examining mRNA complexity by annotation region using MapReduce

I became interested in how annotated mRNA regions (e.g., 5′ UTR, coding, and 3′ UTR) vary in information content, speculating that coding regions (CDS) of transcripts will be generally more complex than other regions due to their role in specifying protein recipes. Measuring sequence complexity using Shannon entropy validated this hypothesis, at least with regard […]

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test driving Amazon Web Services’ Elastic MapReduce

Hadoop provides software infrastructure for running MapReduce tasks, but it requires substantial setup time and availability of a compute cluster to take full advantage of. Amazon’s Elastic MapReduce (EMR) solves these problems; delivering pre-configured Hadoop virtual machines running on the cloud for only the time they are required, and billing only for the computation minutes […]

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comprehensive, anticipatory design in the age of Big Data

Buckminster (Bucky) Fuller wrote in the 1950s that a strategy of “comprehensive anticipatory design science” [1] was required to create technology and systems suitable to sustainable living and sustainable business. This post examines what Bucky meant by comprehensive anticipatory design and then explores how Big Data can play a role in its deployment. Bucky’s vision […]

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