Dec 18 2011

Quodlibet

A quodlibet is a piece of music combining several different melodies, usually popular tunes, in counterpoint and often a light-hearted, humorous manner. The term is Latin, meaning “whatever” or literally, “what pleases.”


Quodlibet (QUOD) is a suite of network creation, editing and querying software I am currenty developing. QUOD is a software application that displays biochemical pathway data in a way that is interactive and information intensive.

In addition to providing information about genetic-protein interactions QUOD also allows for additional information to be harvested, including data on the effects of natural products on gene-protein expression.

A bit of the Adipocytikine network as displayed in QUOD. Amber nodes indicate high betweenness centrality and in-degree. Dark green tags indicate that a natural product has been associated with the regulation of that node.

Unlike most biochemical pathway/network depiction programs QUOD actually ‘thinks’ in a social network sense in that it analyzes the network and reports on many graph functions including betweeness centralities, page-ranks, and cluster coefficients. This allows an immediate understand of which nodes are acting in a critically important role in the network.

It was designed to be simple, easy to user and fun to edit and develop in. Because it is web-based, no special software is required, other than a modern browser and a decent Internet connection. QUOD runs under the DataPunk platform and is open-access. Curators can use the extensive editing tools to add to, alter, or create entirely new networks.

One of the more powerful aspects of QUOD is its ability to highlight naturopathic procedures and agents that have been shown to exert an influence on the expression or function of elements in a molecular network. This will have a major influence on the future practice of Generative Medicine, since complex patterns of relationships between naturopathic agents and procedures (traditional as well as biomedical) can be superimposed over the network analysis of complex molecular graphs so as to allow clinicians to derive extraordinarily high quality suggestions about specific approaches that may more closely approximate the holism of the Vis Medicatrix Naturae.

Since the project is community-based, we are always looking for volunteers who are interested in helping out. Volunteers need not have any medical or super computer skills, just a passion for exactitude and a desire learn more about the genetics and biology. To learn more about QUODLIBET, you can download the User Guide and visit the Community Forums.

What is needed now is the community of volunteers who would be willing to devote time to curate additional maps. Hopefully this call to action will not prove too disappointing: I can think of no better way to enhance one’s own understanding and knowledge about a complex topic than to build mind-maps. Thus it is to the students of our profession that I direct this challenge, though any interested party with a computer and a decent Internet connection is welcome to help out.

Phase I of our map development program will involve translating the KEGG genomic and metabolic maps into QUOD format. KEGG maps are good and even hyperlink to relevant KEGG entries for enzyme activities, drugs, etc. However KEGG maps are hand drawn and cannot perform network graph computations. However KEGG has done much of the heavy lifting: converting a KEGG map to a QUOD map makes development quick and painless. From there QUOD will link all subsequent maps into clustered networks, allowing for greater and greater information processing.

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