Installation: Download Adobe Air and install it, from this site: http://www.adobe.com/products/air/. Also, download AirDrupalFlexDemo4 app, and unzip it. You can then open the Air file directly (e.g., by double-clicking on a Mac).

Once the AirDrupalFlexDemo4 app has opened, expand it to full-screen, and click on each of the tabs at the top to load the corresponding pages. (If you have any trouble getting any of the pages to load, please let me know.)

AirDrupalFlexDemo4: This demo is built on Adobe Air, and the basic Air app uses a Flex TabNavigator component to provide tabbed access to a specific set of web pages (URLs linked to by each tab). Each tab links to a web page consisting of either pure HTML, pure Flex, or mixed Flex / HTML web pages and data. The first 8 tabs are pure HTML, Tab 7 is a mixed HTML / Flex page, and Tab 8 is a pure Flex page, with a multi-component dashboard.

A list of some of the advantages of using an Air desktop app vs. a regular web app is presented here (link)

Note: the back button / reload in the Air TabNavigator app is set up only on Tab 0, to allow free navagation around and within the gClusters web app. Such navigation is not intended for the other tab pages. The only way the other tabs can be reloaded is via the "back" control within the browser. If those pages must be reloaded, the whole Air app must be reloaded.

Tab 0: links to a live, online version of the original gClusters genomics web app, which was built on the Frontier / Radio CMS, which is now being ported to Drupal.

Tab 1: the gClusters gene page for the gene "neuralized" (neur). Each Gene Page in gClusters provides a graphic display of the gene in a 40 Kb region of the genome, along with neigboring genes. In the data tracks below gene tracks, the computationally-derived "clusters" of transcription factor binding sites are shown. This is an Ajax app, where the images in the gene pages can be immediately expanded or collapsed out of view by clicking once on the image, without the entire page having to be redrawn.

A table showing the clusters found near the gene is shown at the top left, including the specific sites found within the cluster, with their specific order and orientation shown. These clusters were computationally identified within the entire genome DNA sequence using regular expression-based pattern matching modelled on specific experimentally-studied genes in the neural differentiation pathway.

Scrolling down in page shows the genetic, biochemical, and other biological fuction data known for this gene, as mined systematically from the online genetic database, Flybase.

Gene Function Info (Automatically mined systematically from FlyBase:)
Biological Function: cell division, neurogenesis, etc.
Molecular Function: DNA-binding, etc.
Genetic interaction with other genes: Brd, Dl, etc.
Gene Expression pattern: neuroblast, etc.
Mutants Effect: central nervous system, neuroblast, etc.

This Gene Function information would be used by a biologist to decide whether ther the computationally-identified clusters of DNA binding sites in the gene promoters are likely to be functional in programming neural-specific gene expression, based on the experimentally defined Gene Function data mined from Flybase. This would then be used to prioritize whether this particular gene, neur, is one which should be experimentally tested by mutating one or more of the DNA binding sites seen in its cluster.

Tab 2: demo illustration of the same information, but displayed in a Drupal 5 site (DrupalFlexLJ).

Tab 2: demo illustration of the same information, but displayed in a Drupal 5 site (AcquiaDrupal126).

Tabs 4, 5, and 6 show similar Gene Function data that has been pulled from an XML data source, rather than mined (by XML-RPC) from the online Flybase genomics database. An XML file of "Unififed Gene Page" data for all 14,000 fly genes has been created, which include much of the same Gene Function data