Cluster for Bioinformatics
David Hoover, 21 May 2008
Using Rosetta on the
Biowulf Cluster (PDF)
David Hoover, 4 Dec 2007
Gene Synthesis using
DNAWorks (Powerpoint file)
David Hoover, 15 Nov 2006
Structural Biology on
the Biowulf Cluster
Overview of structural biology applications on the cluster, and tips on parallelizing large scale structural biology programs using scripts.
David Hoover, 10 Jan 2006
Tutorial and examples for using the UCSC Genome Browser.
David Hoover, 14 Nov 2006
Basic Security for
Steve Bailey, 10 Jul 2003
Large-Scale Sequence Analysis on the NIH Biowulf
Steven Fellini & Susan Chacko, 29 Oct 2002
Also, see here for some online Linux tutorials.