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To access the wireless network:

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

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  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 2nd Epigenome Informatics Workshop Houston, Texas, September 9th 2010

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

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

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

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

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

  10. Self-introduction of workshop participants

  11. Workshop schedule

  12. Workshop schedule

  13. Workshop schedule

  14. NIH Epigenomics Roadmap Initiative DNA methylation Histone modifications Chromatin accessibility RNA-seq Reference Epigenomes 50 Disease Epigenomes 10 Chromatin accessibility samples 5 100s

  15. Data Flowwww.roadmapepigenomics.org

  16. Creating a Data Commons Data Level (0-4) definitions

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

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

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

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

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

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

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

  24. Human Epigenome Atlas Release 1www.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 Roles Users Groups Access Projects Tools Genboree Workbench Genome-centric databases

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