Software

The BMSR develops, distributes and supports five software packages for advanced biomedical modeling and simulation applications: ADAPT, EONS, LYSIS, PNEUMA, and TARGETgene

ADAPT is a set of high-level programs for simulation, data analysis and design of experiments, designed primarily for basic and clinical research modeling and data analysis applications involving pharmacokinetic and pharmacodynamic systems. It is developed under the supervision of Professor David Z. D’Argenio.

RAD-ADAPT is a standalone ADAPT application for modeling and analysis of clonogenic assays in radiation biology. It is developed by Dr. Yaping Zhang and Professor David Z. D’Argenio.

LYSIS (the Greek word for “solution”) is an interactive modular software package of programs performing high-level tasks that can be used for linear and nonlinear time-series analysis, and system modeling and simulation. It is developed under the supervision of Professor Vasilis Z. Marmarelis.

PNEUMA is a Simulink-based set of programs designed to model human cardiorespiratory and sleep-state control. A major goal of this set of software modules is to allow the user to perform virtual experiments and computer simulations of the interactions between the respiratory and cardiovascular systems under conditions of changing sleep-wake states, such as what occurs in the various forms of sleep-disordered breathing. It is developed under the supervision of Professor Michael C.K. Khoo.

EONS is an interactive program that allows the conceptual modeling of a synapse. It was designed to provide users with a computational tool to better understand the interactions between elements within the synapse, as well as the influence of its geometry. It is developed under the supervision of Professor Theodore W. Berger.

TARGETgene is a MATLAB tool for identifying possible therapeutic targets and drug candidates in cancer and other diseases using high-throughput experimental data and gene network-based approaches. The graphical user interface enables mapping and analysis of the genetic network at the functional systems level. It is developed by Dr. Chia-Chin Wu and Professor David Z. D’Argenio.