Object-oriented behavior modeling for biological systems

To effectively model complex biological systems biologists need methods to organize and analyze the flood of complex genomic and proteomic data being produced. The issue of handling systems complexity has already been addressed in other fields. Specifically the computer science field has defined object-oriented methodologies and architectures to handle the complexity in software systems. To demonstrate how these tools can be used to define the behaviors of a biological system and its components, we have set forth to model the behaviors exemplified by influenza A. Although, the genome of influenza A has been well studied, putting the available information into a format that is usable to biologists poses significant challenges. Here, we have used reverse engineering and literature searches to define behaviors associated with the influenza infection process and its viral components. Using object-oriented principles, static and dynamic models were developed that emulate behaviors found in the viral infection and reproduction processes.