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Events/GCC2012/Program/Includes

This page is not intended to be viewed directly. Rather it contains several snippets of wiki markup that are then included on the GCC2012 Program page inside tables. Doing it this way makes the wiki markup much, much easier.


Session1

9:10

Slides, Video (start @ 7:10)
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project

9:40

Slides, Video (start @ 31:55)
Integration of S-MART, a toolbox to aid RNA-seq data analysis in Galaxy
Yufei Luo, Unité de recherche en Génomique-Info, INRA

10:00

Slides, Video part 1 (start @ xx:yy), part 2
Connecting Galaxy to a Data Repository
Richard Park, Boston University & Center for Biomedical Informatics at Harvard Medical School

10:20

Slides, Video (starts @ 11:45)
Role of Galaxy in a bioinformatic plant breeding platform
Vincent Maillol and Jean-Francois Dufayard, INRA and CIRAD

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Session2

11:10

Galaxy Pipeline for Faster Whole Genome Genotype Calling on the GeneTitan Platform
Oleksiy Karpenko, University of Illinois Chicago

11:30

Slides, Video (starts @ 18:15)
Integrating Galaxy with Globus Online: Lessons learned from the CVRG project
Bo Liu, Computation Institute, University of Chicago and Argonne National Laboratory

11:50

Slides, Video (starts @ 42:35)
Scalable data management and computable framework for large scale longitudinal studies

12:10

PDF, PPT, Video part 1 (starts @ 58:45), part 2
Nebula - A Web-Server for Advanced ChIP-Seq Data Analysis
Alban Lermine, Institut Curie

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Session3

1:50

Establishing a National Genomics Virtual Laboratory with Galaxy CloudMan

2:10

Slides, Source, Video part 1 (starts at 22:00), part 2
Keeping Track of Life Science Data
Björn Grüning, Albert-Ludwigs-University Freiburg

2:30

PPT, PDF, Video (starts at 3:00)
Easier Workflows & Tool Comparison with Oqtans+

2:50

Slides, Video (starts @ 19:25)
CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences
Gregory Minevich, Columbia University

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Session4

3:40

GPS: a real-time recommendation system for ChIP-Seq analysis
Hanfei Sun, Dana-Farber Cancer Institute

4:00

Slides, Video (starts @ 16:45)
Integration of Taverna workflows on a Galaxy-based platform for large-scale genomics analysis
Tin-Lap Lee, The Chinese University of Hong Kong

4:20

PDF, PPTX, Video part 1 (starts @ 35:30), part 2
NGS analysis for Biologists: experiences from the cloud
Karen Reddy, Johns Hopkins University

4:40

Slides, Video (starts @ 8:40)
The Galaxy Visualization Framework
Jeremy Goecks, Emory University

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Session5

9:10

Slides, Video (starts @ 7:55)
High level distributed processing pipelines with Galaxy
Brad Chapman, Harvard School of Public Health

9:30

PDF, Keynote, Video (starts @ 28:30)
Proteomics tools for Galaxy
Ira Cooke, La Trobe University

9:50

PDF,PPT, Video (starts @ 48:05)
Using Galaxy for Molecular Assay Design
James Ireland, 5AM Solutions

10:10

PDF, PPTX, Video part 1 (starts @ 1:07:10), part 2, part 3
The National Center for Genome Analysis Support and Galaxy
Richard LeDuc, Indiana University

END_INCLUDE

Session6

10:55

Integration of SeqWare within Galaxy
Zhibin Lu, Ontario Institute for Cancer Research

11:15

PDF, PPSX, Video (starts at 13:40)
Window2Galaxy – Enabling Linux-Windows Hybrid Workflows
Liram Vardi, Agilent Labs

11:35

PDF, PPTX, Video (starts @ 35:15)
NBIC Galaxy to Strengthen the Bioinformatics Community in the Netherlands
David van Enckevort, Netherlands Bioinformatics Centre

11:55

PDF, PPTX, Video part 1 (starts @ 54:10), part 2
GenomeSpace
Ted Liefeld, Broad Institute

END_INCLUDE

Session7

1:10

Tool Shed and Changes to Galaxy Distributions
Greg von Kuster, Penn State University

1:30

Lightning Talks

PDF, PPTX, Video (starts @ 24:40)
Customizing Galaxy for a Hospital Environment
Larry Helseth, NorthShore University HealthSystem

Slides, Video (starts @ 30:30)
ObjectStore
Nate Coraor, Penn State University

PDF, PPTX, Video (starts @ 36:35)
Galaxy and Condor: Challenges with harnessing widely-distributed resources
Jaime Frey, University of Wisconsin-Madison

Link, Video (starts @ xx:yy)
Interactive metagenomic visualization in Galaxy
Brian Ondov, NBACC

Slides, Video (starts @ xx:yy)
Reusable / Scalable Workflows
Clare Sloggett, VLSCI

Slides, Video (starts @ xx:yy)
The Galaxy VM Launcher
John Chilton, University of Minnesota

Slides, Video (starts @ xx:yy)
Differential Expression with Diagnostic Plots using sam2counts and DESeq
Nikhil Joshi, UC Davis

PDF, PPT, Video
Galaxy-P
Pratik Jagtap, University of Minnesota

The Genomic Hyperbrowser: Prove Your Point
Geir Kjetil Sandve, University of Oslo

Slides, Video (starts @ 6:10)
ChemicalToolBoX
Björn Grüning, Albert-Ludwigs-University Freiburg

2:45

Video (starts @ 12:35)
Closing Remarks
Anton Nekrutenko, Penn State University, James Taylor, Emory University

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Day1Lunch

Lunch: Sponsored by EMC Isilon

EMC Isilon
Implications of a Galaxy Community Cloud in Clinical Genomics
Sanjay Joshi, Chief Technical Officer (CTO), Life Sciences, EMC Isilon
EMC Isilon Sponsor Presentation
Video

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IonTorrent

Ion Torrent
Ion Torrent: Open, Accessible, Enabling
Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products
Ion Torrent Sponsor Presentation
PDF, PPT, Video

END_INCLUDE