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Introducing Datapunk, the first bioinformatic portal for naturopathic medicine.

Datapunk is a unique web-based suite of programs that provides an assortment of bioinformatic services, developed and programmed by Dr. Peter D'Adamo and The Center of Excellence in Generative Medicine, in association with the University of Bridgeport.

Diagnosis

Choose a diagnosis and the ICD-9 results will display here.



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. 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.


Detail from the Quodlibet map 'Apoptosis.'
Highly significant nodes are colored in varying shades of gold. Nodes with natural products known to be associated with their expression have green tags linked to them.

Unlike most biochemical pathway/network depiction programs QUOD actually 'thinks' in the sense in that it analyzes the network in real time and reports on many graph functions including betweeness centralities, page-ranks, and cluster coefficients. This allows an immediate understanding of which nodes are acting in a critically important role in the network. Multiple maps can be combined into multi-map mashups and for which any number of provocative anayltics can easily be run.

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.



Hunch: A Collaborative Clinical Instance Developer

Hunch is a program that turns crowd-sourced wisdom into tangible informatics.

HUNCH is a clinical scenario development platform that uses semiotic structuring. Every tile (anything from an ICD code to an acupuncture point) has a unique ID that gives it a semiotic (symbolic) significance. When these tiles are placed in an 'instance' (the workspace that describes the encounter) their location in the grid (matrix) gives them an additional 'semantic' significance (the grid coordinates acting as a sort of primitive ontology). This simple device provides great information value: even an instance with as little as 5-10 tiles provides much more information relevance that a typical history, with the advantage of being capable of being subsequently algorithmically harnessed.

HUNCH has an intuitive drag and drop interface that converts your clinical scenario into a coded matrix, which can then be saved, and further developed you and others. HUNCH does this by helping you build your case history into an instance. You constuct an instance by dragging and dropping various descriptive 'tiles' onto a grid, which you can then save, print out, etc. You can even invite others to participate in the further development/ refinement of your instance.



The Hunch Instance Developer
Click the image to learn more about Hunch.
Click here to watch a video and download the User Guide


As instance data begins to accumulate it can be mined for patterns, frequencies of occurence, the safety and efficacy of agents employed. At that point HUNCH will then gradually morph into an expert system, a combination of the knowledge base and an inference engine.

Discover the Molecular Logo for any naturopathic agent, singly or in combination.

WATUSSI is a bioinformatics application that develops 'molecular logos' for combinations of natural products.



A Watussi Molecular Logo for three natural products
Click the image to learn more about Watussi.


WATSUSSI is dreadfully easy to use. Just select any number of agents from a checklist of natural products; then select the maps you wish to display, and finally play with the data diagrams. WATUSSI also will display protein-protein interactions (PPI) data for the genes displayed in the logo. This give additional insight into the epistatic-phenotypic influences that the agent may exercise.

However, under no circumstances should you ever press the button icon at the upper right hand part of the screen.



In a nutshell, Datapunk NaSH (Naturopathic Subject Headings)is a web-based interpreter that will allow NDs to super-impose an analytic framework ('semantic veneer') on top of the existing NCBI Entrez system. Editors and tag the results of PubMed seaches and associate specific genes, proteins or naturopathic gents with the PubMed article. Linking naturopathic agents to gene-protein expression adds them to the molecular network maps used in Quodlibet and Watussi.

To curate NaSh tagging, a registered user logs into Datapunk and performs conventional literature seaches from the DataPunk search bar (the form at the top of this screen) instead of the traditional Pubmed interface. Once they've been presented with the results of their search they will be presented with a form at the bottom of the artcile to allow them to add tag data. Only the 'curation data' (the semantic veneer) is saved on the Datapunk server, leaving the US taxpayers to do the actual heavy lifting.



Using NaSH.
Click the image to view a typical NaSh entry secreen.



To curate NaSh tagging, a registered user logs into Datapunk and performs conventional literature seaches from the DataPunk search bar (the form at the top of this screen) instead of the traditional Pubmed interface. Once they've been presented with the results of their search they will be presented with a form at the bottom of the artcile to allow them to add tag data. Only the 'curation data' (the semantic veneer) is saved on the Datapunk server, leaving the US taxpayers to do the actual heavy lifting.

Data Visualizations



VEGF signaling pathway network in QUODLIBET main canvas
Click the image to explore the graph.


The same network in QUOD Roamer
Click the image to explore the graph.


Taxonomy of Common Probiotic Strains
Click the image to explore the graph.


Lectin Classification and Taxonomy
Click the image to explore the interactive graph.