Welcome to Datapunk Datapunk is being developed and programmed by Dr. Peter D'Adamo and The Center of Excellence in Generative Medicine, in association with the University of Bridgeport.
It is a unique web-based suite of programs that provide an assortment of informatic services. These include: - A stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI) that performs all the traditional NCBI functions and covers a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature.
- A method to enrich returned results with additional levels of semantic significance
- Network analysis tools and mash-ups that combine and synthesize results from diverse external bioinformatic sources, including KEGG (Kyoto Encyclopedia of Genes and genomics), Online Medellian Inheritance in Man (OMIM), UniProt and the Human Gene and Protein Database (HGPD)
- Quodlibet (QUOD), a suite of network creation, editing and querying software. QUOD is a software application that displays biochemical pathway data in a way that is interactive and information intensive. QUOD networks combine topological analysis, combinatorics and a variety of unique graph algorithms to produce the framework for the analysis of emergent phenomena.
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."
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.
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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Data Visualizations
VEGF signaling pathway network in QUODLIBET main canvas
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The same network in QUOD Roamer
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Taxonomy of Common Probiotic Strains
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Lectin Classification and Taxonomy
Click the image to explore the interactive graph.
Pharmacological Actions of Medicinal Plants and Their Constituents
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Join us. Would you like to become a DATAPUNK referee? It's free and membership allows you to benefit from the Datapunk semantic veneer. Datapunk refereeing is currently open to licensed naturopathic physicians, students currently in attendance in a CNME approved naturopathic educational facility, and by invitation. Refereeing on Datapunk is easy, intuitive. To join Datapunk click here.
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