Modern web applications present new challenges in managing software complexity for developers used to traditional web frameworks. This talk presents a layered approach, a rich Javascript application built on top of a JSON Linked Data web service; and the lessons learned building the ENCODE Portal, a central hub for a large collaborative genome sequencing project. As web users, our expectations for the sites we interact with have been transformed over the past few years. Meeting those expectations with traditional web frameworks has become increasingly difficult. Building pages first with server-side templates followed by progressive enhancement in JavaScript has begun to feel like building a site twice, and tends to fragile interactions that are difficult to reason about or test. In building the ENCODE Portal, we took a layered approach with a web application sitting atop a web service. This helped to clearly delineate responsibilities between the server-side Python – information architecture, access control and validation – and browser-side Javascript – page display and form generation. Our web service is built to expose JSON Linked Data (JSON-LD), a standard for expressing the semantic content of JSON formatted data, exposing and connecting them with other resources on the Semantic Web. This opens up the possibility for others to present or integrate our data in new ways, but even within a single application exposing type information on resources has allowed us to avoid duplicating routing logic on both browser and server. Separating the web service from the web application also allowed us to open up programmatic submission of metadata. Consortium labs script the transfer of experimental metadata from their internal information management systems into the same web service that drives the portal.