Search · four archives
Search · four archives
14 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…
Ragnar Bjornsson
We introduce ASH, a multi-scale, multi-theory modeling program for quantum mechanics (QM), molecular mechanics (MM), and hybrid calculations, written in the Python programming language. ASH is written in response to the increasingly diverse computational chemistry software landscape that features more QM and MM…
Antonina Dobrowolska, Julian Świerczyński, Paweł Tecmer, Emil Sujkowski + 5 more
Python Frameworks for Next-Generation GPUs: A Comparative Study of CuPy and PyTorch on the Hopper and Grace Hopper Architecture Authors: Antonina Dobrowolska, Julian Świerczyński, Paweł Tecmer, Emil Sujkowski, Somayeh Ahmadkhani, Grzegorz Mazur, Klemens Noga, Jeff Hammond, Katharina Boguslawski In this work, we…
Indranil Saha, Daniel Willimetz, Lukáš Grajciar
Molecular simulations are invaluable for analysing molecular systems, but existing post-processing tools are often limited by a lack of customization, interactivity, and efficiency with large datasets. To address this, we developed CRISP (Comprehensive Repository for Insightful Simulation Post-Processing), an…
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…
Fabian Woller, Lis Arend, Christian Fuchsberger, Markus List + 1 more
To demonstrate the practical applicability of NApy on a real-world dataset, all statistical tests were performed on the CHRIS study data both without any parallelization (single thread) and with heavy parallelization (64 threads). For correlations, pandas was used as comparison as it was the fastest compared to other…
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…
Ignacio Martín, Gorka Zamora‐López, Jan Fousek, Michael Schirner + 4 more
This study introduces TVB C++, a streamlined and fast*C++ Back-End for The Virtual Brain (TVB), a renowned platform and a benchmark tool for full-brain simulation. TVB C++ is engineered with speed as a primary focus while retaining the flexibility and ease of use characteristic of the original TVB platform. Positioned…
Han Zhang, John Jonides
We present PupEyes, an open-source Python package for preprocessing and visualizing pupil size and fixation data. PupEyes supports data collected from EyeLink and Tobii eye-trackers as well as any generic dataset that conforms to minimal formatting standards. Developed with current best practices, PupEyes provides a…
Aliaksandr V. Yakutovich, Daniel Hollas, Edan Bainglass, Jusong Yu + 15 more
With ever-increasing computational capabilities, robust and automated research workflows have become essential for orchestrating large numbers of interdependent simulations. However, significant technical expertise is still required to configure execution environments, define calculation inputs, interpret outputs, and…
Darshan Mandge, Anıl Tuncel, Aurélien Jaquier, Ilkan Kilic + 5 more
The diversity of labs, tools, and data formats in neuroscientific research has historically posed challenges for data sharing and collaboration. Researchers often needed to convert data between various formats and adapt their software to new environments, which could divert attention from their main research goals.…
Fanwang Meng, Marco Martínez González, Valerii Chuiko, Alireza Tehrani + 7 more
Selector is a free, open-source Python library for selecting diverse subsets from any dataset, making it a versatile tool across a wide range of application domains. Selector implements different subset sampling algorithms based on sample distance, similarity, and spatial partitioning, along with metrics to quantify…
Aljoša Hafner, George Kourousias, Marco De Simone, Roberto Pugliese + 1 more
MAPI is a modular web-based framework designed to unite legacy analysis code with heterogeneous backends (edge, on-premises, high-performance computing, cloud), dramatically accelerating data analysis workflows and offering a scalable flexible blueprint for modernizing synchrotron data analysis.
Konrad Krämer, Pierre Tremouilhac, Fabian Mauz, Christoph Grathwol + 2 more
We developed OpenStats, a user-friendly web application that brings the power of the R language to researchers through a high-level interface and broad support for statistical methods such as t-tests and ANOVA. OpenStats was integrated into our electronic lab notebook Chemotion ELN via its third-party API, enabling…