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Feature Article #1

Supporting Haiti

On Friday the 29th of January, I will be taking a week’s leave of absence from my day to day responsibilities at Bioteam and traveling to Haiti with a medical relief team.
I’ll be going with a group called Family Health Ministries. We’ll go overland through the Dominican Republic to a clinic where my wife [...]

cdwan | January 26th, 2010 | Continued

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Feature Article #2

Maximizing Utility on the Cloud

For the 2009 BioIT World Conference in Europe I was invited with short notice to give a 60 minute talk centering on practical Cloud approaches for life science organizations. The talk was not really technical in nature and had to hit a huge number of topic areas as well. Overall feedback was positive and a [...]

chrisdag | October 16th, 2009 | Continued

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Feature Article #3

Storage for Next-Gen Sequencing

Presenter slides from the 2009 Storage for Next-Generation Sequencing Workshop(s)

blogadmin | October 16th, 2009 | Continued

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Feature Article #4

Grid Engine & Amazon EC2

Talk slides from 2009 Sun HPC Workshop in Germany. This was my “Grid Engine & Amazon EC2″ talk.

chrisdag | September 9th, 2009 | Continued

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Feature Article #5

Slides from the Amazon AWS 2009 StartUp Event

Talk slides from Chris Dagdigian’s presentation “Utility Computing for Cynics” at the 2009 NYC stop of the Amazon AWS StartUp Tour can be downloaded here:
2009-NYC-AWS-BioTeam

A few pictures from the event are posted below. It was a great event, standing room only for all of the presentations.

chrisdag | June 1st, 2009 | Continued

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Feature Article #6

Antibody Docking in the Amazon Cloud

Adam Kraut has written up his experiences with a Pfizer protein docking experiment on Amazon AWS in a recent BioIT World column:
“… 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 [...]

blogadmin | May 29th, 2009 | Continued

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Feature Article #7

Bio-IT World Keynote Slides

Presentation slides from Chris Dagdigian’s talk at the 2009 Bio-IT World

blogadmin | April 28th, 2009 | Continued

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Grid Engine 6.2 on Mac OS X

Installing Grid Engine 6.x on modern versions of Mac OS X (client and server)
As of early 2010, Grid Engine is effectively not installable out of the box on modern version of Mac OS X. We have seen this recently with server and client versions of OS X 10.5.* as well as the new Snow Leopard [...]

7Feb2010 | chrisdag | 0 comments | Continued
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Safely back to the Dominican

We said our goodbyes this morning, gave away most of our supplies (blankets, sleeping pads, spare clothing, water bottles, etc) to the families still sleeping outdoors in the neighborhood near the clinic, and made our way to the border with the Dominican.
We drove the FHM vans all the way through to the Dominican Republic, stopped [...]

6Feb2010 | cdwan | 0 comments | Continued
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Thursday clinic

Another interesting day is wrapping up down here. We had yet another record breaking day – with 315 patients. This is an all time single day record for Family Health Ministries. Perhaps more interesting, we broke the kilo-patient barrier with our week’s total well over 1,000.
We’re making do with supplies. Our [...]

4Feb2010 | cdwan | 0 comments | Continued
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State of the city

We just returned from a drive around Cite Soleil and downtown. The devastation there is much, much worse than what we’ve been seeing around the clinic. We’ve basically been in a suburb – the houses are spaced a bit further apart and two story buildings were rare. Therefore, while the devastation is [...]

3Feb2010 | cdwan | 0 comments | Continued
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Tuesday, in Haiti

This will be a quick update, because I suspect that I would be asleep long before I could even summarize our entire trip.
We’re in the ‘Blanchard’ or ‘Terre Noir’ neighborhood, perhaps a mile north of Cite Soleil – in Port au Prince. The clinic building where we are working survived the earthquake in remarkably [...]

2Feb2010 | cdwan | 0 comments | Continued
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Supplies

I write this from JFK airport in New York, having successfully gotten out of the house at 5am carrying four duffel bags containing just under 200lbs of (mostly) donated supplies. Our clothing and personal gear are in our carry on luggage.
I remain overwhelmed by the deep vein of compassion and generosity we have tapped. [...]

29Jan2010 | cdwan | 1 comment | Continued
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Cluster user training

On the same trip to India, I found myself in the position of delivering a training session to a room with incredibly varied backgrounds and skill levels. Some folks had never edited a file on the Unix command line before. Others just wanted to know where MPICH was installed. This set of [...]

21Dec2009 | cdwan | 0 comments | Continued
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Inquiry Cluster Admin Slides

I recently took a trip to Kolkata, India to train users and administrators of an Apple / Inquiry compute cluster there. The slides I developed for that trip may be of general interest, and so I’m sharing them here. The intent of these slides is to provide an overview of the administrative tools [...]

21Dec2009 | cdwan | 0 comments | Continued
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Setting up LOM on an Apple XServe from the command line

Apple provides a GUI for setting up the IP address and authentication information on the LOM. The problem, for me, with using a GUI for something like this is that it’s nearly impossible to script and automate. When I’m setting up a cluster of even a dozen nodes, going through a remote desktop to a GUI becomes intolerable in a hurry. This post shares my recipe for getting the LOM ports on the network and accessible, using only the command line.

3Dec2009 | cdwan | 0 comments | Continued
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