Genome Modeling System

The Genome Modeling System (GMS) is a sophisticated, highly-developed framework for managing processing and analysis pipelines for many kinds of sequence data at scales from the single investigator lab to large data-intensive institutes. Emphasis is on atomic tracking and absolute repeatability, with underlying information management handled by a structured relational database. GMS offers many novel features, including installation as a system image, facilities for structured user-development and ready extension, federated capability to optionally operate across institutions, and “intelligent computing”. For example, GMS’ complete awareness of all prior computations allow it to skip component computations that would be repeated, even if part of a different overall pipeline (short-cutting) and it can automatically parallelize computations, when appropriate. GMS is built entirely on free engines, like the OpenLava job scheduler and the PostgreSQL RDBMS, and relies on no commercial software. It has been used at the Genome Institute for almost 5,000 whole genomes and 44,000 exomes. See what GMS can do for you!


A series of classes called Genome Model Basics have been presented at the Genome Institute during the first quarter of 2013. An additional series tentatively titled Genome Model Not So Basic is also scheduled. These presentations are meant to be the basis of presentations tailored for external users of the GMS and to extend and expand the general GMS documentation.