Summary:

The workshop is organized by the Bioinformatics Research Laboratory at Baylor College of Medicine (http://brl.bcm.tmc.edu/epiCenter/index.rhtml).  This 2-day hands-on workshop aims to facilitate exchange of methods, tools, resources, and practical knowledge required for "omic" research, with an emphasis on epigenomic analysis using bioinformatic tools integrated within the Genboree Workbench.

The first day will focus on analytical tools and methods for epigenomic profiling and analysis.  A major focus will be on methylation profiling, including profiles generated using Illumina Human Methylation 450 BeadChips, bisulfite sequencing, RRBS, and MeDIP-Seq. Analysis of other types of epigenomic profiles will also be covered, including histone marks (ChIP-Seq), transcription factor binding (ChIP-seq), chromatin accessibility, and transcriptome profiling (RNA-Seq).  Specific analytical tools that will be covered include MACS, LIMMA, TopHat, CuffLinks, Cuffdiff, and Spark.

The second day will introduce integrative analysis involving a diversity of epigenomic profiling data in the public domain. The dramatic increases of the volume and diversity of this profiling data create both opportunities and challenges. We will illustrate integrative analyses using reference epigenomes produced by the NIH Roadmap Epigenomics Initiative (www.epigenomeatlas.org), and epigenomes produced by the ENCODE consortium and by members of the International Human Epigenome Consortium (IHEC).  As time allows, we will also include example analyses of data generated by other large consortia such as the 1000 Genomes Project, International Cancer Genome Consortium, and the growing epigenomic profiling data in the NIH GEO archives and the UCSC Genome Browser databases.

Analyze Your Data At the Workshop:

The workshop will emphasize hands-on data analysis through a series of use cases.  Participants will be asked to complete a few introductory online use cases prior to arriving on-site. Workshop participants will be able to upload their data prior to arrival and then learn how to conduct epigenomic analyses of their own data at the workshop, using tools in the Genboree Workbench.  We have allocated up to 50GB storage to each participant for uploading of their data onto Genboree prior to the workshop. Prepared datasets will be available for workshop attendees that do not have data to upload, or do not wish to upload their data. Instructions for uploading data will be provided following registration.

Target Participants:

The workshop is tailored to researchers involved in "omic" research at all levels (principal investigators, postdoctoral fellows, graduate students, technical staff). The main workshop track will be aimed at non-bioinformaticians and an additional special track will be tailored to Bioinformaticians, Software Architects, and Developers.

Main Track For Researchers (non-bioinformaticians)

Researchers using epigenomic profiling in the context of basic and disease studies are particularly encouraged to attend. The target participant is a researcher who performs hands-on data analyses using various bioinformatics tools, but does not have the scripting or advanced programming skills (or interest) to develop new tools, or to customize existing tools.  We have reserved a total of 20 seats for participants recruited specifically from laboratories participating in the NIH Roadmap Epigenomics Initiative.  The total number of participants will be limited to 40.  The last three workshops were each oversubscribed, so we encourage you to register early.

Special Parallel Track for Bioinformaticians, Software Architects, and Developers

This track will focus on issues of data and tool integration, and collaborative research using the concept of the "programmable web", REST APIs, and on the Genboree cyberinfrastructure for scalable genome-centric collaborative research. This session will include 1) Genboree architecture and programming, and 2) integration of tools and data via Genboree REST APIs.  If you are a bioinformatician searching for a system that would support many collaborations, a tool developer considering deployment of your tool through the Genboree Workbench, a database developer wishing to deploy your database through Genboree, or just getting started using a scripting language such as Perl, Python, or Ruby in a UNIX/Linux environment and are exploring ways to increase your productivity using the emerging concept of the "programmable web" and Genboree REST APIs specifically, we encourage you to attend. This track will occupy a 2-3-hour block of time each of the two days, a total of 4-6 hours, depending on the degree of interest and length of discussions.

The CIBR center (http://www.bcm.edu/research/cibr) is a co-sponsor of this workshop.  The CIBR Center is a resource to help students and faculty address the broad range of analytical problems posed by the complexity of high throughput biological datasets. The goal of the center is to help bridge the translational gap from data to models, and from models to drug discovery and personalized therapy by fostering collaborations and developing original quantitative approaches to biological and clinical problems.

