TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system

The Infrared Imaging Spectrograph (IRIS) for TMT: Data Reduction System

IRIS (InfraRed Imaging Spectrograph) is the diffraction-limited first light instrument for the Thirty Meter Telescope (TMT) that consists of a near-infrared (0.84 to 2.4 $\mu$m) imager and integral field spectrograph (IFS). The IFS makes use of a lenslet array and slicer for spatial sampling, which will be able to operate in 100's of different modes, including a combination of four plate scales from 4 milliarcseconds (mas) to 50 mas with a large range of filters and gratings. The imager will have a field of view of 34$\times$34 arcsec$^{2}$ with a plate scale of 4 mas with many selectable filters. We present the preliminary design of the data reduction system (DRS) for IRIS that need to address all of these observing modes. Reduction of IRIS data will have unique challenges since it will provide real-time reduction and analysis of the imaging and spectroscopic data during observational sequences, as well as advanced post-processing algorithms. The DRS will support three basic modes of operation of IRIS; reducing data from the imager, the lenslet IFS, and slicer IFS. The DRS will be written in Python, making use of open-source astronomical packages available. In addition to real-time data reduction, the DRS will utilize real-time visualization tools, providing astronomers with up-to-date evaluation of the target acquisition and data quality. The quicklook suite will include visualization tools for 1D, 2D, and 3D raw and reduced images. We discuss the overall requirements of the DRS and visualization tools, as well as necessary calibration data to achieve optimal data quality in order to exploit science cases across all cosmic distance scales.Comment: 13 pages, 2 figures, 6 tables, Proceeding 9913-165 of the SPIE Astronomical Telescopes + Instrumentation 201

CIDPro: Custom Instructions for Dynamic Program Diversification

Timing side-channel attacks pose a major threat to embedded systems due to their ease of accessibility. We propose CIDPro, a framework that relies on dynamic program diversification to mitigate timing side-channel leakage. The proposed framework integrates the widely used LLVM compiler infrastructure and the increasingly popular RISC-V FPGA soft-processor. The compiler automatically generates custom instructions in the security critical segments of the program, and the instructions execute on the RISC-V custom co-processor to produce diversified timing characteristics on each execution instance. CIDPro has been implemented on the Zynq7000 XC7Z020 FPGA device to study the performance overhead and security tradeoffs. Experimental results show that our solution can achieve 80% and 86% timing side-channel capacity reduction for two benchmarks with an acceptable performance overhead compared to existing solutions. In addition, the proposed method incurs only a negligible hardware area overhead of 1% slices of the entire RISC-V system