Search · four archives
Search · four archives
16 papers · ranked by Valyu relevance
Zeyi Zhang, Carlos Mora Perez, Patrick Kwon, Martin Head‐Gordon + 1 more
PARSEC.py is a Python-based real-space Kohn-Sham density functional theory (real-space KS-DFT) framework designed to provide a user- and developer-friendly platform for first-principles electronic-structure simulations. Discretization on real-space grids eliminates basis-set approximations, while enabling systematic…
Maximilian H. Kriebel, Paweł Tecmer, Marta Gałyńska, Aleksandra Leszczyk + 1 more
Coupled-Cluster Implementations: A Comparison Between CPUs and GPUs Authors: Maximilian H. Kriebel, Paweł Tecmer, Marta Gałyńska, Aleksandra Leszczyk, Katharina Boguslawski In this work, we benchmark several Python routines for time and memory requirements to identify the optimal choice of the tensor contraction…
Gregor Mönke, Tim Schäfer, Mohsen Parto-Dezfouli, Diljit Singh Kajal + 3 more
'Stefan Fürtinger' 'Joscha Tapani Schmiedt' 'Pascal Fries'] We introduce an open-source Python package for the analysis of large-scale electrophysiological data, named SyNCoPy, which stands for Systems Neuroscience Computing in Python. The package includes signal processing analyses across time (e.g., time-lock…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Leonid Bystrykh
Genome biology shows substantial progress in its analytical and computational part in the last decades. Differential gene expression is one of many computationally intense areas; it is largely developed under R programming language. Here we explain possible reasons for such dominance of R in gene expression data. Next…
Michael J. O’Brien, David Silva-Sánchez, Geoffrey Woollard, Kwanghwi Je + 5 more
While cryo-electron microscopy (cryo-EM) has come to prominence in the last decade due to its ability to resolve biomolecular complexes at atomic resolution, advancements in experimental and computational methods have made cryo-EM promising for investigating intracellular organization and heterogeneous molecular…
Chaoming Wang, Tianqiu Zhang, Xiaoyu Chen, Sichao He + 4 more
'Si Wu' 'Marcel Stimberg' 'Panayiota Poirazi'] Elucidating the intricate neural mechanisms underlying brain functions requires integrative brain dynamics modeling. To facilitate this process, it is crucial to develop a general-purpose programming framework that allows users to freely define neural models across…
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall + 16 more
Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility…
Guillaume Viejo, Daniel Levenstein, Sofia Skromne Carrasco, Dhruv Mehrotra + 8 more
'Dhruv Mehrotra' 'Sara Mahallati' 'Gilberto R Vite' 'Henry Denny' 'Lucas Sjulson' 'Francesco P Battaglia' 'Adrien Peyrache' 'Caleb Kemere' 'Timothy E Behrens'] Datasets collected in neuroscientific studies are of ever-growing complexity, often combining high-dimensional time series data from multiple data acquisition…
Daniel P. Marshall, Elie S. Farah, Eric D. Musselman, Nicole A. Pelot + 2 more
of model nerve fibers to electrical stimulation PyFibers: A Python package to simulate nerve fiber responses to electrical stimulation Authors: Daniel P. Marshall, Elie S. Farah, Eric D. Musselman, Nicole A. Pelot, Warren M. Grill, Alain Nogaret Computational modeling of peripheral nerve fibers is a key tool for…
Miranda Mundt, William E. Hart, Emma S. Johnson, Bethany Nicholson + 1 more
'John D. Siirola'] Title: Summary Pyomo is an open-source optimization modeling software that has undergone significant evolution since its inception in 2008. Pyomo has evolved to enhance flexibility, solver integration, and community engagement. Modern collaborative tools for open-source software have facilitated the…
Vladislav Skorpil, Vaclav Oujezsky, Arcangelo Castiglione, Gianni D’Angelo
'Gianni D’Angelo'] This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are…
David Montero, César Aybar, Miguel D. Mahecha, Francesco Martinuzzi + 2 more
'Maximilian Söchting' 'Sebastian Wieneke'] Spectral Indices derived from multispectral remote sensing products are extensively used to monitor Earth system dynamics (e.g. vegetation dynamics, water bodies, fire regimes). The rapid increase of proposed spectral indices led to a high demand for catalogues of spectral…
James B. Aimone, Omar Awile, Markus Diesmann, James C. Knight + 2 more
At the turn of the millennium the computational neuroscience community realized that neuroscience was in a software crisis: software development was no longer progressing as expected and reproducibility declined. The International Neuroinformatics Coordinating Facility (INCF) was inaugurated in 2007 as an initiative to…
Matthew Carlucci, Tadas Bareikis, Karolis Koncevičius, Povilas Gibas + 4 more
'Algimantas Kriščiūnas' 'Art Petronis' 'Gabriel Oh' 'Anna Bernasconi'] Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is…
Loriano Storchi, Laura Bellentani, Jeff Hammond, Sergio Orlandini + 3 more
the Relativistic Dirac–Kohn–Sham Method with GPU: A Pre-Exascale Implementation of BERTHA and PyBERTHA Authors: ['Loriano Storchi' 'Laura Bellentani' 'Jeff Hammond' 'Sergio Orlandini' 'Leonardo Pacifici' 'Nicoló Antonini' 'Leonardo Belpassi'] In this paper, we present the recent advances in the computation of the…