DIVERSE: a Software Toolkit to Integrate Distributed Simulations with Heterogeneous Virtual Environments

We present DIVERSE (Device Independent Virtual Environments- Reconfigurable, Scalable, Extensible), which is a modular collection of complimentary software packages that we have developed to facilitate the creation of distributed operator-in-the-loop simulations. In DIVERSE we introduce a novel implementation of remote shared memory (distributed shared memory) that uses Internet Protocol (IP) networks. We also introduce a new method that automatically extends hardware drivers (not in the operating system kernel driver sense) into inter-process and Internet hardware services. Using DIVERSE, a program can display in a CAVE™, ImmersaDesk™, head mounted display (HMD), desktop or laptop without modification. We have developed a method of configuring user programs at run-time by loading dynamic shared objects (DSOs), in contrast to the more common practice of creating interpreted configuration languages. We find that by loading DSOs the development time, complexity and size of DIVERSE and DIVERSE user applications is significantly reduced. Configurations to support different I/O devices, device emulators, visual displays, and any component of a user application including interaction techniques, can be changed at run-time by loading different sets of DIVERSE DSOs. In addition, interpreted run-time configuration parsers have been implemented using DIVERSE DSOs; new ones can be created as needed. DIVERSE is free software, licensed under the terms of the GNU General Public License (GPL) and the GNU Lesser General Public License (LGPL) licenses. We describe the DIVERSE architecture and demonstrate how DIVERSE was used in the development of a specific application, an operator-in-the-loop Navy ship-board crane simulator, which runs unmodified on a desktop computer and/or in a CAVE with motion base motion queuing

Rapid, modular and reliable construction of complex mammalian gene circuits

We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 transcription units and 33 basic parts. We show robust gene expression control of multiple transcription units by small molecule inducers in human cells with transient transfection and stable chromosomal integration of these circuits. This framework enables development of complex gene circuits for engineering mammalian cells with unprecedented speed, reliability and scalability and should have broad applicability in a variety of areas including mammalian cell fermentation, cell fate reprogramming and cell-based assays.Synthetic Biology Engineering Research Center (SA5284-11210)United States. Defense Advanced Research Projects Agency (HR0011-12-C-0067)United States. Defense Advanced Research Projects Agency (DARPA-BAA-11-23)National Science Foundation (U.S.) (CBET-0939511)National Institutes of Health (U.S.). (5-R01-CA155320-02

Visualising Class Cohesion with Virtual Worlds

An understanding of cohesion is an important factor in software design. However, cohesion is difficult to quantify, particularly for OO, and attempts to develop metrics have had limited success. We advocate the use of visualisation techniques to provide a richer view of cohesion than is possible with a single numeric value. In this paper we describe the application of ANGLE for 3D graph layout and the use of XSLT transformations both to select the ingredients for visualisations and to determine their presentation details. We discuss our experiences with the use of virtual worlds as a presentation medium both on the desktop and in immersive environments and report early results from ongoing empirical work

DIVERSE: a Software Toolkit to Integrate Distributed Simulations with Heterogeneous Virtual Environments.

We present DIVERSE (Device Independent Virtual Environments- Reconfigurable, Scalable, Extensible), which is a modular collection of complimentary software packages that we have developed to facilitate the creation of distributed operator-in-the-loop simulations. In DIVERSE we introduce a novel implementation of remote shared memory (distributed shared memory) that uses Internet Protocol (IP) networks. We also introduce a new method that automatically extends hardware drivers (not in the operating system kernel driver sense) into inter-process and Internet hardware services. Using DIVERSE, a program can display in a CAVE^TM, ImmersaDesk^TM, head mounted display (HMD), desktop or laptop without modification. We have developed a method of configuring user programs at run-time by loading dynamic shared objects (DSOs), in contrast to the more common practice of creating interpreted configuration languages. We find that by loading DSOs the development time, complexity and size of DIVERSE and DIVERSE user applications is significantly reduced. Configurations to support different I/O devices, device emulators, visual displays, and any component of a user application including interaction techniques, can be changed at run-time by loading different sets of DIVERSE DSOs. In addition, interpreted run-time configuration parsers have been implemented using DIVERSE DSOs; new ones can be created as needed. DIVERSE is free software, licensed under the terms of the GNU General Public License (GPL) and the GNU Lesser General Public License (LGPL) licenses. We describe the DIVERSE architecture and demonstrate how DIVERSE was used in the development of a specific application, an operator-in-the-loop Navy ship-board crane simulator, which runs unmodified on a desktop computer and/or in a CA..

Expression, purification and crystallization of the ecto-enzymatic domain of rat E-NTPDase1 CD39

The ecto-enzymatic domain of rat E-NTPDase1 CD39 was expressed and purified and diffraction-quality crystals of the enzyme were obtained

Triad of polar residues implicated in pH specificity of acidic mammalian chitinase

Acidic mammalian chitinase (AMCase) is a mammalian chitinase that has been implicated in allergic asthma. One of only two active mammalian chinases, AMCase, is distinguished from other chitinases by several unique features. Here, we present the novel structure of the AMCase catalytic domain, both in the apo form and in complex with the inhibitor methylallosamidin, determined to high resolution by X-ray crystallography. These results provide a structural basis for understanding some of the unique characteristics of this enzyme, including the low pH optimum and the preference for the β-anomer of the substrate. A triad of polar residues in the second-shell is found to modulate the highly conserved chitinase active site. As a novel target for asthma therapy, structural details of AMCase activity will help guide the future design of specific and potent AMCase inhibitors