BioTeam Inc.

Talk slides from 2008 OSGC event

blogadmin — Mon, 19 May 2008 15:17:30 +0000

Here are the talk slides from ChrisDag’s presentations at the 2008 Open Source Grid & Cluster Conference (http://www.opensourcegridcluster.org/).

SGE 6.2beta ‘unboxing’ screencast

blogadmin — Fri, 16 May 2008 19:42:30 +0000

Click on the video still image below to watch a recorded screencast where Chris Dagdigian “unboxes” the freshly released Grid Engine 6.2beta release. The video is Quicktime (not the usual Flash based screencast) and is fairly large in order to show terminal detail.

Comments & feedback appreciated. We are still trying to figure out the value-vs-effort equation as it relates to online video and screencasts.

The direct link is here: http://www.screencast.com/t/rXw612Cv

Mike Cariaso wins the 23andMe “Win your Genome” contest

blogadmin — Thu, 15 May 2008 17:56:45 +0000

Congratulations are in order for Mike who was announced as the winner of the “Win your Genome” contest being run by 23andMe. The announcement can be read online here:

http://spittoon.23andme.com/2008/05/14/and-the-winner-is/

Inquiry in the Cloud

cdwan — Mon, 12 May 2008 20:41:43 +0000

Bioteam has ported our award winning iNquiry software to the Amazon EC2 cloud computing environment. Some initial questions and answers are available here: inquiry-ec2

The Cloud, on NPR

briano — Mon, 05 May 2008 16:18:42 +0000

Yes, the Cloud is hot. We just listened to a brief, non-technical piece on Cloud Computing on National Public Radio:

http://www.npr.org/templates/story/story.php?storyId=90180142&ft=1&f=1019

The issues they touch on include security, using the Cloud to compute your genealogy, and how the consumer has access to super-computation for the first time.

Bio-IT World Conference Presentations

blogadmin — Thu, 01 May 2008 14:07:51 +0000

Images from Day 1 “Infrastructure Track” at the 2008 Bio-IT World Conference & Expo

Download links for both presentations:

Chris Dagdigian: “Trends from the Trenches” (cdagdigian-bioit08-v1.pdf)

Chris Dwan: “The Cutting Edge Can Hurt You” (Dwan_BioITWorld_2008.pdf)

Genetic Engineering News: Managing Data from Next-Gen Sequencing

blogadmin — Thu, 17 Apr 2008 01:21:17 +0000

Bill Van Etten has a piece in the April 2008 issue of Genetic Engineering News.

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:

WikiLIMS - Next-Gen Data Management

blogadmin — Thu, 17 Apr 2008 01:04:04 +0000

Excerpt from Mike Cariaso’s recent column in Bio IT World:

“…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:

BioInform writeup on IT limitations in next-gen sequencing shops

blogadmin — Sun, 30 Mar 2008 16:35:31 +0000

BioTeam principal consultants William Van Etten and Chris Dagdigian are quoted in a March 2008 BioInform article entitled “As Next-Gen Sequencers Push IT Limits, Labs Respond With a Range of Informatics Answers.”

Click on the image to download the full article in PDF form.

BioInform writeup on WikiLIMS

blogadmin — Sun, 30 Mar 2008 16:24:08 +0000

Excerpt from a February 2008 BioInform article on WikiLIMS entitled “BioTeam Turns to Wiki Technology to Build Flexible LIMS for Next-Gen Sequence Data”

“… The wikiLIMS system is
“something of a shared brain”
for a lab, “where we can all
agree on a common dialog, a
common vocabulary, common
semantics, and we have the
infinite memory of a hard
drive.”

The full article in PDF form is available here: