News and Blog

News and Blog

Will Spooner

Commercialisation of scientific software; the case for open-source.

September 29, 2010 / no comments / in Bioinformatics / by Will Spooner
September 29, 2010 no comments in Bioinformatics by Will Spooner
Since the Fort Lauderdale agreement in 2003, genomics has had perhaps the most 'open' attitude to data sharing of any field of science, and this is reflected in attitudes to software, where open-source is the norm.

 

 

Much like the Apache web..

Changing understandings

Reading an article on the BBC website ('Computers show how wind could have parted Red Sea') this morning reminded me how sometimes our understanding of the world can change.  Here is a case of what many people would have thought of as  being a..

Single point of failure

This should be common sense really, but the weakest point of any software system is the point that is non-redundant and cannot be avoided. No matter how many alternative paths you have that pass through that point, if none of the paths can get to..

Abel Ureta-Vidal

Amazon S3 as a File System in Amazon EC2

September 20, 2010 / 3 Comments / in AWS, Big data technology, EC2, S3 / by Abel Ureta-Vidal

As a cloud application developer, shared storage on EC2 is particularly challenging when GBs of data has to be accessed by 100s of EC2 instances. One particular option we explored is leveraging our Amazon S3 storage to mount on EC2 instances and use..

Where in the world are the bioinformaticians?

As Eagle expands, we hire new staff from time-to-time to cope with the increased workload. (We're not currently hiring by the way, this is a general comment piece...)

European Conference on Computational Biology, Ghent ( ECCB10)

In a couple of weeks I shall be attending the ECCB10 conference in Ghent. I have just been reading through the talks and needless to say it looks interesting. I shall be presenting a poster this time, on "An Ensembl-based pipeline for microRNA..

DBCLS BioHackathon

In February 2008 I attended a BioHackathon held at DBCLS in Tokyo to work on semantic data in open-source bioinformatics toolkits. My role at the time was to represent BioJava along with my erstwhile BioJava colleague Mark Schreiber, and the two of..

Debian Ensembl update

Eagle's DebianMed contribution of a fully-working .deb file to install Ensembl is almost complete. The demonstration version 57 contains only minor issues now that need to be resolved before it can be released through the Debian package management..

Abel Ureta-Vidal

Eucalyptus has now a serious competitor

I discovered in this article by Joseph Forn that Eucalyptus, the well known open source infrastructure software to establish cloud environment, is in fact not 100% open source. The story goes that a code contributor, namely NASA, using Eucalyptus..

ProServer Das, Ensembl and EC2

If you use the ProServer DAS server with some Ensembl-based adaptors ( maybe you want to server data from Ensembl, or maybe you have genomic data and want to serve it with some extra annotation that is in Ensembl ) then you may  have come across..

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