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. Request: 30,000 SUs and 12 months Advanced User Support Abstract: This startup project will explore how best to leverage Blacklight at the Pittsburgh Supercomputing Center for next-generation sequencing data and genome analysis applications. The following software systems will be installed, and appropriate components selected, tested and benchmarked to enable the development of a TeraGrid research proposal: (1) Applied Biosystems Bioscope package. (2) CLC Bio software. Both ABI and CLC will support this project with trial licenses and developer expertise. Below we provide additional background on these two packages. AB Bioscope - This package was installed and run successfully during the friendly user period on Blacklight. There were some efficiency issues, which will be addressed when Blacklight enters production in early January. CLC Bio Genomics Workbench / server -The CLC software is split into a server and clients. Both have essentially identical analytical tools from the user perspective, but the server allows clients to initiate multiple jobs at once (whereas the clients are limited to single jobs at a time, typically). The server is what we run in our lab. The CLC Genomics server can queue multiple jobs at once, and with multiple nodes attached, can parallel process jobs. The """"""""client"""""""" Workbenches are graphical, wizard driven tools that are relatively simple for biologists to run. This can run in X-windows. The clients function as very capable desktop solutions, but can also be the """"""""client"""""""" when you have access to the CLC Bio server solution. CLC Bio Assembly Cell - This is the CLC Bio command line product, where CLC Bio first implements new development in these algorithms after which they get migrated to both the CLC Genomics Workbench, and the Genomics Server products. We plan to focus on this first, and see how it could support research that could only be done on Blacklight. Then we will investigate how Blacklight can fit into the Client-Server model. We have obtained a trial license for this product, for our tests on Blacklight. Advanced User Support During the friendly user period we have worked with Drs. Jana and Sanielevici at PSC. Their continued support of our work will be very important during this startup project.

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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Yonkunas, Michael; Buddhadev, Maiti; Flores Canales, Jose C et al. (2017) Configurational Preference of the Glutamate Receptor Ligand Binding Domain Dimers. Biophys J 112:2291-2300
Earley, Lauriel F; Powers, John M; Adachi, Kei et al. (2017) Adeno-associated Virus (AAV) Assembly-Activating Protein Is Not an Essential Requirement for Capsid Assembly of AAV Serotypes 4, 5, and 11. J Virol 91:
Subramanian, Sandeep; Chaparala, Srilakshmi; Avali, Viji et al. (2016) A pilot study on the prevalence of DNA palindromes in breast cancer genomes. BMC Med Genomics 9:73
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
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
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
Lee, Tai Sing (2015) The visual system's internal model of the world. Proc IEEE Inst Electr Electron Eng 103:1359-1378
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
Jurkowitz, Marianne S; Patel, Aalapi; Wu, Lai-Chu et al. (2015) The YhhN protein of Legionella pneumophila is a Lysoplasmalogenase. Biochim Biophys Acta 1848:742-51

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