Collaboratory

Abstract: Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

Abstract: Contents: Introduction. Part I: Theoretical Approaches to Coordination and Collaboration. T.W. Malone, K. Crowston, The Interdisciplinary Study of Coordination. R.J. Boland, Jr., R.V. Tenkasi, Communication and Collaboration in Distributed Cognition. E.H. Durfee, D. Damouth, P.J. Gmytrasiewicz, M.J. Huber, T.A. Montgomery, S. Sen, Coordination as Distributed Search. S. Kraus, J. Wilkenfeld, Strategic Negotiation in Multiagent Environments. T.W. Malone, K-Y. Lai, K.R. Grant, Two Design Principles for Collaboration Technology: Examples of Semiformal Systems and Radical Tailorability. T. Marschak, On Economies of Scope in Communication. S. Reiter, Knowledge, Discovery, and Growth. Part II: Collaboration Technology for Specific Domains. P. Dewan, V. Mashayekhi, J. Riedl, Infrastructure and Applications for Collaborative Software Engineering. C.A. Jasek, P.M. Jones, Cooperative Support for Distributed Supervisory Control. R. Furuta, P.D. Stotts, Trellis: A Formally Defined Hypertextual Basis for Integrating Task and Information. J. Pasquale, Problems of Decentralized Control: Using Randomized Coordination to Deal With Uncertainty and Avoid Conflicts. D.E. Shackelford, J.B. Smith, F.D. Smith, The Architecture and Implementation of a Distributed Hypermedia Storage System. Part III: Studies of Collaboration. R.C. Arkin, T. Balch, Communication and Coordination in Reactive Robotic Teams. G. Fischer, J. Grudin, R. McCall, J. Ostwald, D. Redmiles, B. Reeves, F. Shipman, Seeding, Evolutionary Growth, and Reseeding: The Incremental Development of Collaborative Design Environments. S.R. Hiltz, D. Dufner, J. Fjermestad, Y. Kim, R. Ocker, A. Rana, M. Turoff, Distributed Group Support Systems: Theory Development and Experimentation. R. Kling, K.L. Kraemer, J.P. Allen, Y. Bakos, V. Gurbaxani, M. Elliott, Transforming Coordination: The Promise and Problems of Information Technology in Coordination. C.M. Neuwirth, D.S. Kaufer, R. Chandhok, J.H. Morris, Computer Support for Distributed Collaborative Writing: A Coordination Science Perspective. G.M. Olson, J.S. Olson, Technology Support for Collaborative Workgroups. Part IV: Organizational Modeling. T. Berger, N.M. Kiefer, Central Coordination of Decentralized Information in Large Chains and Franchises. K.M. Carley, Organizational Performance, Coordination, and Cognition. R.E. Levitt, Y. Jin, G.A. Oralkan, J.C. Kunz, T.R. Christiansen, Computational Enterprise Models: Toward Analysis Tools for Designing Organizations. C. Lewis, R. Reitsma, E.V. Wilson, I. Zigurs, Extending Coordination Theory to Deal With Goal Conflicts. W-P. Wang, D.L. Kleinman, P.B. Luh, Modeling Team Coordination and Decisions in a Distributed Dynamic Environment. Part V: Collaboratories. G.C. Bowker, S.L. Star, Social Theoretical Issues in the Design of Collaboratories: Customized Software for Community Support Versus Large Scale Infrastructure. H. Chen, B.R. Schatz, A Path to Concept-Based Information Access: From National Collaboratories to Digital Libraries. G.M. Olson, D.E. Atkins, R. Clauer, T. Weymouth, T.A. Finholt, A. Prakash, C. Rasmussen, F. Jahanian, Technology to Support Distributed Team Science: The First Phase of the Upper Atmospheric Research Collaboratory (UARC).