The 1st Epigenome Informatics Workshop
September 10th-12th, 2009, Houston, Texas
There will be five sessions spread of 2.5 days. Sessions 1-3 will be coducted by EDACC staff. Session 4 will be conducted by REMC and disease project representatives. Session 5 will focus on potential collaborative projects between EDACC and other NIH Epigenomics Roadmap Initiative members.
The workshop will include 3 exercises (as part of Sessions 1-3). The following data generated by the consortium may be used for the exercises:
| H1 cell line | IMR90 cell line | |
|---|---|---|
| ChIP-seq | 6 marks | ? |
| Methylome | Bisulfite-seq MRE-seq MeDIP-seq |
Bisulfite-se3 MRE-seq MeDIP-seq |
| smRNA-seq | yes | yes |
| mRNA-seq | yes | yes |
Thursday, Sep 10th
| Session 1: Data Flow and Genboree This session will have dual focus: (a) Epigenomic Data Flow and (b) Introduction to Genboree | |
|---|---|
| 9:00am-9:45am 9:45am-10:00am |
Opening and Introduction – Art Beaudet and Aleks Milosavljevic Data flow overview – Aleks Milosavljevic Metadata, raw and analysis data, data flow |
| 10:00am-10:30am | Genboree feature overview – Alan Harris Databases, tracks, projects, groups, users, access control |
| 10:30am-10:45am | Break |
| 10:45am-12noon | Genboree Exercises – Alan Harris |
| 12noon-1:00pm | Lunch |
Session 2: Primary Data and Pipelines ( Galaxy and Genboree integration, Tools) This session will have dual focus: (a) Primary data Analysis and (b) Galaxy/Genboree integration | |
| 1:00pm-1:30pm | Galaxy-Genboree integration – Alan Harris Integration of Galaxy pipelines and Genboree via Genboree APIs |
| 1:30pm-2:15pm | Primary Data Analysis Pipelines – Cristi Coarfa Read mapping via Pash. Defining and computing Level 2, 3 data for various assays and pipelines. Defining verification procedures. |
| 2:15pm-3:45pm | Primary Data Analysis Exercises – Cristi Coarfa Running Genboree-integrated EDACC-hosted Galaxy reference pipelines to perform primary analysis for various assays. |
| 3:45pm-4:00pm | Break |
| 4:00pm-5:00pm | Data Analysis Tools – Wei Li MACS, BS-seq, others. |
| 5:00pm-6:00pm | EDACC Housewarming party (Suite 400D) |
| 6:30pm-8:00pm Dinner | (Trevisio restaurant, Texas Medical Center) |
| Session 3: Integrative Data Analysis and Visualization and Genboree APIs This session will have dual focus: (a) Integrative Data Analysis and (b) EDACC-hosted methods and tools relevant of Intregrative Analysis: Virtual Genome Painting and Genboree APIs | |
|---|---|
| 9:00am-10:00am | Integrative Data Analysis and Visualization – Cristi Coarfa Finding differenecs: ChIP-seq, MACs and multiscale. Visualization in the context of UCSC tracks ( by using UCSC service or Genboree warehousing ) |
| 10:00am-10:15am | Integrative Data Analysis and Visualization Exercises – Cristi Virtual Genome Painting, Circos. |
| 10:15am-11:00am | Break |
| 11:00am-12noon | Using Genboree APIs to retrieve integrated data sets– Andrew Jackson Retrieving data for integrative analysis of multiple marks, clustering and heatmap visualization. |
| 12noon-1:00pm | Lunch |
| Session 4: Participant-supplied topics: problems, solutions, and opportunities addressable in collaboration between REMCs or disease-focused projects and EDACC | |
A sampling of problems/solutions/opportunities that may be addressed:
1. Sharing pre-publication data among members of collaboratring groups. Examples: sharing pre-publication data generated by REMCs among REMCs; sharing pre-publication data generated by disease projects among disease projects.
2. Pash mapping service for all assays ( EDACC automatically generating upon REMC data submission Level 1 data in SAM format for all assays )
3. Developement of reference pipelines: defining and computing Level 2, 3 data for all assays
4. Defining verification procedures and coordinating REMCs verfication and EDACC verification.
5. Defining epigenome similarity measures (multiscale) to identify global/local similarities and differences.
6. Warehousing external epigenomic and other data sets of relevance for integrative analysis
7. Developing, integrating, and serving up visualization tools: VGP, Circos, heatmaps, others
8. Integrative analysis: Serving up integrated data sets via Genboree APIs
| 1:00pm-1:15pm | Introduction |
| 1:15pm-1:45pm | UW: Bob Thurman |
| Multiscale analysis, chipseq and chromatin accessibility. | |
| 1:45pm-2:15pm | UCSF/UBC/UCSC: Nina? |
| Histone modification marks algorithms and analysis | |
| 2:15pm-2:45pm | UCSD: Lee Edsall |
| Comparing lanes, peak calling, bisulfite sequencing mapping. | |
| 2:45pm-3:15pm | Broad: Noam Shoresh |
| Discussion of topics of interest rather than a presentation. Peak calling, segmentation, analysis issues. | |
| 3:15pm-3:30pm | Break |
| 3:30pm-4:30pm | Disease projects |
| 4:30pm-5:00pm | Summary |
| Session 5: Outline of potential collaborative projects | |
|---|---|
| 9:00am-9:45am | Outline of Collaborative Project 1 |
| 9:45am-10:30am | Outline of Collaborative Project 2 |
| 10:30am-10:45am | Break |
| 10:45am-11:30am | Outline of Collaborative Project 3 |
| 11:30am-12:00noon | Closing Remarks and Adjourn – Aleks Milosavljevic |
This page last reviewed on May 6, 2014