Elasticsearch, RethinkDB and the Semantic Web

June 11, 2014


Everyone is handling big data nowadays, or at least, so it seems. Hadoop is very popular among the Big Data wranglers and it is often mentioned as the de facto solution. I have dabbled into working with Hadoop over the past years and found that: yes, it is very suitable for certain kinds of data […]

Adding Furigana Support to Firefox

June 2, 2014


So here we go, you learned your hiragana, katakana and perhaps even forayed into deep mysteries as to why ha (は) is a lot of times pronounced wa (わ). Time to read some Japanese newspapers, right? Wrong! There are still a few thousand kanji to learn, which is about as exciting as getting a root […]

Analyzing the Biostar: Fourth Anniversary

April 8, 2014


I am slightly behind schedule this year, but I finally got around to follow-up with my annual investigation into Biostar’s forum quality (1st year, 2nd year, 3rd year, and bonus blog posts). It is very exciting to see that this long-term project is producing valuable insights into many more metrics than four years ago, that it […]

Posted in: Bioinformatics

BaseSpace Ruby SDK: Genomics Cloud Computing

August 5, 2013


BaseSpace is Illumina’s cloud computing platform that aims to provide a scalable computing environment for genome sequencing and analysis. This blog post gives a short overview about BaseSpace Ruby SDK, which helps App developers by providing a framework for accessing the BaseSpace RESTful API. Introduction BaseSpace is a new cloud computing platform that went public for […]

Posted in: Bioinformatics

EC2Workflow: A Workflow Framework for the Elastic Compute Cloud

June 16, 2013


In this blog post I present a framework for executing workflows in Amazon’s Elastic Compute Cloud (Amazon EC2). The framework — EC2Workflow — is based on the fully automated and scalable text mining pipeline Open Access Mortar (opacmo) which I have been working on for the past two years. EC2Workflow is application agnostic implementation of the text […]

Posted in: Bioinformatics

Uh-oh, Biostar: Three Years of User Metrics Analysis

March 15, 2013


It is March again and that calls for another annual follow-up of my investigations (1st year, 2nd year and bonus blog posts) into Biostar’s forum quality. Biostar is a public internet forum for the bioinformatics community where registered users can get help on a wide range of topics. Over the years I became convinced that […]

Posted in: Bioinformatics

opacmo: Release 4 adds support for Amazon’s Elastic Compute Cloud

December 17, 2012


Open Access Mortar (opacmo) is a rich text-mining resource that is powered by opacmo’s unique generic text-mining pipeline implementation. Earlier releases of opacmo supported text-mining on single machines, such as laptops, as well as Oracle Grid Engine high-performance computing clusters. With the newest release of opacmo 4, it is also possible to run the text-mining […]

Posted in: Bioinformatics

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