28 papers · ranked by Valyu relevance
Temitayo Adefemi
—Parallelization has become a cornerstone of modern computing, influencing everything from high-performance supercomputers to everyday mobile devices. This paper presents a comprehensive guide on the fundamentals of parallelization that every computer scientist should know, beginning with a historical perspective that…
Rajendra Purohit, K. R. Chowdhary, Sunıl Dutt Purohıt
—Arrival of multicore systems has enforced a new scenario in computing, the parallel and distributed algorithms are fast replacing the older sequential algorithms, with many challenges of these techniques. The distributed algorithms provide distributed processing using distributed file systems and processing units…
Brijender Kahanwal
Nowadays, we are to find out solutions to huge computing problems very rapidly. It brings the idea of parallel computing in which several machines or processors work cooperatively for computational tasks. In the past decades, there are a lot of variations in perceiving the importance of parallelism in computing…
Claudia Misale, Giulio Ferrero, Massimo Torquati, Marco Aldinucci
In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all be abstracted to a…
Gianni D'Angelo, Salvatore Rampone
Background The huge quantity of data produced in Biomedical research needs sophisticated algorithmic methodologies for its storage, analysis, and processing. High Performance Computing (HPC) appears as a magic bullet in this challenge. However, several hard to solve parallelization and load balancing problems arise in…
José Colmenares, Antonella Galizia, Jesús Ortiz, Andrea Clematis + 1 more
'Walter Rocchia'] The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological…
Predrag Brođanac, Josip Novak, Ivica Boljat
Today, almost every computer has at least one multicore processor. To remain in stride with hardware developments, numerous university faculties oriented towards computer science have introduced parallel programming as an integral part of their courses. The question is, given the availability of parallel architectures…
Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon + 3 more
Parallel computing divides calculations into smaller problems and solves these simultaneously, using multiple computing elements (hereafter “workers”). In the biological sciences, many computationally intensive problems are “embarrassingly parallel” , where almost all calculations can be completed in parallel. Common…
Sebastian Nanz, Scott West, Kaue Soares da Silveira, Bertrand Meyer
—Developers face a wide choice of programming languages and libraries supporting multicore computing. Ever more diverse paradigms for expressing parallelism and synchronization become available while their influence on usability and performance remains largely unclear. This paper describes an experiment comparing four…
Pierre Carrier, Bill Long, Richard Walsh, Jef Dawson + 4 more
High Performance Computing (HPC) Best Practice offers opportunities to implement lessons learned in areas such as computational chemistry and physics in genomics workflows, specifically Next-Generation Sequencing (NGS) workflows. In this study we will briefly describe how distributed-memory parallelism can be an…
Idan Mosseri, Lee-or Alon, Re’em Harel, Gal Oren
Parallelization schemes are essential in order to exploit the full benefits of multi-core architectures, which have become widespread in recent years. In shared-memory architectures, the most comprehensive parallelization API is OpenMP. However, the introduction of correct and optimal OpenMP parallelization to…
Fan Xu, Li Shen, Zhiying Wang, Bo Su + 2 more
Exploiting potential thread-level parallelism (TLP) is becoming the key factor to improving performance of programs on multicore or many-core systems. Among various kinds of parallel execution models, the software-based speculative parallel model has become a research focus due to its low cost, high efficiency…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Xiandong Meng, Yanqing Ji
This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications-hidden Markov models (HMM). We show the detailed performance…
Eric Wright, Mauricio Ferrato, Alex Bryer, Robert Searles + 2 more
Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging…
Abhishek Kulkarni, Andrew Lumsdaine
We evaluate and compare four contemporary and emerging runtimes for high-performance computing (HPC) applications: Cilk, Charm++, ParalleX and AM++. We compare along three bases: programming model, execution model and the implementation on an underlying machine model. The comparison study includes a survey of each…
Patryk Orzechowski, Artur Pańszczyk, Xiuzhen Huang, Jason H. Moore
Biclustering (called also co-clustering) is an unsupervised technique of simultaneous analysis of rows and columns of input matrix. From the first application to gene expression data, multiple algorithms have been proposed. Only a handful of them were able to provide accurate results and were fast enough to be suitable…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Patrick Mukala
| Article Info | ABSTRACT | | --- | --- | | | A myriad of applications ranging from engineering and scientific | | | simulations, image and signal processing as well as high-sensitive data | | | retrieval demand high processing power reaching up to teraflops for their | | | efficient execution. While a standard serial…
Debaleena Basu, Aditya Murthy
We use sequences of saccadic eye movements to continually explore our visual environments. Previous studies have established that saccades in a sequence may be programmed in parallel by the oculomotor system. In this study, we tested the neural correlates of parallel programming of saccade sequences in the frontal eye…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Costanza Pascal, Herzeel Charlotte, Verachtert Wilfried
elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Alexander S. Shved, Blake E. Ocampo, Elena S. Burlova, Casey L. Olen + 2 more
The construction, management and analysis of large in silico molecular libraries is critical in many areas of modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, "molli", which is a Python 3 cheminformatics module that provides a streamlined interface for manipulating large in silico libraries.…
Authors not listed
The python package ArchOnML ("Archive-On-Machine-Learning") is introduced, which can perform virtual screening projects covering up to millions of structural derivatives through the use of Kernel Ridge Regression models. It supports the full workflow of setting up calculation inputs for external quantum chemistry…
Authors not listed
Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…
Peter Kraus, Edan Bainglass, Francisco F. Ramirez, Enea Svaluto-Ferro + 7 more
Compliance with good research data management practices means trust in the integrity of the data, and it is achievable by a full control of the data gathering process. In this work, we demonstrate tooling which bridges these two aspects, and illustrate its use in a case study of automated battery cycling. We…