Archive for the 'Bioinformatics' Category

Apr 21 2013

Remembering the Memorable

One of the features of any network is the appearance of motifs, patterns that recur within a network much more often than expected via any sort of random occurence. The first four notes of Beethoven’s Fifth Symphony are an example of a motif: This opening phrase is one of the most widely recognized in music. […]

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Mar 20 2012

Fruity Loops and Arrowheads

One of the features of any network is the appearance of motifs, patterns (sub-graphs) that recur within a network much more often than expected at random. These small circuits can be considered as simple building blocks from which the network is composed. This analogy is quite useful, since many of these motifs would appear to […]

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Dec 21 2011

Concept Nodes

This entry is about an editing function in QUODLIBET. QUODLIBET is a computer program that creates, edits and queries biomedical networks. In addition to providing information about genetic-protein-phenotype interactions QUODLIBET also allows for additional information to be harvested, including data on the effects of natural products on gene-protein expression.  We are always looking for volunteers […]

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Nov 12 2011

Beautiful Data

It has been said that if one really wants to learn something, they should teach it. However we may want to expand that aphorism, to perhaps if one really wants to learn something, they should teach it, organize it or animate it. The commonality between science and art is in trying to see profoundly – […]

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Oct 26 2011

Walking on Eggshells

Published by under Bioinformatics,Perl

After a self-declared coding holiday, I was back at things this weekend working on the Pathscrubber module of the Datapunk platform. A recently developed vexing problem that needed to be addressed was actually two problems intertwined. If you used Pathscrubber and clicked on any gene/protein node, PS would query Entrez-gene for the descriptive text and […]

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