Analyzing the Biostar: Fourth Anniversary

April 8, 2014

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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

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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

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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

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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

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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

opacmo: Third Prize Winner in the Springer API Challenge 2.0

August 15, 2012

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At the end of May I submitted Open Access Mortar (opacmo) as an entry to the Springer API Challenge 2.0 competition. The extensions that I made to opacmo’s web interface for the competition have been described in an earlier blog post, which essentially integrate search results of Springer’s Metadata API and provide a comparative analysis […]

Posted in: Bioinformatics

BioMart: Automating Mart Updates

July 18, 2012

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BioMart is a federated database system that provides web interfaces and web services for relational database management systems and offers tools for configuring and deploying optimised database schemas as marts. A mart is an instance of a data warehouse, which is a collection of schemas that are optimised for a given purpose. In BioMart’s case, the schemas are […]

Posted in: Bioinformatics
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