News and Blog

News and Blog

Abel Ureta-Vidal

Changing MySQL DB parameter on Amazon RDS instance

November 16, 2010 / 2 Comments / in Amazon, AWS, Big data technology, Blog, MySQL, RDS / by Abel Ureta-Vidal

MySQL instances on Amazon RDS service usually comes with default MySQL configuration settings, which might not always work for our needs. For example: we had to change max_allowed_packet DB parameter value to allow importing large DNA sets. This is..

Ensembl 60 top tip #1

Ensembl 60 came out yesterday. For those of you who are technical developers like us who do in-depth hacking of the source code, there's two things that have changed which you need to be aware of:

Abel Ureta-Vidal

SaaS (Software as a Service) a blessing for bioinformatics users?

In these tough economic conditions more and more organisations are looking for ways to reduce their operational and maintenance costs. Businesses are turning towards SaaS (Software as a Service) model because they no longer have to worry about..

Importing Ensembl into Amazon RDB

Ensembl very kindly distributes their databases on Amazon as public datasets in a variety of forms. The most straightforward to use is the set of MySQL database files that can simply be copied into a MySQL server's data directory and they will..

Public or Private Cloud, or maybe Hybrid?

Last week I noticed that a new world record had been set... and I'm afraid I'm not talking about the common wealth games, but rather about another advance in private cloud computing. The record was set ( or rather reset, as they already held it ) by..

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..

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..

JSON for Ajax

JSON is so much easier to work with in Javascript than XML. This makes it perfect for coding responses from AJAX-backed web services.

Solutions without problems

There are so many good ideas floating around in the bioinformatics open-source world that its hard to know what to do about them all. Sometimes it feels like almost every day yet another paper has been published on some fantastic piece of software..

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