Cloud computing infrastructures are providing resources on demand for tackling the needs of large-scale distributed applications. To adapt to the diversity of cloud infras- tructures and usage, new operation tools and models are needed. Estimating the amount of resources consumed by each application in particular is a difficult problem, both for end users who aim at minimizing their costs and infrastructure providers who aim at control- ling their resources allocation. Furthermore, network provision is generally not controlled on clouds. This paper describes a framework automating cloud resources allocation, deploy- ment and application execution control. It is based on a cost estimation model taking into account both virtual network and nodes managed by the cloud. The flexible provisioning of network resources permits the optimization of applications performance and infrastructure cost reduction. Four resource allocation strategies relying on the expertise that can be cap- tured in workflow-based applications are considered. Results of these strategies are confined virtual infrastructure descriptions that are interpreted by the HIPerNet engine responsible for allocating, reserving and configuring physical resources. The evaluation of this framework was carried out on the Aladdin/Grid'5000 testbed using a real application from the area of medical image analysis.