To achieve the goals of this project, vast amounts of heterogeneous data must be collected, analyzed and warehoused. Tools will be developed to make the research environment more conducive to using multiple techniques on single systems and to integrate the data from the different Core projects for a system-level understanding. To start quickly, standards for data transmission will be negotiated with the data creators. In the long term, better data handling tools will be delivered to the labs that have common interfaces allowing multiple kinds of data to be handled in a more intuitive way. After validation within the lab, data will be transferred to the Project Database where it can have different statuses such as """"""""creator private,"""""""" """"""""project private"""""""" and """"""""public."""""""" Any data without a """"""""private"""""""" annotation is transferred to the public Science Database. A """"""""What's New"""""""" page will show recent and expected updates to the database across all projects and cores. The same web interfaces, tools and annotation capabilities will be available to Project members and the scientific community. This goes far beyond the normal web sites for communication and data browsing. We will provide """"""""portals"""""""" for collaboration and """"""""hooks"""""""" for data access equivalent to the access internal to our collaboration. The data model will have a significant impact on future modeling efforts. The current gene based systems will be extended to arbitrarily connected graphs of sequence data, genes, gene products, etc. This will be specialized to the global networks of physical interactions or signaling. Within a cell, the activation of the subnetworks that are fixed by development, stimulated by perturbation or misfunctioning owing to disease will be explored. The open source model will be adopted for our tools. We are currently distributing VERA, SAM and Dapple. We will release Cytoscape in February and the data system SBEAMS will also be distributed.
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