This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We propose to develop a networked environment for the collaborative assembly, analysis, and sharing of a number of multi-terabyte datasets. We will test its effectiveness by working with content providers who will use the system to build a large repository of important biological data, by having additional collaborators use the system to work on open research questions, and by observing use of the system by the general scientific community. The system is applicable to any area of research that involves collection and analysis of large image and volumetric datasets such as optical sections, CT, MRI, and EM. Its greatest value is with data that must be interactively shared by multiple users, is too large for distribution as DVDs, and that must be used in 3D aligned form. The primary user interface, to access full system functionality, will be a platform independent (PC, Mac, Linux, UNIX) native mode client program derived in part from the current PSC Volume Browser. It will provide highly interactive and dynamic performance by making use of accelerated graphics hardware features such as texture mapping, blending, coordinate transforms and 3D shading called from OpenGL. Less graphically intensive access to portions of the system will also be provided through conventional web browsers. The processes needed to co-register large numbers of serial sections and to recognize 3D structures are computationally and memory intensive. CASCADE will handle the majority of the collaboratory interactions. We established SuperWorm (, a confluence of two software groups (PSC's Biomedical Initiative;Spring, Pitt), two content generating researchers (Hall, AECOM;Fetter, UCSF) and five beta-test researchers plus an experienced software evaluator (Gadd, Pitt). This group will develop and integrate tools for collaboration, visualization, analysis, high speed networking and supercomputing into a single working environment to enable effective distributed collaborations and to support the wide-spread sharing of expensive and voluminous (multi-terabyte datasets) TEM datasets.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZRG1-BCMB-Q (40))
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Carnegie-Mellon University
Biostatistics & Other Math Sci
Schools of Arts and Sciences
United States
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Lee, Wei-Chung Allen; Bonin, Vincent; Reed, Michael et al. (2016) Anatomy and function of an excitatory network in the visual cortex. Nature 532:370-4
Murty, Vishnu P; Calabro, Finnegan; Luna, Beatriz (2016) The role of experience in adolescent cognitive development: Integration of executive, memory, and mesolimbic systems. Neurosci Biobehav Rev 70:46-58
Zhang, Yimeng; Li, Xiong; Samonds, Jason M et al. (2016) Relating functional connectivity in V1 neural circuits and 3D natural scenes using Boltzmann machines. Vision Res 120:121-31
Ramakrishnan, N; Tourdot, Richard W; Radhakrishnan, Ravi (2016) Thermodynamic free energy methods to investigate shape transitions in bilayer membranes. Int J Adv Eng Sci Appl Math 8:88-100
Kuhlman, Chris J; Anil Kumar, V S; Marathe, Madhav V et al. (2015) Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results. Data Min Knowl Discov 29:423-465
Sha, Huizi; Zou, Zhengyun; Xin, Kai et al. (2015) Tumor-penetrating peptide fused EGFR single-domain antibody enhances cancer drug penetration into 3D multicellular spheroids and facilitates effective gastric cancer therapy. J Control Release 200:188-200
Ramakrishnan, N; Radhakrishnan, Ravi (2015) Phenomenology based multiscale models as tools to understand cell membrane and organelle morphologies. Adv Planar Lipid Bilayers Liposomes 22:129-175
Feng, Rentian; Tong, Qin; Xie, Zhaojun et al. (2015) Targeting cannabinoid receptor-2 pathway by phenylacetylamide suppresses the proliferation of human myeloma cells through mitotic dysregulation and cytoskeleton disruption. Mol Carcinog 54:1796-806
Black, Jessica J; Clark, Duncan B; Martin, Christopher S et al. (2015) Course of alcohol symptoms and social anxiety disorder from adolescence to young adulthood. Alcohol Clin Exp Res 39:1008-15
Wachinger, Christian; Golland, Polina; Kremen, William et al. (2015) BrainPrint: a discriminative characterization of brain morphology. Neuroimage 109:232-48

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