Enabling Systems Biology: A Scientific Problem-Solving Environment.
ABSTRACT Biologists today are striving to solve multidisciplinary, complex systems biology questions. To successfully address these
questions, software tools must be created to allow scientists to capture data and information, to share this information,
and to analyze the data as elements of a complete system. At Pacific Northwest National Laboratory, we are creating the Computational
Cell Environment, a biology-centered collaborative problem-solving environment with the goal of providing data retrieval,
management, and analysis through all aspects of biological study. A horizontal prototype called SysBioPSE, demonstrates this
vision. Our initial work is centered on developing the Distributed Data Management and Analysis subsystem, which is a specific
tool for retrieving data from multiple heterogeneous data stores, providing storage facilities that support pedigree tracking
and data and information analysis under a common user interface. With time, many such individual subsystems will be developed
and integrated to fulfill the Computational Cell Environment vision.
Conference Proceeding: Computing through scientific abstractions in SysBioPSE.[show abstract] [hide abstract]
ABSTRACT: At Pacific Northwest National Laboratory, we are researching and developing scientific computing environments for biologists and bioinformaticists. Important issues for us are how to motivate biologists to use new computational technologies and how to best incorporate and integrate disparate computational resources into computational biology research. In recent efforts, we have focused on the development of tools that support specific scientific abstractions or models that may be used as cognitive computational frameworks for biologists. The specific tools allow biologists to view and organize their computational work along the scientific concepts and theories that are under investigation, the experimental processes that are being carried out, and the logical structures and properties of the scientific data being examined and explored. This collection of tools and their underlying framework comprise a system known as SysBioPSE (system biology problem solving environment)Proceedings of the IEEE International Conference on Systems, Man & Cybernetics: The Hague, Netherlands, 10-13 October 2004; 01/2004