Two concurrent workshops will be held on the morning of Sat June 22, 2013. See the registration page for fees.

W1: Next-generation sequencing data analysis with GenomeSpace and Galaxy
Michael Reich (Broad Institute of MIT and Harvard) and Dave Clements (Emory University)

This workshop give an overview of the next-generation sequencing data analysis pipeline, focusing on RNA-seq, and participants will learn how to run this analysis using GenomeSpace and Galaxy. GenomeSpace brings together diverse computational tools into one place, enabling scientists without programming skills to easily combine their capabilities. Among the genomic tools available through GenomeSpace is Galaxy, an open, web-based platform for data intensive biomedical research. During the workshop, participants will learn how to load public RNA-seq data into GenomeSpace and analyze such data with Galaxy tool suites for quality assessment and RNA-seq analysis.

Workshop program:

9:00 – 9:15 Next-generation sequencing data analysis workflow outline

9:15 – 10:15 GenomeSpace: introduction to the project and loading of the data

10:15 – 11:00 Galaxy: introduction to the project and data quality assessment

11:00 - 11:30 Coffee break

11:30 - 12:30 RNA-seq data analysis with Galaxy

W2: Using the DOE Systems Biology Knowledgebase (KBase) to perform analysis and modeling of genomics data
Michael Sneddon (Lawrence Berkeley National Laboratory) and Ric Colasanti (Argonne National Laboratory).

The DOE Systems Biology Knowledgebase (KBase, is an emerging community resource designed to integrate diverse biological data within a unified computational framework to enable predictive biology.  One of the key drivers of KBase is the idea that biological models can be used as an effective tool for aggregating and understanding experimental and genomic data from multiple, disparate sources.  KBase provides a user-friendly platform for conducting large-scale data analysis on scalable computing infrastructure, building and simulating models of cellular behavior and function, and generating and testing hypotheses of gene and protein function.  KBase is an open and extensible framework for secure sharing of data, tools, and scientific conclusions in systems biology.

This KBase workshop will begin with an overview of the project, followed by a tutorial that will show how to build genome-scale metabolic models from a raw microbial genome sequence with KBase.  We will demonstrate how these models can be constrained with experimental data, then used to generate new hypotheses and test biological assumptions.  The workshop will conclude with information on how you can work with us by contributing data or software tools and a discussion of future KBase development plans.  No prior programming or modeling experience is necessary to participate.

FGED 2013 Conference in Seattle

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