The Encyclopedia of DNA Elements project (ENCODE) has been producing data for over eight years to investigate DNA and RNA binding proteins, chromatin structure, transcriptional activity and DNA methylation on a variety of human and mouse tissues and cell lines.

As the complexity and diversity of the data grows, the tools required to organize, search and access the data in meaningful ways need to be more sophisticated. The ENCODE Data Coordination Center (DCC) have built a web resource, the ENCODE Portal, to distribute the results of these experiments. This system allows external researchers to write their own interfaces to access, analyze and visualize the ENCODE data. It also facilitates the integration of the ENCODE data with other similar large-scale data sets like Epigentics Roadmap and modENCODE. Web-based faceted browsing and search are supported, as is programmatic access through the ENCODE REST API with JSON (JavaScript Object Notation) objects to facilitate the access of ENCODE experimental metadata using a web portal.

Here we present our implementation and give examples of how researches can use these tools to gain access to ENCODE. The ENCODE Data Analysis Center (DAC) have specified uniform processing pipelines for four ENCODE datatypes: ChIP-seq, RNA-seq, DNase-seq, and whole-genome bisulfite sequencing. The DCC have implemented these pipelines and deployed them to a cloud-based platform.

In this workshop you will explore hands on access to ENCODE data and metadata via the ENCODE Portal and programatic access to all the data via a REST API. You will also use the unified processing pipelines via the DNAnexus web site. The ENCODE Portal is https://www.encodeproject.org/. The DCC codebase is freely available at https://github.com/ENCODE-DCC/.