C-ME: Collaborative Molecular Modeling Environment

Collaborative Modeling Environment (C-ME) is a smart client that allows researchers to organize information, visualize it using a common contextual 2D or 3D basis, and share that information with other researchers utilizing Microsoft Office Server System 2007 (MOSS 2007) as a data store, Vista’s Windows Presentation Foundation for the graphics display and visual studio 2005 / C# as a development platform.  C-ME addresses two important aspects of collaboration: context and information management.  C-ME allows a researcher to use a 3D atomic structure model or a 2D image (e.g. an image of a slide containing cancer cells) as a contextual basis on which to attach annotations to specific atoms or groups of atoms of a 3D atomic structure or to user-definable areas on a 2D image.  These annotations (Office documents, URLs, Notes, and Screen Captures) provide additional information about the atomic structure or cellular imagery and are stored on a Microsoft Office System Server (MOSS 2007) and are accessible to other scientists using C-ME provided they have appropriate permission in the Active Directory.  Storing and managing the annotations on MOSS allows us to maintain a single copy of the information accessible to a collaborating group of researchers. Contributions to this single copy of information via additional annotations are again immediately available to the entire community.
C-ME data organization is hierarchical with projects being at the top and containing one or more entities, which can be either a 3-dimensional atomic coordinate file (PDB format) or a 2-dimensional image file (PNG, JPG format).  Each entity can then be annotated as described above with one or more annotations.  We are currently in the process of improving the initial implementation by enhancing the existing 3D and 2D annotation capabilities to better match researchers’ needs, increasing drag-and-drop/one-click functionality for efficiency and standardization of the GUI under Vista, and further leveraging the search and indexing capabilities of MOSS 2007. We are also looking for outside users to install and evaluate C-ME.
Future directions for C-ME include features to publish annotations to a WordML document, more granular use of access control lists to grant/deny access at the file level, extension of the API to enable access to 3rd party SQL databases and XML data sources and application output. 
Acknowledgments:
The C-ME development team includes members of Interknowlogy, Microsoft and the Kuhn-Stevens laboratories at The Scripps Research Institute. Support for C-ME is in part provided by the NIH NIGMS Protein Structure Initiative under grant U54-GM074961 and through NIH-NIAID Contract HHSN266200400058C.