1. To access the wireless network: Please bookmark the following link, which will allow each of you to become set-up as a Rice visitor online: https://docs.rice.edu/confluence/display/ITTUT/Connect+on-campus After connecting to the link above, Scroll down and select to connect to the non-secure wireless network "Rice Visitor"

2. Introduction to the Second Epigenome Informatics Workshop Aleksandar Milosavljevic Epigenomics Data Analysis and Coordination Center (EDACC) Presented at the 2 nd Epigenome Informatics Workshop Houston, Texas, September 9 th 2010

3. Announcement Modules 1-8 will be partially recorded and distributed.

4. Welcome to the Texas Medical Center Rice UniversityBaylor College of Medicine Downtown Houston

5. Workshop Sponsors and Funders

6. NIH Epigenomics Roadmap Project Hypothesis: Origins of health and susceptibility to disease are, in part, result of epigenetic regulation Goal: Transform biomedical research by Developing comprehensive reference epigenome maps Developing new technologies for epigenomic analyses

7. (adapted from John Satterlee’s talk March, 2009) EDACC Data Coordination Mapping Centers Health and disease New Tech. Novel Marks NCBI Data Distribution

8. Workshop purpose 1.Educate participants about the cyberinfrastructure developed at EDACC to support analyses of epigenomic data. 2.Explore ways in which EDACC and REMCs can enable disease projects. 3.Exchange experience in epigenomic data analysis tools and methods. 4.Explore collaborative opportunities. Explore opportunities for collaborative building, analysis and uses of Human Epigenome Atlas

9. Introductions EDACC Director Dr. Aleksandar MilosavljevicModules 1,6,7 EDACC Co-director Dr. Arthur L. Beaudet Dr. R. Alan HarrisModules 2,3 Dr. Cristian CoarfaModules 4,5,9 Dr. Wei Li Dr. Robert A. Waterland Mr. Andrew R. JacksonModule 8 Workshop coordinator Ms. Elke Norwig-Eastaugh elken@bcm.edu Full list of EDACC / BRL members: http://www.brl.bcm.tmc.edu

10. Self-introduction of workshop participants

11. Workshop schedule

14. NIH Epigenomics Roadmap Initiative 5100s samples DNA methylation Histone modifications Chromatin accessibility RNA-seq 50 Reference Epigenomes Disease Epigenomes Chromatin accessibility 10

15. Data Flow www.roadmapepigenomics.org www.roadmapepigenomics.org

16. Creating a Data Commons Data Level (0-4) definitions “chip” data“seq” data Level 0imagereads Level 1extracted featuresmapped reads Level 2normalized intensities raw signal (read density) Level 3epigenomic state of an individual sample Level 4results of integrative analyses involving more than one sample

17. Creating a Data Commons: Metadata Extended NCBI Short Read Archive XML (SRA-XML) Data Levels 0-4

18. Data Flow Mapping Centers EDACC NCBI Archive and Portal Verify Level 1-3 analyses Create Genboree project and verify run data Reference primary analysis pipeline Journal Publication Perform Level 4 Analyses and publish

19. NCBI Epigenomics Portal http://www.ncbi.nlm.nih.gov/epigenomics

20. Human Epigenome Atlas Release 1 (June 14 th, 2010 based on April 1 st, 2010 freeze ) www.epigenomeatlas.org www.epigenomeatlas.org Assays Samples Experiments

21. Human Epigenome Atlas Release 1 www.epigenomeatlas.org www.epigenomeatlas.org Assays

22. Human Epigenome Atlas Release 1 www.epigenomeatlas.org www.epigenomeatlas.org Samples

23. Human Epigenome Atlas Release 1 www.epigenomeatlas.org www.epigenomeatlas.org Experiments

24. Human Epigenome Atlas Release 1 www.epigenomeatlas.org www.epigenomeatlas.org Samples Data Downloads April - Jul 2010 ( not including NCBI ) :

25. EDACC Aim: Cyberinfrastructure for Building, Analyzing and Using the Human Epigenome Atlas

26. Genboree Genome-centric databases Users Groups Roles Access Projects Genboree Workbench Tools