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The Genome Institute at Washington University has developed a high-throughput, fault-tolerant analysis information management system called the Genome Modeling System (GMS), capable of executing complex, interdependent, and automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. GMS includes a full system image with software and services, expandable from one workstation to a large compute cluster.

GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its federated data management system that also supports external collaboration. Most importantly, rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS provides systematic integration between the two. The GMS thus promotes versioned data tracking of ad hoc analyses while facilitating rapid development of formal pipelines.

As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395 BL) and produced an integrated analysis of these data. The results are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations.

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Step-by-step instructions for installing the sGMS	Technical documentation about the internals of the sGMS	Tutorials for running different analyses using the sGMS	Frequently asked questions about the sGMS