Computing through scientific abstractions in SysBioPSE

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)