SUMMARY: Drug discovery targeting G protein-coupled receptors (GPCRs), the largest known class of therapeutic targets, is challenging. To facilitate the rapid discovery and development of GPCR drugs, we built a system, PanGPCR, to predict multiple potential GPCR targets and their expression locations in the tissues, side effects and possible repurposing of GPCR drugs. With PanGPCR, the compound of interest is docked to a library of 36 experimentally determined crystal structures comprising of 46 docking sites for human GPCRs, and a ranked list is generated from the docking studies to assess all GPCRs and their binding affinities. Users can determine a given compound's GPCR targets and its repurposing potential accordingly. Moreover, potential side effects collected from the SIDER (Side-Effect Resource) database and mapped to 45 tissues and organs are provided by linking predicted off-targets and their expressed sequence tag profiles. With PanGPCR, multiple targets, repurposing potential and side effects can be determined by simply uploading a small ligand. AVAILABILITY AND IMPLEMENTATION: PanGPCR is freely accessible at https://gpcrpanel.cmdm.tw/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The activity scheduling of sensors to alternately wake up for sensing obligation such that the network lifetime can be efficiently prolonged is a very important issue in wireless sensor networks (WSNs). Target area coverage is a new coverage problem in wireless sensor networks. The paper addresses the target area coverage problem and schedules sensors to alternatively wake up to collaboratively cover and sense the target area. A geometric-based activity scheduling scheme, named GAS scheme, for WSNs to fully cover a target area is proposed. By means of computational geometry, the sensors can self-determine when to sleep or wake up while preserving the sensing coverage. GAS is able to find as few sensors as possible to cover the target area, which is termed a cover set. In addition, GAS can find as many number of cover sets as possible to be alternately in charge of the sensing task. Simulation results show that GAS can efficiently schedule the sensor when to switch between active and sleep modes. Furthermore, the network lifetime can be prolonged significantly in comparison with the state-of-the-art schemes.

UNLABELLED: Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k(2) times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis. AVAILABILITY: Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/~chromaligner.

The paper proposes a fragment and rate matching (FaRM) MAC protocol for wireless local area networks (LANs) to resist the frequent changing of channel quality and increase the network throughput. In wireless environments, channel quality varies with time. FaRM dynamically detects the current SNR to estimate the channel quality through the control frame exchanges. A Finite State Markov Chain (FSMC) is adopted to predict the variation of the channel condition. According to the results generated from FSMC, FaRM enables a station to select an appropriate transmission rate as well as an acceptable fragment length dynamically to transmit in order to both increase the reliability and shorten the channel access time of the transmission. The simulation results show FaRM has better performance, higher transmission reliability, and lower transmission delay time by fragment and rate matching.

The paper considers the target coverage problem in wireless heterogeneous sensor networks (WHSNs) with multiple sensing units. The paper reduces the problem to a set cover problem and further formulates it as integer programming (IP) constraints. Moreover, two heuristic but distributed schemes, remaining energy first scheme (REFS) and energy efficient first scheme (EEFS), are proposed to solve the target coverage problem. Simulation results show that REFS and EEFS effectively prolong the network lifetime. In addition, EEFS outperforms REFS in network lifetime.

The scheduling algorithm is useful in providing quality of service (QoS). In this paper, a scheduling algorithm, jumping virtual clock (JVC), is developed to has O(I) complexity of calculating virtual time.

Mobile ad hoc networks (MANET) have many applications in the civilian environment, law enforcement, military and disaster recovery arenas. To facilitate these applications, with heavy traffic among nodes, a stable and efficient routing protocol is crucial. In this paper, a signal strength-based, on-demand routing protocol has been proposed, which first uses the earliest established path to forward packets, then changes to the strongest signal strength path for long transmissions. Through exhaustive simulation on ns-2, our routing showed superior performance for various system parameters in a Ricean fading environment. When combined with a multi-rate MAC protocol, the performance was even more distinguished.

This paper considers the multi-node multicast problem in a wormhole-routed 2-D torus/mesh, where an arbitrary number of source nodes each intends to multicast a message to an arbitrary set of destinations. To resolve the contention and the congestion problems, we propose to partition the network into subnetworks to distribute, and thus balance, the traffic load among all network links. Several ways to partition the network are explored. The network-partitioning idea was used in earlier works for single-node broadcast and single-node multicast. This paper contributes in extending its applicability to multi-node multicast and demonstrating its capability to balance load on torus/mesh. Simulation results show significant improvement over existing results for torus and mesh networks.

This paper considers the multi-node multicast problem in a wormhole-routed 20 torus/mesh, where an arbitrary number of source nodes each intending to multicast a message to an arbitrary, set of destinations. To resolve the contention and the congestion problems, we propose to partition the network into subnetworks to distribute, and thus balance, the traffic load among all network links. Several ways to partition the network are explored. Simulation results show significant improvement over existing results for torus and mesh networks.

The one-to-all broadcast is the most primary collective communication pattern in a multicomputer network. We consider this problem in a wormhole-routed torus which uses the all-port and dimension-ordered routing model. We derive our routing algorithms based on the concept of "span of vector spaces" in linear algebra. For instance, in a 3D torus, the nodes receiving the broadcast message will be "spanned" from the source node to a line of nodes, to a plane of nodes, and then to a cube of nodes. Our results require at most 2(k-1) steps more than the optimal number of steps for any square k-D torus. Existing results, as compared to ours, can only be applied to tori of very restricted dimensions or sizes and either rely on an undesirable non-dimension-ordered routing or require more numbers of steps.

In this paper, a network-partitioning approach for one-to-all broadcasting on wormhole-routed networks is proposed. To broadcast a message, the scheme works in three phases. First, a number of data-distributing networks (DDNs), which can work independently, are constructed. Then the message is evenly divided into submessages, each being sent to a representative node in one DDN. Second, the submessages are broadcast on the DDNs concurrently. Finally, a number of data-collecting networks (DCNs), which can work independently too, are constructed. Then, concurrently on each DCN, the submessages are collected and combined into the original message. Our approach, especially designed for wormhole-routed networks, is conceptually similar but fundamentally very different from the traditional approach of using multiple edge-disjoint spanning trees in parallel for broadcasting in store-and-forward networks. One interesting issue is on the definition of independent DDNs and DCNs, in the sense of wormhole routing. We show how to apply this approach to tori, meshes, and hypercubes. Thorough analyses and comparisons based on different system parameters and configurations are conducted. The results do confirm the advantage of our scheme, under various system parameters and conditions, over other existing broadcasting algorithms.

The one-to-all broadcast is the most primary collective communication pattern in a multicomputer network. We consider this problem in a wormhole-routed torus which uses all-port and dimension-ordered routing model. We derive our routing algorithms based on the concept of "span of vector spaces" in linear algebra. For instance, in a 3-D torus, the nodes receiving the broadcast message will be "spanned" from the source node to a line of nodes, to a plane of nodes, and then to a cube of nodes. Our results require at most 2(k-1) steps more than the optimal number of steps for any square k-D torus. Existing results, as compared to ours, can only be applied to tori of very restricted dimensions or sizes, and either rely on an undesirable non-dimension-ordered routing or require more numbers of steps.