Cloud computing promises to change the way scientists will tackle future research challenges by providing transparent access to distributed heterogeneous data sources and to high-end computing facilities for performing computationally demanding and data-intensive modeling, simulation and analysis tasks. In this article we describe the Vienna Cloud Environment (VCE), a service-oriented Cloud infrastructure based on standard virtualization and Web service technologies for the provisioning of scientific applications, data sources, and scientific workflows as virtual appliances that hide the details of the underlying software and hardware infrastructure. The VCE is based on a virtual appliance model within a component-based service provision framework, which supports the configuration of application, data, and workflow services from a set of basic service components providing capabilities like job or query execution, data transfers, QoS negotiation, data staging, and error recovery. The virtual appliance model constitutes an easy way to provision applications, data sources, and workflows in the Cloud and a standard way of accessing and integrating the appliances into client applications. VCE has been developed and utilized in the context of several projects for the realization of IT infrastructures within bio-medical and molecular modeling domains.