Environment Modules are a convenient way for users to dynamically
set paths, library paths, and other required environment variables
for an application. Instead of typing shell-dependent commands,
for example, a user could now type:
module load ThisApp
to set up all environment variables for the program ThisApp, and:
module unload ThisApp
to unset all those environment variables.
Almost all the scientific applications, libraries, and interpreters
such as Perl, Python and Java on Helix & Biowulf now use modules.
Details are on the application webpages.
If you are not familiar with the use of modules, please see
for an introduction.
Please contact email@example.com with any questions.
There will be a general downtime for the NIH Biowulf Cluster
during the morning and afternoon of Saturday July 20th.
Both the cluster and the login node will be unavailable during
If you are planning on submitting long-running jobs without
checkpointing or large swarms, please keep this date in mind
as all jobs will be deleted from the system.
Additional details will be included in a reminder e-mail
several days before the scheduled downtime.
Please send questions or comments to firstname.lastname@example.org.
The Helix Systems staff maintains a small collection of 1000 genomes
data (vcf files) in /fdb/1000genomes/. We are considering maintaining
a copy of the BAM files (alignments) from 1000 Genomes.
These files are very large (currently 132 TB total, and growing), and
since disk space is always in short supply, we need to seriously consider
their value to the Helix/Biowulf user community before downloading them.
* Have you ever used the 1000 Genomes BAM files?
* Do you currently have a copy of any of the 1000 Genomes data on your
* Do you plan to use the 1000 Genomes BAM files? If so, when?
Thanks for your input!
Helix Systems Staff.
For NIH Helix & Biowulf users who have Linux or Mac systems in their labs,
there is a new file transfer program available for the Helix Systems.
'bbcp' is a high-performance version of scp which can provide significantly
increased file transfer performance over scp. You can use 'bbcp' on
Biowulf or Helix to transfer files to your local Linux or Mac system; you
can also download a version of 'bbcp' for your local system and use it
For details on using 'bbcp' on Biowulf see the section entitled
"Commandline File Transfer: Macs & Unix/Linux: bbcp" at
The Helix/Biowulf staff will present a series of classes in April 2013.
Classes are free but registration is required. Helix/Biowulf users will
have priority enrollment, and new users are highly encouraged to attend.
Introduction to Linux
Date & Time: Wed, Apr 10, 9 am - 4 pm
Location: Bldg 12A, Rm B51.
This class is intended as a starting point for individuals new to Linux and
UNIX. The class will center on basic UNIX/Linux concepts: logging in,
navigating the file system, commands for interacting with files, running
and viewing processes, checking disk space and other common tasks. The class
will also cover the use of some services specific to Helix/Biowulf usage.
Bash Shell Scripting for Helix and Biowulf
Date & Time: Wed, Apr 17, 10 am - 4 pm
Location: Bldg 12A, Rm B51.
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.
This class will give a hands-on tutorial on how to create and use bash
shell scripts in a Linux environment.
NIH Biowulf Cluster: Scientific Computing
Date & Time: Wed, Apr 24, 9 am - 4 pm
Location: Bldg 12A, Rm B51
Morning: 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.
Afternoon: Hardware and network configuration, types of nodes, selection
of nodes using properties, system software, parallel programs,
The Helix Systems staff is pleased to announce a utility tool that
lets users monitor their usage of CPU and storage on Biowulf and Helix.
To view your usage, go to
You will need to authenticate with your NIH login username and password.
This utility is only available within the NIH network.
The website also displays papers that cited Helix and Biowulf during
this period. If you have additional papers that are not listed, please
let us know by sending email to email@example.com
Helix Systems Staff.
Recent publication citing Helix/Biowulf resources:Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space
Gelio Alves and Yi-Kuo Yu DOI: 10.1021/pr301139y (2013) J. Proteome Research
Recent publication citing Helix/Biowulf resources:Degenerate polymerase chain reaction strategy with DNA microarray for detection of multiple and various subtypes of virus during blood screening
K. Takizawa, T. Nakashima, T Mizukami et al. DOI: 10.1111/trf.12193 (2013) Transfusion
Recent publication citing Helix/Biowulf resources:RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells
MA Alhoot, SM Wang, SD Sekaran RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells (2012) PLoS One
Recent publication citing Helix/Biowulf resources:Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase
H. Sepasi Tehrani, A.A. Moosavi-Movahedia, H. Ghourchian, F. Ahmad, A. Kiany, M.S. Atri, Sh Ariaeenejad, K. Kavousi & A.A. Sabourya DOI:10.1080/07391102.2012.742460 (2012) J. Biomol. Struct. Dynamics