The 5th Epigenome Informatics Workshop

October 4th & 5th, 2012 at Baylor College of Medicine in Houston, Texas


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.

There will be two special parallel sessions for bioinformaticians and software engineers on data and tool integration using the concept of the “programmable web” and REST APIs and on the support for scalable genome-centric collaborative research. Genboree architecture, REST-APIs and Genboree deployment issues will be discussed.

The first day will focus on analytical tools and methods for epigenomic profiling and analysis from the public domain that are already integrated within the Genboree Workbench. A major focus will be on methylation profiling, including whole genome bisulfite sequencing, RRBS, MeDIP-Seq, and Illumina Human Methylation (450K Array). Other types of epigenomic profiles will also be covered, including histone marks (ChIP-Seq), transcription factor binding (ChIP-seq), chromatin accessibility, transcriptome profiling (RNA-Seq), and genome resequencing. Specific analytical tools that will be covered include MACS, LIMMA, TopHat, CuffLinks, Cuffdiff, and Atlas-SNP2.

The second day will focus on data integration. Dramatic increases in the diversity of assays and quantity of epigenomic profiling data in the public domain create both opportunities and challenges. Regarding the diversity of assays, we will focus on the integration of epigenomic and genomic variation. Regarding integration of data in the public domain, we will focus on integrative analyses involving reference epigenomes produced by the NIH Roadmap Epigenomics Initiative (, the epigenomes produced by the ENCODE consortium and other members of the International Human Epigenome Consortium (IHEC), with a secondary focus on the 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 at the workshop and to learn how to conduct epigenomic analyses of their own data. We have allocated approximately 15-20GB disc storage to each participant and will work with each registrant individually to coordinate any changes to quotas (if required) and the uploading of their data onto Genboree prior to the workshop. For workshop attendees that do not have data to upload, or do not wish to upload their data, prepared datasets will be available for the hands-on use cases. Additional instructions will be provided following registration.

Target Participants:

Researchers (non-bioinformaticians)

Researchers using epigenomic profiling in the context of basic and disease studies are particularly encouraged to participate. The target participant is a researcher who performs hands-on data analyses using various software tools, but does not have the resources, scripting or advance programming skills (or interest) to develop new tools, or to customize existing bioinformatic tools. We have reserved a total of 25 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 two workshops were each oversubscribed, so we encourage you to register early.

Bioinformaticians, Software Architects, and Developers

A new track at this workshop 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. The list of topics will include 1) Genboree architecture and programming, 2) integration of tools and data via Genboree REST APIs, and 3) Genboree deployment. 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.

Program Overview:

Day 1 - Analysis of study-specific epigenomic profiling data:

1. Review of working with Genboree: setting up and managing accounts, groups, projects, 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).

3. Hands-on case studies: epigenomic variation between tissues, between individuals, and in cancer.

4. Hands-on case studies: Introduction to Chip-Seq and RNA-Seq, and 450K analysis in the context of basic biology and disease etiology.

Special parallel 2-3 hour session for bioinformaticians, software architects, and developers: Data and tool integration using the concept of the “programmable web” and REST APIs. 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:

5. Hands-on data analysis: Participant time to perform analysis on own data sets, or to finish up use cases from Day 1.

6. Integrative analysis of genomic and epigenomic variation.

7. 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 ( Standards developed by the NIH Roadmap Epigenomics Initiative currently under consideration for adoption by the International Human Epigenome Consortium will also be discussed.

Special parallel 2-3 hour session for bioinformaticians and software engineers: Data and tool integration using the concept of the “programmable web” and REST APIs. Support for scalable genome-centric collaborative research. Genboree architecture, REST-APIs and Genboree deployment issues will be discussed.


Workshop Venue:

The workshop will be held in Room M421 in the Michael DeBakey building at Baylor College of Medicine.

PLEASE NOTE: Participants will be expected to bring their own laptops.

Registration Fee:

There is a registration fee of $250.00 to attend this workshop. A continental breakfast each morning, breaks, lunches and an optional hosted dinner are included in this price. You will receive payment information after workshop acceptance.

Travel, transportation, and lodging costs are NOT covered and participants will be expected to make their own arrangements.

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/from airport:

Taxis are easily available at both airports outside the baggage claim area. On the day of departure we will be happy 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


We have arranged a small room block for attendees at a rate of $89.00 + tax per night. Directions on how to book this block will be sent with your workshop acceptance confirmation.


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 Thursday evening (details to follow).



This page last reviewed on December 18, 2019