BioSPICE: Access to the Most Current Computational Tools for Biologists

TLDR

BioSPICE seeks to give biologists access to the latest computational tools by building a framework that will grow to include notebooks, a model repository, and wet‑lab support. Its core is the BioSPICE Dashboard, a graphical environment combining Open Agent Architecture and NetBeans that unifies diverse software modules, data sources, models, and simulation engines across a distributed network, allowing users to build workflows and connect components, with a project website supporting community exchange. By the program midpoint, the BioSPICE community has assembled a software system from about 20 laboratories, integrated under the Dashboard and establishing a methodology for continuous software integration.

Abstract

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.