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Advances in genomics are creating new opportunities to integrate systems modeling and bioinformatics. The goal of the first SysMod meeting is to create a forum for systems modelers and bioinformaticians to discuss common research questions and methods. The meeting will cover the full range of methods used in systems modeling, including qualitative and quantitative and dynamical and steady modeling, as well as cover the full range of applications of systems modeling including basic science, bioengineering, and medicine. The first SysMod meeting will in particular focus on areas of systems modeling which are, or could be, deeply integrated with bioinformatics, including logical, rule-based, and constraint-based modeling.