You can also download it via this short link: http://biote.am/mini

Excerpt:

“IT MAY NO LONGER BE FAIR to characterize large pharmaceutical firms as late adopters of information technology (IT).

Having spent the past five years catching up to other industries in the deployment of enterprise software systems that link researchers and laboratories companywide, big drug firms are now starting to push data storage and processing onto the Internet to be managed for them by companies such as Amazon, Google, and Microsoft on computers in undisclosed locations…“

Article link: http://pubs.acs.org/cen/email/html/cen_coverstory_87_8721cover.html

“… The new docking architecture at Pfizer employs nearly the entire suite of services offered by Amazon. A huge array of Rosetta workers can be spun up on EC2 by a single protein engineer and managed through a web browser.”

Full article link here:

http://www.bio-itworld.com/issues/2009/may-jun/antibody-docking-EC2.html

This post is a follow-up to the article discussing Bill Van Etten’s OS X Launchd scripts for Grid Engine.

We now have a perl script that will automatically create site-appropriate launchd plist files for Grid Engine – the files are constructed by querying the SGE environment variables and running one of the SGE utility scripts. This may be a more convenient method than downloading our plist files and hand-editing them via the Apple plist editor program.

The new-in-Leopard “launchd” framewortk is Apple’s preferred system for handling system services and daemons. For more background on why launchd may be critical to Grid Engine on 10.5 systems (especially OS X Server 10.5.4 and later …) please visit the Grid Engine wiki page covering Apple Launchd:

http://wiki.gridengine.info/wiki/index.php/GridEngine_launchd

Download the script here:

sge-launchd-scriptmaker

Chris Dagdigian recently test-drove Univa UD’s UniCluster Express, integrated it with the Amazon Elastic Compute Cloud (EC2).

Links to the Howto Whitepaper and various screencast video recordings are available via the gridengine.info post:

http://gridengine.info/articles/2008/07/14/univa-ud-unicluster-express-and-amazon-ec2

Excerpt:

“…One terabyte of data is not large by today’s standards. An external terabyte disk can be purchased for less than a few hundred dollars at any office supply store. Accumulating one terabyte per day, maintaining it for rapid online access, and archiving it for permanent storage is a familiar problem to the sequencing center and maybe even the core facility, but this is a novel problem for the small research group and individual principal investigator.“

Link to the full article:

GEN 2008, “Managing Data from Next-Gen Sequencing” (p.42,44)

Link to a PDF reprint:

“…We’re now capturing data electronically with no human intervention required. A single device doing this isn’t particularly compelling, but two or more can be. The wiki becomes an electronic lab notebook written entirely by your machines. Because it can be viewed and edited with a Web browser, scientists can begin by using it as a web portal to recently completed analyses. Each discovery can be recorded into the wiki, one click away from the supporting raw data. Simple programs can build reports from or read and write into the wiki. An automatic full history of every page provides a safety net, and a way to view how our understanding of the data has evolved. This enables cycles in which humans and software each complement the other’s strengths.”

Read the full article here:

http://www.bio-itworld.com/issues/2008/april/inside-box-wikilims.html

Download a PDF reprint here:

William Van Etten has produced new scripts for the Apple OS X “Launchd” framework used by Mac OS X 10.5 “Leopard” systems. Moving forward it seems that Apple eventually intends to phase out the SystemStarter methods for starting/stopping daemons and services in favor of the newer launchd mechanisms.

A Wiki entry over at http://gridengine.info explains some of the problems with Launchd and shows an (older) potential workaround.

The new scripts referenced in this blog post take advantage of a newly discovered (by us) environment variable called “SGE_ND” — if this variable is set, the SGE daemons will not fork off and daemonize (something that Apple Launchd does not allow). By including the “SGE_ND=1” environment variable into the Grid Engine startup environment we are able to produce launchd-compatible scripts that function well at automatically enabling Grid Engine startup and shutdown (and theoretically automatic restart of crashed daemons).

Bill has created three launchd.plist(s)…

1) sgeqmaster.plist
2) sgeschedd.plist
3) sgeexecd.plist

Using these plists, one can load with …

launchctl load /Library/LaunchDaemons/net.sunsource.gridengine.sgeqmaster.plist
launchctl load /Library/LaunchDaemons/net.sunsource.gridengine.sgeschedd.plist
launchctl load /Library/LaunchDaemons/net.sunsource.gridengine.sgeexecd.plist

and start/stop with…

launchctl start net.sunsource.gridengine.sgeqmaster
launchctl start net.sunsource.gridengine.sgeschedd
launchctl start net.sunsource.gridengine.sgeexecd

launchctl stop net.sunsource.gridengine.sgeqmaster
launchctl stop net.sunsource.gridengine.sgeschedd
launchctl stop net.sunsource.gridengine.sgeexecd

If these scripts are installed in “/Library/LaunchDaemons/” they will also activate automatically on system boot or restarts.

Download link & Installation Instructions

The .plist scripts are available here: sge_launchd.tgz

To install them:

1. Download the gzipped tarball
2. Examine each .plist file in a text editor or the Apple “Plist Property Editor” program – there will be paths and variables that may have to be altered to match your local site configuration in each file
3. Install as root in “/Library/LaunchDaemons/”

To make an Apple 10.5.x system aware of the new scripts without rebooting or restarting, use the “launchctl load” command shown above.