14 papers · ranked by Valyu relevance
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…
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…
Robert Wolff, Alessia Polito, Alessio Paolo Buccino, Michela Chiappalone + 1 more
Title: Summary High-density multi-electrode arrays enable the recording of in vitro neuronal activity with exceptional spatial and temporal resolution. Here, we describe a protocol for analyzing these extensive datasets by using two complementary tools. The nicespike tool implements a full electrophysiological data…
Stephen R Piccolo, Harlan P Stevens
Using OpenAI’s Chat Completions API, we evaluated the ability to translate the example solutions and test code for the Python exercises to other programming languages: C++, Rust, Julia, and JavaScript. When invoking the API, we used version “gpt-4-0314” of the model and the default temperature setting of 0.7. For each…
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…
Ayusha Shrestha, Jasper W. Schwarz, Kurtis H. Feng, McKayla M. Spencer + 10 more
During November-December 2020, a disease outbreak involving eastern mudsnakes (Farancia abacura abacura) was documented in the Greater Everglades Ecosystem, Florida, USA. Moribund snakes were observed writhing on riverbanks with concomitant frothy oral discharge. Pathological examination revealed necrotizing enteritis…
Saroja Somasundaram, Nelson J. Johansen, Trygve E. Bakken, Jeremy A. Miller
High-throughput chromatin accessibility assays such as ATAC-seq generate thousands of candidate regulatory elements (peaks), yet no standardized tool exists for assembling the diverse quantitative features needed to prioritize peaks for functional validation. Here we present PyPeakRankR, an open-source Python package…
Shuo Yang, Yuting Liu, Jie Mi, Li‐Jen Chang + 1 more
According to the traditional Chinese veterinary medicine (TCVM) theory, Yin deficiency contributes to the acute onset of eclampsia. This condition arises primarily from the substantial loss of blood and nutrients to the foetus during pregnancy, leading to insufficient nutrition and blood supply. Consequently, the…
Alexander Alsalihi, Robert M. Flight, Hunter N. B. Moseley
The recount3 online resource provides tens of thousands of uniformly processed RNA-seq samples across human and mouse from major sequencing repositories like the Sequence Read Archive. While access to these datasets has traditionally been centered in the R/Bioconductor ecosystem, the growing prominence of Python in…
Tomasz Chady, Zuzanna Karolina Filutowska, Zhiyong Lu
GTF/GFF version 2 and FASTA file formats are widely used in genomics owing to their simplicity and ease of use. Consequently, parsing these files is often the first step in many projects, and can become a bottleneck. Indeed, this was the experience of the authors, who found a Python-based parser to be too slow and…
Michael Antonov, Gábor Csárdi, Szabolcs Horvát, Kirill Müller + 7 more
Networks or graphs are widely used across the sciences to represent relationships of many kinds. The igraph ([https://igraph.org]()) software library supports graph construction, analysis, and visualisation, combining fast and robust performance with a low entry barrier. igraph pairs a fast core written in C with…
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…
Richard Burger, Daniel J. D. Natusch, Richard Shine, Ian P. Vaughan + 2 more
Evaluating sustainable levels of offtake is central to regulating the commercial harvest of wildlife species, but methods developed for temperate-zone mammal and bird species may be inapplicable to tropical rainforest reptiles. For example, population viability models require information on abundance and on rates of…
Jane P. Wesson, Mark A. O'Dea, Andrew J. Currie, Cathy M. Shilton + 2 more
Sunshinevirus was originally isolated in 2008 from a collection of Australian pythons suffering an outbreak of neuro-respiratory disease. Sunshinevirus infection cases, including chronic asymptomatic infections, have subsequently been detected throughout Australia by PCR testing. To investigate the association between…