Workshop website: http://brl.bcm.tmc.edu/workshop.rhtml
The 3rd Epigenome Informatics Workshop
First Call for Participation
March 5-6, 2012
Registration
Deadline: |
Wednesday February
15, 2012 |
Registration
Form: |
Summary:
The workshop is organized by the Epigenome Center at Baylor
College of Medicine as part of the NIH Roadmap Epigenomics Initiative. This
hands-on workshop aims to facilitate exchange of methods, tools, resources, and
practical knowledge required for epigenomic research.
As the amount of publicly available
epigenomic data increases, so will the utility of integrative analyses
combining study-specific data with data in the public domain. To explore this
emerging opportunity, the two days of the workshop have slightly different
emphases.
The first day focuses on epigenomic
profiling and analysis of study-specific data, including methylation assays,
whole genome bisulfite sequencing, RRBS, MeDIP-seq, and Illumina
HumanMethylation 450K Array), histone marks (ChIP-seq), transcription factor
binding (ChIP-seq), chromatin accessibility, and transcriptome profiling
(RNA-seq).
The second day focuses on integrative
analyses that combine epigenomic profiles generated in the context of specific
studies with publicly available data. Special focus will be on the analyses
involving reference epigenomes produced by the NIH Roadmap Epigenomics Initiative,
with a secondary focus on the data generated by ENCODE and TCGA projects and
the growing number of epigenomic profiling data in the NIH GEO archives and the
UCSC Genome Browser databases.
In addition to didactic lectures by
EDACC staff and hands-on exercises, a number of case studies will be included.
Some of the case studies may be presented by workshop participants. For
instructions on how to propose a case study for possible inclusion in the
workshop, see Application Instructions below. The registration deadline is
February 15th, 2012.
Target
Participants:
Researchers using epigenomic profiling
in the context of basic and disease studies are particularly encouraged to
participate. The target participant is a lab member who performs hands-on data
analysis using a scripting language such as Perl, Python, or Ruby in a
UNIX/Linux environment. The workshop will include data analysis exercises.
Because the exercises that require programming will be optional,
non-programmers will also benefit from attending. We have reserved a total of
25 seats for participants recruited specifically from laboratories
participating in the NIH Roadmap Epigenomics Initiative and a limited number of
seats for other participants engaged in the field of epigenomic research.
Program:
Monday,
March 5: Analysis of study-specific epigenomic profiling data
Topics: Whole-genome assays, data
standards, and primary data processing pipelines. Data analysis pipelines for
epigenomic assays with sequencing readouts and chip readouts. We will review
read mapping and derivation of data tracks ready for visualization in genome
browsers. Tools for segmentation, peak calling and comparative analysis of
epigenomic profiles.
Case studies. The case
studies will illustrate applications of epigenomic profiling to gain insights
into basic biology and disease etiology. Case studies may be selected by EDACC
staff from those proposed by workshop participants. For instructions on how to
submit an abstract for a case study presentation, see Application Instructions
below.
Tuesday,
March 6: Integrative analyses combining study-specific and public data
Topics: Metadata standards, data
archives, and data portals. Emerging epigenomic data commons. Submission of
data and metadata to the NCBI GEO/SRA archives. Human Epigenome Atlas (
www.epigenomeatlas.org ). Standards developed by the NIH Roadmap Epigenomics
Initiative currently under consideration for adoption by the International
Human Epigenome Consortium. Integrative frameworks and
cyberinfrastructure for epigenomic research. UCSC custom tracks and data hubs.
NCBI custom tracks. Genboree Workbench.
Case studies –
integrative analysis. The case studies will illustrate combined analysis of
study-specific data with the data available in public data archives and data
portals. Case studies may be selected by EDACC staff from those proposed by
workshop participants. For instructions on how to submit an abstract for a case
study presentation, see Application Instructions below.
***
Logistical
Details:
Participants will be expected to bring
their own laptops. Travel, transportation, and lodging costs are not covered
and participants will be expected to make their own arrangements.
Registration
Fee:
There is a nominal registration fee for
this workshop, payable after application and acceptance.
EARLY REGISTRATION:
Register by January 23rd: |
$75 |
Register by February
15th: |
$100 |
Register after
February 15th (if space is available we
will allow late registrations) : |
$125 |
Air
Travel:
The closest airport to the
The largest airport in
Ground
Transportation:
Taxis are easily available at both
airports outside the baggage claim area. On the day of departure we will be
happy arrange for taxis for you.
Hotel:
We have arranged a block for attendees
beginning Sunday, March 4th at a reduced group rate (ranging from $109/night to
$145/night). You will receive further information in a detailed logistical
email shortly after registration and acceptance to the workshop.
Meals:
We will have coffee, tea, and a small
continental breakfast selection each morning, buffet lunches on Monday and
Tuesday, and breaks will be provided. There will be an optional outing to the
Houston Livestock Show & Rodeo for all attendees on Monday (March 5th)
evening (details to follow).
Case
Study:
If you are interested in presenting a
case study at the workshop please indicate on the registration form. We will
contact you after acceptance to obtain a one-page summary of the case study you
propose and to discuss.
Questions?:
If you have any questions or comments
please feel free to contact Elke Norwig-Eastaugh at [log in to unmask]
We hope to see you in
Registration:
To register, please use the
registration form here: https://www.bcm.edu/genetics/epigenomics/workshop.cfm