title: The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches.
abstract: Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research laboratory or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a Web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of this is to not only provide a common data sharing and archiving system, but also to assist in the building of new collaborations and to spur the development of new tools and technologies.
authors.affiliation: Biosystems Research, Advanced Software R&D, and Exploratory Computer and Software Engineering Departments, Sandia National Laboratories, P.O. Box 969, Livermore, California 94551-0969, USA.
authors.forename: Eizadora T
authors.initials: ET
authors.lastname: Yu
authors.forename: Arie
authors.initials: A
authors.lastname: Hawkins
authors.forename: Irwin D
authors.initials: ID
authors.lastname: Kuntz
authors.forename: Larry A
authors.initials: LA
authors.lastname: Rahn
authors.forename: Andrew
authors.initials: A
authors.lastname: Rothfuss
authors.forename: Kenneth
authors.initials: K
authors.lastname: Sale
authors.forename: Malin M
authors.initials: MM
authors.lastname: Young
authors.forename: Christine L
authors.initials: CL
authors.lastname: Yang
authors.forename: Carmen M
authors.initials: CM
authors.lastname: Pancerella
authors.forename: Daniele
authors.initials: D
authors.lastname: Fabris
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D003299:Cooperative Behavior; D003628:Database Management Systems; D016247:Information Storage and Retrieval; D020407:Internet; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000737:chemistry* / Q000378:metabolism; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012108:Research Personnel; D012984:Software; D018511:Systems Integration
chemical_list: D009696:Nucleic Acids; D011506:Proteins