Multipath TCP, or MPTCP, is a widely-researched mechanism that allows a single application-level connection to be split to more than one TCP stream, and consequently more than one network interface, as opposed to the traditional TCP/IP model. Being a transport layer protocol, MPTCP can easily interact between the application using it and the network supporting it. However, MPTCP does not have control of its own route. Default IP routing behavior generally takes all traffic through the shortest or best-metric path. However, this behavior may actually cause paths to collide with each other, creating contention for bandwidth in a number of edges. This can result in a bottleneck which limits the throughput of the network. Therefore, a multipath routing mechanism is necessary to ensure smooth operation of MPTCP. We created smoc, a Simple Multipath OpenFlow Controller, that uses only topology information of the network to avoid collision where possible. Evaluation of smoc in a virtual local-area and a physical wide-area SDNs showed favorable results as smoc provided better performance than simple or spanning-tree routing mechanisms.
The virtual screening approach for docking small molecules into a known protein structure is a powerful tool for drug design. In this work, a combined docking and neural network approach, using a self-organizing map, has been developed and applied to screen anti-HIV-1 inhibitors for two targets, HIV-1 RT and HIV-1 PR, from active compounds available in the Thai Medicinal Plants Database. Based on nevirapine and calanolide A as reference structures in the HIV-1 RT binding site and XK-263 in the HIV-1 PR binding site, 2,684 compounds in the database were docked into the target enzymes. Self-organizing maps were then generated with respect to three types of pharmacophoric groups. The map of the reference structures were then superimposed on the feature maps of all screened compounds. Only the structures having similar features to the reference compounds were accepted. By using the SOMs, the number of candidates for HIV-1 RT was reduced to six and nine compounds consistent with nevirapine and calanolide A, respectively, as references. For the HIV-1 PR target, there are 135 screened compounds showed good agreement with the XK-263 feature map. These screened compounds will be further tested for their HIV-1 inhibitory affinities. The obtained results indicate that this combined method is clearly helpful to perform the successive screening and to reduce the analyzing step from AutoDock and scoring procedure.
This practices and experience paper describes the coordination, design, implementation, availability, and performance of the Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) Grid Testbed. Applications in high-energy physics, genome annotation, quantum computational chemistry, wildfire simulation, and protein sequence alignment have driven the middleware requirements, and the testbed provides a mechanism for international users to share software beyond the essential, de facto standard Globus core. In this paper, we describe how human factors, resource availability and performance issues have affected the middleware, applications and the testbed design. We also describe how middleware components in grid monitoring, grid accounting, grid Remote Procedure Calls, grid-aware file systems, and grid-based optimization have dealt with some of the major characteristics of our testbed. We also briefly describe a number of mechanisms that we have
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