Nov 12 2011
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 – to develop strategies of seeing and showing. –Edward Tufte
One of the main goals of our Datapunk bioinformatics platform is the development of new and exciting information visualization (InfoViz) tools that can be used to develop new appreciations for the relationships between data. We are currently developing two new InfoViz platofrms that I think have great potential. But more than that, these tools feature stunning interfaces that go a long way towards again proving the fact that information, presented imaginatively, can not only yield amazing secrets, but can be stunningly beautiful as well.
The first InfoViz platform we developed is a full-bodied genomic network depictor called PathScrubber, which runs inside Datapunk. PathScrubber draws network graphs of gene-protein relationships. Each node in the network is click-able and links to a popup that provides information on that gene, through an API to OMIM (Online Mendellian Inheritance in Man). Perhaps more significantly, Datapunk is the first informatics tool that is harvesting scientific references detailing phytochemicals and dietary agents that have been reported in the literature to influence the expression of these gene-proteins.
Simply enter any gene-protein terms you wish to include in your network. Don’t worry about partial terms; PathScrubber will return a list of possible terms for you to consider and you can check which ones are appropriate in the next screen. After the program draws the network, you can zoom in or out with either the mouse or via a slider. Nodes containing genomic expression information on phytochemical or dietary agents are coded orange. PathScrubber has an extensive help page. PathScrubber is programmed in Perl, utilizing Léon Brocard’s GraphViz module to draw the graphs.
Lectins: Classification and Taxonomy
Radio buttons on the top allow for the user to display the tree in different aspects and to chose between a ‘normal’ display, where the categories open up in a linear fashion of a ‘centering’ mode where the newly selected category moves to the center of the tree. Finally branches of the tree often contain hyperlinks to additional information.
Actions of Medicinal Plants