I have just committed a major update to biogeek’s script to fetch pdf-reprints of papers indexed in Pubmed. It is available on github here .

The first version required the Camping rubygem, but I have decoupled that dependency, cleaned up the code a bit and added a few tests.

A major problem for many users of EC2 has been sending emails because of issues with reverse DNS causing it to be regarded as spam many places.

I got it working just fine using the Elastic Load Balancer. I configure exim “dpkg-reconfigure exim4-config” to use my elastic load balancer as it’s Mail Server Name. For example, if I have the website example.com, I make sure the DNS for this site points to my load balancer (and in the load balancer I register the server/s hosting my site). So, when I send mails from somebody@example.com it will reverse DNS correctly.

p.s. you cannot actually point the DNS for example.com to the load balancer since the load balancer is not a IP you have to use CNAME and can only point www.example.com (or any subdomain) to the load balancer. You could point example.com to an elastic IP for one of your servers and have permanently point example.com to www.example.com.

Lately I’ve been playing with Amazon Elastic Compute Cloud (Amazon EC2) and so far I really like what I see. Their virtual setup makes EC2 quite an attractive and flexible alternative to running the servers locally. For example, I could setup a server with EC2, install various bioinformatics tools and take a snapshot of this server. This “copy-paste” of a server allows me, in no time, to provide companies with an advanced and powerful bioinformatics server, which could easily be administrated by either us or the client. Also, this makes it easy for companies/universities to setup a server which provides some service, and as the company and demand for more CPU power grows, it is fast to “copy-paste” your server to add more servers.

Another great thing about EC2 is that in addition to great GUIs like ElasticFox there are also the EC2 API tools, making it possible to script your server management. For example, you can use these tools to dynamically start/stop servers, for example if your servers are very loaded, you could define some server load thresholds and automatically add/remove servers based on these thresholds. Also, since Amazon charge by the hour, you can set your servers to shutdown after office hours if your employees are the only people using your server. Using Ubuntu, this page is a good place to start using the ec2-api-tools (of course you will first need an EC2 account).

You should be aware that once you shutdown your server, all data will be lost. That’s why Amazon also have Elastic Block Storage (EBS). You can, also scripting it with ec2-api-tools, create an EBS volume, which is is your disk space (which according to Amazon should be as fast or faster than local disks), and have your server mount it automatically when you start your server. So you can have the server write its data to this EBS volume and avoid loosing data when you stop your server.

This is only a fraction of the possibilities that I mention here and I am still fairly new to EC2, but so far I am really impressed with it and hope to use it a lot in the future. Thumbs up to the developer team at Amazon for some well thought out solutions.

This just in before the weekend:

Complete Genomics have published its first few genomes, and despite (somewhat) dodgy statistics on the quality of the assembly they are in business. More here.

Nature paper out on the ‘complete’ epigenome hints that embryonic cells may use different mechanisms for gene regulation than more differentiated cells. Abstract here.

Lastly, Microsoft would like to take a step into the world of bioinformatics. What they really want to is to take a strong tradition for open source and wrap it in proprietary frameworks so we can be even more reliant on Microsoft products. Posted here (Gleen Moodys comment) and here (Microsoft statement).

A small neat GUI for generating barcodes which incorporates some error checking. A very useful tool for multiplexing strategies.

Bioconductor 2.5 has been released, and many new packages are included. A fair amount of the new packages are related to analysis of data from sequencing platforms (Chip-seq and RNA-seq) and analysis of miRNA targets, just to mention some of the packages that looked interesting. See the full statement here.

If you have a well-structured data model and an intuitive framework for querying your data it suddenly becomes feasible (and fun) to quickly address smaller scientific questions as they arise. If you use an expressive and intuitive query language it is also a lot easier to share your query/code with people in your group or in a scientific forum. miRMaid (www.mirmaid.org) provides such a software framework for miRNA data. If you are interested in microRNAs, or in doing something similar in your own data domain, then read on.

Tired of clicking your way to the article PDFs you need? Check this out and find out how you can fully automate this process.

Just happened to stumble across this very geeky post on blog updating from emacs and R. I am sure that my fellow geeks and I will be spending some time during the weekend checking this out. Maybe the readers of this blog will be spammed with R-code, even more, in the near future. Have a nice weekend.

A small rant about two different, and very useful methods for analyzing expression data from micro arrays.