The ongoing need of IT support for advancing personalized medicine has led to a plethora of needs for developing new computational algorithms, informatics resource management infrastructures and tools for extracting patient specific clinico-genomic information, and more recently, predicting and optimizing the therapeutic outcome for the individual patient within the EC VPH initiative. This has led to an unprecedented explosion in proposed tools and models for personalized medicine which in turn need specific frameworks for categorizing, querying and accessing such resources in an interoperable and standardized fashion. The proposed personalized medicine workbench is part of the EC funded p-medicine project and aims to create a semantically annotated repository of tools specific to the advancement of personalized medicine by addressing the project's clinical scenarios. Central to this development is the inclusion of a wide range of tools for personalized medicine encompassing biostatistics, bioinformatics, multi-scale predictive modeling and image analysis clinical applications.