Hard SyDR: A Benchmarking Environment for Global Navigation Satellite System Algorithms.

A Global Navigation Satellite System (GNSS) is widely used today for both positioning and timing purposes. Many distinct receiver chips are available as Application-Specific Integrated Circuit (ASIC)s off-the-shelf, each tailored to the requirements of various applications. These chips deliver good performance and low energy consumption but offer customers little-to-no transparency about their internal features. This prevents modification, research in GNSS processing chain enhancement (e.g., application of Approximate Computing (AxC) techniques), and design space exploration to find the optimal receiver for a use case. In this paper, we review the GNSS processing chain using SyDR, our open-source GNSS Software-Defined Radio (SDR) designed for algorithm benchmarking, and highlight the limitations of a software-only environment. In return, we propose an evolution to our system, called Hard SyDR to become closer to the hardware layer and access new Key Performance Indicator (KPI)s, such as power/energy consumption and resource utilization. We use High-Level Synthesis (HLS) and the PYNQ platform to ease our development process and provide an overview of their advantages/limitations in our project. Finally, we evaluate the foreseen developments, including how this work can serve as the foundation for an exploration of AxC techniques in future low-power GNSS receivers.

FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters.

We introduce a version of the epistasis test in FaST-LMM for clusters of multithreaded processors. This new software maintains the sensitivity of the original FaST-LMM while delivering acceleration that is close to linear on 12-16 nodes of two recent platforms, with respect to improved implementation of FaST-LMM presented in an earlier work. This efficiency is attained through several enhancements on the original single-node version of FaST-LMM, together with the development of a message passing interface (MPI)-based version that ensures a balanced distribution of the workload as well as a multigraphics processing unit (GPU) module that can exploit the presence of multiple GPUs per node.

Concurrent and Accurate Short Read Mapping on Multicore Processors.

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

iMODS: internal coordinates normal mode analysis server.

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org.