Program Overview:

Day 1:

Analysis of study-specific epigenomic profiling data:

1. Review of working with Genboree:  setting up and managing accounts, groups, projects, and databases, user privileges, submitting jobs, data analysis, and sharing data with collaborators.
2. Review of introductory use cases and results (introductory use cases should be completed prior to arriving at the workshop), epigenomic variation between tissues, between individuals, and in cancer.
3. Hands-on case studies:  Introduction to Chip-Seq and RNA-Seq, and 450 BeadChip analyses in the context of basic biology and disease etiology.
4. Hands-on data analysis:  Participant time to initiate analysis of own data sets, or advanced use cases for those not uploading their own data.

Special 2-3 hour parallel track for bioinformaticians, software architects, and developers:

1. Data and tool integration using the concept of the "programmable web" and REST APIs.
2. Support for scalable genome-centric collaborative research, Genboree architecture, REST-APIs, and Genboree deployment will be discussed.

Day 2:

Integrative analyses combining study-specific and public data:

1. Hands-on data analysis:  Participant time to perform analysis on own data, or to finish up use cases from Day 1.
2. Integrative data analysis using the Genboree Workbench. The case studies will illustrate analyses that combine study-specific data in the context of data available in public data archives and data portals, including the UCSC genome browser, NCBI GEO archives, ENCODE, submission of data and metadata to the NCBI GEO/SRA archives, and the Human Epigenome Atlas (www.epigenomeatlas.org). Standards developed by the NIH Roadmap Epigenomics Initiative and the International Human Epigenome Consortium will also be discussed.

Special 2-3 hour parallel track for bioinformaticians and software engineers:

1. Data and tool integration using the concept of the "programmable web" and REST APIs. Support for scalable genome-centric collaborative research.
2. Genboree architecture, REST-APIs, and Genboree deployment issues will be discussed (continuation of Day 1).

Workshop Venue:

The workshop will be held at the Hilton Houston Medical Center. Continental breakfast will start at 8:15am on Monday March 4th and sessions will wrap up around 4pm on Tuesday March 5th.

PLEASE NOTE: Participants will be expected to bring their own laptop computers with power cords.  

Registration Free:

There is a registration fee of $350.00 to attend this workshop.  A continental breakfast each morning, refreshments at breaks, lunches and an optional hosted dinner on Monday night are included in this price.   You will receive payment instructions after workshop acceptance.

Travel, transportation, and lodging costs are NOT covered and participants will be expected to make their own arrangements.  The total number of participants will be limited to 40.  Previous workshops were oversubscribed, so we encourage you to register early.

Registration will CLOSE on Wednesday, February 20th at 5pm CT.

Air Travel:

The closest airport to the Texas Medical Center is Houston Hobby (HOU), approximately 20 minutes to the south.  The airlines servicing Hobby include Southwest, JetBlue, Delta and American.

The largest airport in Houston is Houston Intercontinental (IAH), approximately 50 minutes to the north.  This airport is the main hub for United Airlines, and is also serviced by American, Delta, Frontier and Spirit.  There are also daily nonstop flights to many international destinations.

Ground Transportation To And From The Airport:

Taxis are easily available at both airports outside the baggage claim area.  On the day of departure we will be happy to arrange taxis for you.  If you are planning on renting a car and want to drive please let me know so I can give you directions.

SuperShuttle also operates from both Houston airports:
IAH - http://www.supershuttle.com/Locations/IAHAirportShuttleHouston.aspx
Hobby - http://www.supershuttle.com/Locations/HOUAirportShuttleHouston.aspx

Hotels:

We have arranged a small room block for attendees at a rate of $140.00 + tax per night.  Directions on how to book this block will be sent with your workshop acceptance confirmation.  Please note that this workshop is being held during the Houston Livestock Show and Rodeo, and the city will be quite busy; if you would like to stay over the Saturday night before please let me know, as this is the busiest hotel night during rodeo.

Meals:

We will have coffee, tea, and a small continental breakfast selection each morning, buffet lunches and breaks will be provided.  There will be an optional dinner for all attendees on Monday evening (details to follow).

Application Instructions:

To apply please follow this link: http://tinyurl.com/genboreeworkshop
 
If you have any questions or comments please feel free to email me and I will do my best to be of assistance.  We hope to see you in Houston in March!

Ms. Elke Norwig-Eastaugh
Workshop Coordinator
elken@bcm.edu
281-250-4819