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Design a genome browser

Tom designed a “Genome Browser”, intended to illustrate the transformative impact of applying consumer technology to make leading-edge science available to everyone everywhere. The software design challenge was to provide an end-to-end demonstration of “Hex™” in the life science domain. Hex is the language-neutral web- and cloud-based object environment that powers the Zeetix portfolio. He made extensive use of relevant software design patterns in both the browser and the server.

Tom designed the presentation-layer interaction model, alongside the browser DOM, so that the initial set of presentation objects are loaded from the Hex server (based on its persistent object id) and realized, in Javascript, in the browser. He wrapped the Google Map API, hooking relevent browser events to enable an AJAX exchange with the server in response to a mouse click on a specific marker or its icon in the navigation tree. The html content of the resulting “ZeeWindow” is thus collected from the server dynamically in response to the mouse click. The object id of the marker object is passed to the server in the AJAX exchange.

On the server, Tom specialized the various Hex framework classes (written in Python), so that the html request is ultimately handled by a renderer descendent that queries the MySql database (at runtime) and expands a server-side template using data-model information derived from the initial request. The resulting html is serialized (using JSON) and wrapped in a response that is then passed back to the browser, where it is unwrapped, expanded into the appropriate browser-side Javascript and DOM objects, and then passed to the Google API routines that open and display the resulting window.

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Portfolio

ZeeLife

Tom created these two "pre-construction" demos, a GenomeBrowser and a PathwayBrowser. When complete, each will allow the user to browse, annotate, and publish arbitrary data at arbitrary detail—all the way from the karyotype or organism to the sequence or molecular level.

Genome Browser Demo

Genome Browser:  Use the Google Map API to browse a full human genome.

Pathway Browser Demo

Pathways Browser:  Use the Google Map API to browse the human metabolic pathways.

ZeeGuide

ZeeGuide™ is a "Facebook for neighborhoods", a social network comprised of businesses, organizations, and individuals related by physical geography and "affinity".

Partners and resources

Mcvinney & CompanyMcVinney & Company is a Massachusetts-based organizational development and executive consulting company.

WingwareWingware is a Cambridge-based company dedicated to the development and sale of software development tools for the Python programming language.

ApacheZeetix sites are hosted on Apache web servers.

Valid XHTML 1.0 StrictZeetix sites are validated as "XHTML 1.0 Strict" for maximum browser interoperability.

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