13 papers · ranked by Valyu relevance
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Alex M. Ascension, Marcos J. Araúzo-Bravo
Big Data analysis is a discipline with a growing number of areas where huge amounts of data is extracted and analyzed. Parallelization in Python integrates Message Passing Interface via mpi4py module. Since mpi4py does not support parallelization of objects greater than 2^31^ bytes, we developed BigMPI4py, a Python…
Erik De Schutter
The Neural Development Simulator, NeuroDevSim, is a Python module that simulates the most important aspects of development: growth, migration and pruning. It uses an agent-based modeling approach inherited from the NeuroMaC software. Each cycle, agents called fronts execute code. In the case of a growing dendritic or…
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt
The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated quadratic…
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…
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…
Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez
The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a…
Dominique Lavenier, Remy Cimadomo, Romaric Jodin
In this paper, we introduce a new combination of software and hardware PIM (Process-in-Memory) architecture to accelerate the variant calling genomic process. PIM translates into bringing data intensive calculations directly where the data is: within the DRAM, enhanced with thousands of processing units. The energy…
J Kyle Medley, Shaik Asifullah, Joseph Hellerstein, Herbert M Sauro
Mechanistic kinetic models of biological pathways are an important tool for understanding biological systems. Constructing kinetic models requires fitting the parameters to experimental data. However, parameter fitting on these models is a non–convex, non–linear optimization problem. Many algorithms have been proposed…
Constantin Scholl, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis
Motivated by load balance issues in parallel calculations of the phylogenetic likelihood function, we recently introduced an approximation algorithm for efficiently distributing partitioned alignment data to a given number of CPUs. The goal is to balance the accumulated number of sites per CPU, and, at the same time…
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…
Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva, Kirk E. Jordan
De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer…
Christoph Stelz, Lukas Hübner, Alexandros Stamatakis
Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum Likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between…