News:ENCODE Users' Meeting
Entering edit mode
8.7 years ago
Emily 23k

Hi all

I'll be involved in the ENCODE Users' Meeting this month. Here's the advert for it:

Registration for the first ENCODE Users Meeting is now open. Cost and links to abstract submission and registration are available at:

The ENCODE 2015: Research Applications and Users Meeting will be a 2.5-day workshop to learn how to navigate, analyze, use, and integrate ENCODE and mouseENCODE data. The NHGRI-sponsored meeting will be held from June 29 - July 1, 2015 at the Bolger Center ( in Potomac, MD.

This meeting will have both scientific presentations from a distinguished list of invited speakers and hands-on tutorial sessions with the goal of learning how ENCODE and mouseENCODE data has been used and providing opportunities to apply these tools to your own data.

We will have a poster session and select talks from the submitted abstracts. In addition, this meeting will provide opportunities for scientist to interact with people familiar with ENCODE datasets and analysis and foster future collaborations.

Abstract submission deadline: June 1, 2015

Invited Speakers

  • Stephen Baylin, Johns Hopkins School of Medicine
  • Brad Bernstein, Harvard/Massachusetts General Hospital
  • Stephen Chanock, National Cancer Institute
  • Chris Cotsapas, Yale University
  • Nancy Cox, Vanderbilt University
  • Chris Glass, University of California, San Diego
  • Mathieu Lupien, University of Toronto

  • Len Pennacchio, Lawrence Berkeley National Laboratory

  • Katherine Pollard, University of California, San Francisco
  • Wesley Pike, University of Wisconsin-Madison
  • Evan Rosen, Harvard Medical School
  • Shamil Sunyaev, Harvard Medical School
  • Katalin Susztak, University of Pennsylvania
  • and many more

Workshop topics

  • Learn to use resources for viewing, querying, and downloading ENCODE data
  • Run ENCODE processing pipelines on your own data (ChIP-seq, RNA-seq, DNase-seq, DNA methylation)
  • Integrate ENCODE data with those from your lab or major projects
  • Use ENCODE data to:
    • Interpret human variation and personal genomes
    • Interpret cancer genomes
    • Connect genes to their controlling regulatory elements to target genes across the genome
    • Identify likely cell types and pathways underlying non-coding disease associations

We look forward to seeing you in June.

encode ucsc conference functional-genomics ensembl • 2.3k views
Entering edit mode
8.7 years ago

One type of information that I was unable to find (several times when looking to prepare training materials) were full and complete instructions on running a pipeline. Most of the documents are PDF files from presentations. The resources are mostly listings of software tools. What seems to be missing are "code type" of content. Makefiles, command line invocation of tools, Readme-s that one could use. For example a Makefile stored in a git repository that would contain sections:

  • getting data that corresponds to one or more experiments
  • running tools with certain parameters and producing outputs that one is expected to create

that would make the process very explicit and would allow a far easier training of newcomers to the field.


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