Title: Naturally Speaking: A Systems Biology Tool with Natural Language Interfaces (NYU-CS-TR853) Author: Marco Antoniotti, Ian T. Lau, and Bud Mishra Abstract: This short paper describes a systems biology software tool that can engage in a dialogue with a biologist by responding to questions posed to it in English (or another natural language) regarding the behavior of a complex biological system, and by suggesting a set of facts about the biological system based on a timetested generate and test approach. Thus, this bioinformatics system improves the quality of the interaction that a biologist can have with a system built on rigorous mathematical modeling, but without being aware of the underlying mathematically sophisticated concepts or notations. Given the nature of the mathematical semantics of our Simpathica/XSSYS tool, it was possible to construct a well-founded natural language interface on top of the computational kernel. We discuss our tool and illustrate its use with a few examples. The natural language subsystem is available as an integrated subsystem of the Simpathica/XSSYS tool and through a simple Web-based interface; we describe both systems in the paper. More details about the system can be found at: http://bioinformatics.nyu.edu, and its sub-pages.