Jul 2004: Helix Systems downtime: Helix, Nimbus, and Quasar will be unavailable on Monday July 19 starting at 6 PM in order to perform system maintenance. We expect that the systems will be available by no later than 9 PM. Mail coming through Helix will also be inaccessible during this period.

May 2004: Gaussian03 was updated to version B.04. There are changes in Gaussian03 from version B.04 onwards which require that all Gaussian users belong to 'gaussian' group. Helix users who have used Gaussian in the last year have been added to that group already, and new users will be added when they first use Gaussian03. Please see the Gaussian03 webpage for more information about how to run version B.04.

Apr 2004: Helix Systems downtime: Helix, Nimbus, and Quasar will be unavailable on Monday April 26 starting at 6 PM in order to perform system maintenance. We expect that the systems will be available by no later than 9 PM. Mail coming through Helix will also be inaccessible during this period.

Mar 2004: A web interface to PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) version 2.0 is now available. PROSPECT is a threading-based protein structure prediction system. PROSPECT will find distant structural homologs with low sequence identity to a target sequence by protein threading. The job is submitted as batch to Biowulf, and the results will be made available to the user by email when the job is finished. Typically, a threading job against a single structural template library should take 5-10 minutes, while against all libraries should take 25-30 minutes.

Dec 2003: A mirror of the UCSC Genome Bioinformatics Site is now available. The mirror site contains the reference sequences for human (Jul 2003), mouse (Oct 2003), and rat (Jun 2003) genomes, which can be accessed by Genome Browser, Family Browser, Table Browser, and Blat Search, applications designed by Jim Kent and others. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Browser displays an annotated genome as multiple tracks (such as aligned protein sequences and ESTs), and the user can add their own custom tracks to the display. The Family Browser shows expression, homology and other information on groups of genes that can be related in many ways. The Table Browser provides convenient access to the underlying database. Blat quickly maps your sequence to the genome.

Dec 2003: Linkage programs, several linkage analysis programs now available on Helix Systems.

Dec 2003: Irix patch installed which affects all the SGI compilers.

Oct 2003: DNAWorks, automates the design of oligonucleotides for PCR-based gene synthesis.

Oct 2003: Three additional blade systems arrive for biowulf system. 198 1, 2 and 4GB 2.8GHz Xeon nodes.

Sep 2003: EMBOSS, the sequence analysis tools, is now available on Helix Systems.

May 2003: Swish-e search engine on Helix systems homepage is now running.

March 2003: PBS client software has been installed on the Helix systems SGIs so that you can submit jobs to the Biowulf cluster directly from Helix, Nimbus and Quasar.

To submit a Biowulf job from Helix, you would type

qsub -l nodes=1:m1024 job_script

just as on Biowulf. 'qstat' on Helix will show the status of jobs on the cluster.

Of course, the job scripts and files still need to be accessible from the Biowulf nodes, i.e. they should be in your /data directory and not in your helix /home/user area. Note: if you have the line

#PBS -k oe

in your script, the standard error and output files will appear in your Biowulf home directory. If you remove this line, the files will appear in the submitting directory ($PBS_O_WORKDIR, e.g. /data/username/sequences/) which may be more convenient if you are working on Helix.

For more information, see http://biowulf.nih.gov/user_guide#q

March 2003: Installed R version 1.6.2 on Helix SGI Systems

March 2003: Updated R on Biowulf to version 1.6.2.

March 2003: Installed CNS 1.1 on Helix Systems.

October 2002: SAS version 8.2 was installed on Helix Systems. Type 'man sas' at Helix prompt for help.

September 2002: RepeatMasker on Helix: screens DNA sequences of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions

September 2002: Povray on Biowulf: a new easy way to run large Povray jobs which insulates you from the batch system.

July 2002: Gnuplot v3.7 on Biowulf: useful tool for graphs data or mathematical functions in 2 or 3 dimensions

July 2002: Mfold v3.1 on Helix: RNA/DNA secondary structure prediction

June 2002: Gromacs v3.1.4 on Helix, and on Biowulf: a versatile package to perform molecular dynamics

June 2002: Phylip v3.573 on Helix: including SGI Parallel and optimized programs

June 2002: Tree-Puzzle v5.0 and fastDNAml v1.2.2 on Biowulf: Phylogenetic Analysis programs

June 2002: HMMER on Biowulf: easy ways to perform HMMER sequence analysis.

May 2002: EasyBlat & EasyBlast on Biowulf: easy ways to submit BLAT and Blast jobs

April 2002: SquirrelMail: Secure Web Access to Helix Mail

April 2002: With the latest addition of nodes, Biowulf/LoBoS3 is now a 1.2 TERAFLOP System!

March 2002: MySQL relational database management system available: contact staff@helix.nih.gov for more information.

October 2001: The new 1.4 GHz Athlon nodes are now on Biowulf