Workshop website: http://brl.bcm.tmc.edu/workshop.rhtml

The 3rd Epigenome Informatics Workshop
First Call for Participation
March 5-6, 2012
Baylor College of Medicine, Houston, Texas 

Registration Deadline:
Wednesday February 15, 2012

Registration Form:
https://www.bcm.edu/genetics/epigenomics/workshop.cfm


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 DETAILS

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 & 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. 

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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: $75.00
Register by February 15th: $100.00 
Register after February 15th (if space is available we will allow late registrations): $125.00
 
AIR TRAVEL:
The closest airport to the Texas Medical Center is Houston Hobby (HOU), approximately 20 minutes to the south. The major airlines servicing Hobby include Southwest, Air Tran, JetBlue, Delta and American.
The largest airport in Houston is Houston Intercontinental (IAH), approximately 50 minutes to the north. This airport is serviced by most major airlines and is a hub airport for Continental / United. There are daily nonstop flights to/from many international destinations as well.

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 STUDIES:
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 Houston in March!

REGISTRATION:
To register, please use the registration form here: https://www.bcm.edu/genetics/epigenomics/workshop.cfm