The Virtual Notebook Environment (ViNE) is a platform-independent, web-based interface designed to support a range of scientific activities across distributed, heterogeneous computing platforms. ViNE provides scientists with a web-based version of the common paper-based lab notebook, but in addition, it provides support for collaboration and management of computational experiments. Collaboration is supported with the web-based approach, which makes notebook material generally accessible and with a hierarchy of security mechanisms that screen that access. ViNE provides uniform, system-transparent access to data, tools, and programs throughout the scientist's computing infrastructure. Computational experiments can be launched from ViNE using a visual specification language. The scientist is freed from concerns about inter-tool connectivity, data distribution, or data management details. ViNE also provides support for dynamically linking analysis results back into the notebook content. In this paper we present the ViNE system architecture and a case study of its use in neuropsychology research at the University of Oregon. Our case study with the Brain Electrophysiology Laboratory (BEL) addresses their need for data security and management, collaborative support, and distributed analysis processes. The current version of ViNE is a prototype system being tested with this and other scientific applications.