MPI-dot2dot: A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Tandem Repeats (TRs) are segments that occur several times in a DNA sequence, and each copy is adjacent to other. In the last few years, TRs have gained significant attention as they are thought to be related with certain human diseases. Therefore, identifying and classifying TRs have become a highly important task in bioinformatics in order to analyze their disorders and relationships with illnesses. Dot2dot, a tool recently developed to find TRs, provides more accurate results than the previous state-of-the-art, but it requires a long execution time even when using multiple threads. This work presents MPI-dot2dot, a novel version of this tool that combines MPI and OpenMP so that it can be executed in a cluster of multicore nodes and thus reduces its execution time. The performance of this new parallel implementation has been tested using different real datasets. Depending on the characteristics of the input genomes, it is able to obtain the same biological results as Dot2dot but more than 100 times faster on a 16-node multicore cluster (384 cores). MPI-dot2dot is publicly available to download from https://sourceforge.net/projects/mpi-dot2dot.This work was supported by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 / AEI / 10.13039/501100011033), and by Xunta de Galicia and FEDER funds (Centro de Investigación de Galicia accreditation 2019-2022 and Consolidation Program of Competitive Reference Groups, under Grants ED431G 2019/01 and ED431C 2021/30, respectively). The authors would like to thank the Galician Supercomputing Center (CESGA) for providing access to the Finis Terrae II supercomputer. Open Access funding provided thanks to the CRUE-CSIC agreement with Springer NatureXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431C 2021/3

Study of fault-tolerant software technology

Presented is an overview of the current state of the art of fault-tolerant software and an analysis of quantitative techniques and models developed to assess its impact. It examines research efforts as well as experience gained from commercial application of these techniques. The paper also addresses the computer architecture and design implications on hardware, operating systems and programming languages (including Ada) of using fault-tolerant software in real-time aerospace applications. It concludes that fault-tolerant software has progressed beyond the pure research state. The paper also finds that, although not perfectly matched, newer architectural and language capabilities provide many of the notations and functions needed to effectively and efficiently implement software fault-tolerance

The Pan-STARRS Moving Object Processing System

We describe the Pan-STARRS Moving Object Processing System (MOPS), a modern software package that produces automatic asteroid discoveries and identifications from catalogs of transient detections from next-generation astronomical survey telescopes. MOPS achieves > 99.5% efficiency in producing orbits from a synthetic but realistic population of asteroids whose measurements were simulated for a Pan-STARRS4-class telescope. Additionally, using a non-physical grid population, we demonstrate that MOPS can detect populations of currently unknown objects such as interstellar asteroids. MOPS has been adapted successfully to the prototype Pan-STARRS1 telescope despite differences in expected false detection rates, fill-factor loss and relatively sparse observing cadence compared to a hypothetical Pan-STARRS4 telescope and survey. MOPS remains >99.5% efficient at detecting objects on a single night but drops to 80% efficiency at producing orbits for objects detected on multiple nights. This loss is primarily due to configurable MOPS processing limits that are not yet tuned for the Pan-STARRS1 mission. The core MOPS software package is the product of more than 15 person-years of software development and incorporates countless additional years of effort in third-party software to perform lower-level functions such as spatial searching or orbit determination. We describe the high-level design of MOPS and essential subcomponents, the suitability of MOPS for other survey programs, and suggest a road map for future MOPS development.Comment: 57 Pages, 26 Figures, 13 Table

Design of a Wearable Balance Control Indicator

Each year, one in three elderly fall. Studies show that many factors contribute to an elderly person\u27s risk of falling, but if the factors causing imbalance are improved, a person\u27s risk of falling may be reduced. A device that detects and alerts the user of an off-balance situation before the fall occurs could identify a specific need for improved balance control. This MQP describes the design, testing, and verification of a prototype wearable device that is worn on the right hip during the sit-to-stand activity (STS) to detect and notify the user of an unbalanced STS. By signaling an off-balance situation during STS, our device notifies the user of poor balance control and identifies the need for balance control improvement

Mariner Venus/Mercury 1973 study

Mariner Venus/Mercury 1973 flyby mission and description of spacecraft and subsystem