26 papers · ranked by Valyu relevance
Immo Schuetz, Harun Karimpur, Katja Fiehler
Virtual reality (VR) is a powerful tool for researchers due to its potential to study dynamic human behavior in highly naturalistic environments while retaining full control over the presented stimuli. Due to advancements in consumer hardware, VR devices are now very affordable and have also started to include…
Jin Hyun Cheong, Eshin Jolly, Tiankang Xie, Sophie Byrne + 2 more
'Matthew Kenney' 'Luke J. Chang'] Studying facial expressions is a notoriously difficult endeavor. Recent advances in the field of affective computing have yielded impressive progress in automatically detecting facial expressions from pictures and videos. However, much of this work has yet to be widely disseminated in…
Elizaveta Lavrova, Sergey Primakov, Zohaib Salahuddin, Manon Beuque + 3 more
'Damon Verstappen' 'Henry C. Woodruff' 'Philippe Lambin'] Medical image analysis plays a key role in precision medicine as it allows the clinicians to identify anatomical abnormalities and it is routinely used in clinical assessment. Data curation and preprocessing of medical images are critical steps in the…
Márton Á Goda, Peter H Charlton, Joachim A Behar
Objective. Photoplethysmography is a non-invasive optical technique that measures changes in blood volume within tissues. It is commonly and being increasingly used for a variety of research and clinical applications to assess vascular dynamics and physiological parameters. Yet, contrary to heart rate variability…
Jens Lucht, Paul Meyer, Leon Merten Lohse, Tim Salditt + 1 more
We present HoToPy, a toolbox for X-ray holo-tomography in Python. It offers state-of-the-art phase retrieval methods for synchrotron and laboratory sources as well as tomographic reconstruction and alignment methods.
Haocheng Zhu, Ulrik Beierholm, Ladan Shams, Michael Moutoussis
Psychological and neuroscientific research over the past two decades has shown that the Bayesian causal inference (BCI) is a potential unifying theory that can account for a wide range of perceptual and sensorimotor processes in humans. Therefore, we introduce the BCI Toolbox, a statistical and analytical tool in…
Johnathan Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar + 10 more
Computational Pathology (CPath) has seen rapid growth in recent years, driven by advanced deep learning (DL) algorithms. These algorithms typically share the same sequence of steps. However, due to the sheer size and complexity of handling large multi-gigapixel whole-slide images, there is no open-source software…
William R. P. Nourse, Clayton Jackson, Nicholas S. Szczecinski, Roger D. Quinn + 2 more
'Roger D. Quinn' 'Mingguo Zhao' 'Biao Hu'] One developing approach for robotic control is the use of networks of dynamic neurons connected with conductance-based synapses, also known as Synthetic Nervous Systems (SNS). These networks are often developed using cyclic topologies and heterogeneous mixtures of spiking and…
Christoph Redies, Ralf Bartho, Lisa Koßmann, Branka Spehar + 3 more
'Ronald Hübner' 'Johan Wagemans' 'Gregor U. Hayn-Leichsenring'] Over the past two decades, researchers in the field of visual aesthetics have studied numerous quantitative (objective) image properties and how they relate to visual aesthetic appreciation. However, results are difficult to compare between research…
Laura Wiggins, Stuart Lacy, Graeme Park, Joanne Marrison + 5 more
We previously developed the CellPhe toolkit^1^, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image analysis tools and to enhance interoperability with widely used software for cell segmentation and tracking, we developed…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Randy Heiland, Daniel Bergman, Blair Lyons, Julie Cass + 4 more
Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of objects. Hopefully the model will be defined using some format specification, e.g., a markup language, that will provide easy model sharing (and a minimal step toward reproducibility).…
Alex Sheng
We develop a simple and straightforward methodology to create AI computer agents that can carry out diverse computer tasks and self-improve by developing tools and augmentations to enable themselves to solve increasingly complex tasks. As large language models (LLMs) have been shown to benefit from nonparametric…
Muhammad Aziz
Computational chemistry software designed to compute the chemical properties of compounds falls under the category of dry research. The computational calculation of chemicals is a broad term. In this current study, chemical properties are estimated through computational methods, which is valuable for newly synthesis…
Dimitar Georgiev, Simon Vilms Pedersen, Ruoxiao Xie, Álvaro Fernández-Galiana + 2 more
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the…
Himaghna Bhattacharjee, Jackson Burns, Dionisios Vlachos
The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Yangyang Li, Rendong Yang
We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows.…
Wei Cheng, Xiangrong Zhu, Wei Hu
Code sharing and reuse is a widespread use practice in software engineering. Although a vast amount of open-source Python code is accessible on many online platforms, programmers often find it difficult to restore a successful runtime environment. Previous studies validated automatic inference of Python dependencies…
Anselm W. Hahn, Joseph Zsombor-Pindera, Pierre Kennepohl, Serena DeBeer
In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows…
François Moreews, Jean-Baptiste Bougaud, Emmanuelle Becker, Florence Gondret + 1 more
Biological Pathway Exchange (BioPAX) is a standard language, represented in OWL, that aims to enable the integration, exchange, visualization and analysis of biological pathway data. While public databanks increasingly provide datasets in BioPAX format, their use remains below potential. Users may encounter challenges…
Serena Cofano, Giacomo Benedetti, Matteo Dell’Amico
Our analysis highlights issues related to dependency versions, metadata files, remote dependencies, and optional dependencies. Additionally, we identified a systematic issue with the lack of standards for metadata in the PyPI ecosystem. This includes inconsistencies in the presence of metadata files as well as…
Siamak Farshidi, Amir Saberhabibi, Behbod Eskafi, Niloofar Nikfarjam + 4 more
Context: Selecting third-party software packages in open-source ecosystems such as Python is challenging due to the significant number of alternatives and the limited availability of transparent evidence to compare them. Generative AI tools are commonly used in development workflows, yet their suggestions often…
Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes + 2 more
'Claire Samuels' 'Herbert M. Sauro'] SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the drawing canvas. It supports the visualization and editing of compartments, species, and…
Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao + 1 more
SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) is a powerful and versatile software tool designed to computationally estimate the kinetics and thermodynamics of complex molecular processes, particularly emphasizing the process of receptor-ligand binding and unbinding. We present a suite of tutorials for…