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Updated WikiLIMS Presentation
Download the 11-14-2009 version of the WikiLIMS Overview presentation by clicking on the graphic below:
SSH tunnels part 3: Reverse tunnels
The problem addressed here is the same as the previous two, except that the remote administrator won’t open up *any* ports in their firewall. Machines on the customer’s network can connect out onto the internet, but there is no direct way to connect to them from out here. This post describes how to set up a pair of tunnels that meet in the middle, allowing me access to machines that don’t even have a public IP address.
SSH Tunnels – part 2
In a previous post I described how and why one might set up a very simple ssh tunnel in order to access a web server or a remote desktop server on a machine with a restrictive firewall. This post goes one step deeper, showing how to chain tunnels together.
SSH Tunnels For Beginners
A basic introduction to ssh tunnels: As a first puzzle, assume that a friendly administrator gave me an ssh account on her web server. However, her organization’s security scheme only allows me to get to port 22. I can ssh in, but I can’t really debug some problem with the web browser because port 80 is still blocked. Assume as well that we’ve already called up the network administrator, who offered to think about it – laughed maniacally – and hung up on us.
Binding Apple’s Open Directory from the Command Line
Here is a trick I use a couple of times a month to get finicky compute nodes in a Apple compute clusters to correctly bind to their LDAP / Open Directory master. This started working as of OS X 10.4, and to my knowledge it still works as of OS X 10.6.1. Bioteam uses a [...]
Trends and Observations, October 2009
Slides from an invited talk to a group of Pharmaceutical IT folks. The topic was very broad, “trends and changes in what I’ve seen.” We used these as a jumping off point for a couple of hours of conversation. Direct link to the slides: Click Here (or on the picture below).
2009 PRISM Forum Presentation
Talk slides from the 2009 PRISM Forum SIG meeting on “Biomarker Discovery” have been posted here. The talk was a short one and pretty non-technical – aimed at listing out some of the key problems and focus areas in environments where the scientific protocols and technology changes faster than the underlying research IT infrastructure. Direct [...]
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 [...]
Storage for Next-Gen Sequencing
Presenter slides from the 2009 Storage for Next-Generation Sequencing Workshop(s)
Instead of spending 20 minutes to format an ext3 volume every time you need one, you could just snapshot a ...
Let me add a few remarks about Ext3 as well.
The reason we usually recommend Ext3 instead of XFS is because ...
I'm using these slides to tune SGE 6.2 @ European Space Agency, thanks a lot! 
Great post.
Can you also try our native scale out NFS protocol? Next 3.1 release of Gluster will include it ...
So far my mental architecture is shaping up to be something like this:
Use the ephemeral disks for scratch space and ...
This shows that on-demand HPC still has a ways to go, it is very unfortunate that only ext3 is supported ...
We have had sge62u3 working fine in a 10.5 cluster using cron to startup the sge_execd process on clients. Trying ...
Instead of increasing your disk image size, you could have decreased the memory by writing a very short C program ...