The invention relates to a framework system and methods for connecting a plurality of tools. The system comprises a plug-in mechanism configured to dynamically load the plurality of tools, a data pool having storage space configured to store data sets associated with the plurality of tools, a linking mechanism configured to establish communications links between the loaded plurality of tools to enable coordinated operation of the loaded plurality of tools, a session component configured to record the process history of the operations of the loaded plurality of tool and the system states corresponding to the process history of the operations and an annotation module configured to associate user-provided data corresponding to one or more of the stored data sets.