ENCODE Uniform Data Processing Pipelines: Wrap-up – J. Seth Strattan

ENCODE Uniform Data Processing Pipelines: Wrap-up – J. Seth Strattan


Seth Strattan:
Okay, so we are out of time. So, I’ll wrap it up. I told you that our goal for this entire
project was to deploy these relatively complicated pipelines in a way that anybody can run. Now,
we’ve chosen this DNX as platform. Many of you in this session have asked how you
can run the code on your own cluster, and I’ve given you a link to our get hub [spelled
phonetically] repository here, where all of the code that actually runs behind these pipelines
is available for download. And I wanted to tell you that tonight at the poster session,
Ben and I both have posers. Ben has a poster on the RNA pipeline, and I have a poster on
ChIP pipeline. And we would be very happy to talk to you more about big picture questions,
or small picture questions, anything that you want to talk about. Come to the poster
session, and you can get to us after the session through [email protected] So,
that will go to our group, and we all see those messages. So, if you have any additional
questions about the pipeline or how to run them, or you would like to talk to us about
them, then contact us through encode help, or get one of our cards, or email us and contact
us directly, because one of the goals of our project is to make this so that you can run
it. So if you need more help, please contact us. We don’t have time for additional questions,
but I will follow-up with you. But I do want to acknowledge some of the people that contributed
to the development of these pipelines. One of the software engineers who wrote most of
the RNA-seq is not here today. His name is Tim Drazier [spelled phonetically] and I wanted
to make sure that his name was mentioned, because we’ve been running his code all
day long. You know Mike and Eurie, because Mike introduced us, and Eurie has been here
as well. Other members of the data coordinating center are listed here. These pipelines have
all been defined by members of the ENCODE consortium outside of the data coordinating
center, as part of the working groups that focus on the particular assay. So, there’s
an RNA-seq working group that defined the RNA-seq pipeline and so forth. Their names
are listed here, and this has been sort of a — if you want we’d talk about private/public
partnerships, this has been a collaboration with DNAnexus and a number of their senior
engineers have been with us throughout this process. And so, their names are listed here.
And particularly thanks to Joe and George for coming all the way from California to
help today. So, that’s all we’ve got, and thanks for coming to the workshop. [applause] Male Speaker:
So, I’d like to thank Ben and Seth for doing all this today. They’ve been working hard
for the past couple of weeks, but I want to congratulate you. I mean, you may not realize
it, but you’re the first sort of public group to actually run these pipelines, which
is very significant because you couldn’t ever run ENCODE pipelines before yourself
unless you had access to some nice, expensive cluster, and maybe some bioformatics people
to run them. So, congratulations to you. I think there were many, many hands that went
up, that you actually were successful. I hope you can use it again, and you know, you’ve
got this free account for $100, and play as much as you want. Certainly, you know, we’re
around to answer questions, but George and Joe are back there still. They’ll be around
for a couple of hours. So, certainly find them during the break, but thank you a lot
for putting up with this, you know, demo, and we’ve learned a lot. And I hope you
have too. Thank you. [applause] [end of transcript]

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