URI: http://hdl.handle.net/2144/1240

Recently Added

  • HIL: designing an exokernel for the data center 

    Hennessey, Jason; Tikale, Sahil; Turk, Ata; Kaynar, Emine Ugur; Hill, Chris; Desnoyers, Peter; Krieger, Orran (ACM, 2016-10)
    We propose a new Exokernel-like layer to allow mutually untrusting physically deployed services to efficiently share the resources of a data center. We believe that such a layer offers not only efficiency gains, but may ...
  • An Experiment on Bare-Metal BigData Provisioning 

    Turk, Ata; Gudimetla, Ravi S.; Kaynar, Emine Ugur; Hennessey, Jason; Tikale, Sahil; Desnoyers, Peter; Krieger, Orran (8th USENIX Workshop on Hot Topics in Cloud Computing (HotCloud 16), 2016-06)
    Many BigData customers use on-demand platforms in the cloud, where they can get a dedicated virtual cluster in a couple of minutes and pay only for the time they use. Increasingly, there is a demand for bare-metal bigdata ...
  • Hardware as a service - enabling dynamic, user-level bare metal provisioning of pools of data center resources. 

    Hennessey, Jason; Hill, Chris; Denhardt, Ian; Viggnesh, Venugopal; Silvis, George; Krieger, Orran; Desnoyers, Peter (2014 IEEE High Performance Extreme Computing Conference (HPEC ‘14), 2014-09)
    We describe a “Hardware as a Service (HaaS)” tool for isolating pools of compute, storage and networking resources. The goal of HaaS is to enable dynamic and flexible, user-level provisioning of pools of ...
  • Using OpenStack for an Open Cloud eXchange(OCX) 

    Desnoyers, Peter; Hennessey, Jason; Holden, Brent; Krieger, Orran; Rudolph, Larry; Young, Adam (2015-03)
    We are developing a new public cloud, the Mas- sachusetts Open Cloud (MOC) based on the model of an Open Cloud eXchange (OCX). We discuss in this paper the vision of an OCX and how we ...
  • A protocol and calibration method for accurate multi-camera field videography 

    Theriault, Diane H.; Fuller, Nathan W.; Jackson, Brandon E.; Bluhm, Evan; Evangelista, Dennis; Wu, Zheng; Betke, Margrit; Hedrick, Tyson L. (The Company of Biologists, Ltd., 2014-02-27)
    Stereo videography is a powerful technique for quantifying the kinematics and behavior of animals, but it can be challenging to use in an outdoor field setting. We here present a workflow and associated software for ...
  • Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation 

    Giordano, Joti; Ge, Yongchao; Gelfand, Yevgeniy; Abrusán, György; Benson, Gary; Warburton, Peter E (Public Library of Science, 2007-7-13)
    The constant bombardment of mammalian genomes by transposable elements (TEs) has resulted in TEs comprising at least 45% of the human genome. Because of their great age and abundance, TEs are important in comparative ...
  • Spectral affinity in protein networks 

    Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-11-29)
    BACKGROUND. Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network ...
  • 3'-UTR SIRF: A Database for Identifying Clusters of Whort Interspersed Repeats in 3' Untranslated Regions 

    Andken, Benjamin B.; Lim, In; Benson, Gary; Vincent, John J.; Ferenc, Matthew T.; Heinrich, Bianca; Jarzylo, Larissa A.; Man, Heng-Ye; Deshler, James O. (BioMed Central, 2007-7-30)
    BACKGROUND. Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a ...
  • Finding Local Communities in Protein Networks 

    Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-9-18)
    BACKGROUND. Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is ...
  • TRDB—The Tandem Repeats Database 

    Gelfand, Yevgeniy; Rodriguez, Alfredo; Benson, Gary (Oxford University Press, 2006-12-14)
    Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory ...
  • Biological Context Networks: A Mosaic View of the Interactome 

    Rachlin, John; Cohen, Dikla Dotan; Cantor, Charles; Kasif, Simon (2006-11-28)
    Network models are a fundamental tool for the visualization and analysis of molecular interactions occurring in biological systems. While broadly illuminating the molecular machinery of the cell, graphical representations ...