29 papers · ranked by Valyu relevance
Guillaume Lemaître, Fernando Nogueira, Christos K. Aridas
imbalanced-learn is an open-source python toolbox aiming at providing a wide range of methods to cope with the problem of imbalanced dataset frequently encountered in machine learning and pattern recognition. The implemented state-of-the-art methods can be categorized into 4 groups: (i) under-sampling, (ii)…
Quinn Thibeault, Jacob Anderson, Aniruddh Chandratre, Giulia Pedrielli + 1 more
'Giulia Pedrielli' 'Georgios Fainekos'] Abstract. In this paper, we present the Python package PSY-TaLiRo which is a toolbox for temporal logic robustness guided falsification of Cyber-Physical Systems (CPS). PSY-TaLiRo is a completely modular toolbox supporting multiple temporal logic offline monitors as well as…
Henrik Podéus, Gustav Magnusson, Sasan Keshmiri, Kajsa Tunedal + 3 more
When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition, hierarchical system building, and time-dependent input handling, particularly within the…
Ciaran M Welsh, Nicola Fullard, Carole J Proctor, Alvaro Martinez-Guimera + 6 more
PyCoTools is an open source Python package designed to assist COPASI users in the task of modelling biological systems. PyCoTools offers an alternative high level interface to COPASI tasks including time courses, parameter scans and parameter estimations. While COPASI implements the heavy computation, PyCoTools…
Lucas S P Rudden, Samuel C Musson, Justin L P Benesch, Matteo T Degiacomi + 1 more
Models rationalizing sparse and low-resolution information on biomolecular structure, dynamics and interactions can provide key insight into biological function at the atomic level. Such models are generally produced by exploiting or combining collections of available molecular structures so as to recapitulate…
João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
The pdb-tools are a collection of Python scripts for working with molecular structure data in the PDB format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely…
Paulo Roberto Pereira Santiago, Abel Gonçalves Chinaglia, Kira Flanagan, Bruno L. S. Bedo + 4 more
Multimodal Toolbox Authors: ['Paulo Roberto Pereira Santiago' 'Abel Gonçalves Chinaglia' 'Kira Flanagan' 'Bruno L. S. Bedo' 'Lígia Yumi Mochida' 'Juan Aceros' 'Aline Bononi' 'Guilherme M. Cesar'] Biomechanics and Motor Control Laboratory, School of Physical Education and Sport, USP, Brazil Graduate Program 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…
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…
Johnny Hay, Eilidh Troup, Ivan Clark, Julian Pietsch + 2 more
'Tomasz Zieliński' 'Andrew Millar'] Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and…
Kiri Choi, J. Kyle Medley, Caroline Cannistra, Matthias König + 3 more
In this article, we present Tellurium, a powerful Python-based integrated environment designed for model building, analysis, simulation and reproducibility in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source integrated development environment (IDE) composed of multiple libraries…
Christoph Redies, Ralf Bartho, Lisa Koßmann, Branka Špehar + 3 more
research Authors: ['Christoph Redies' 'Ralf Bartho' 'Lisa Koßmann' 'Branka Špehar' '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…
Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche + 4 more
'Michael Crusoe' 'Hedi Peterson' 'Jon Ison' 'Hervé Ménager'] Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such…
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…
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…
Hamed Tahmooresi, Abbas Heydarnoori, Alireza Aghamohammadi
—Python is a popular, widely used, and general-purpose programming language. In spite of its ever-growing community, researchers have not performed much analysis on Python's topics, trends, and technologies which provides insights for developers about Python community trends and main issues. In this article, we examine…
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…
Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
'Morris A. Swertz'] Background Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science.…
Peter K. G. Williams, Casey Law, Geoffrey C. Bower
New and upgraded radio interferometers produce data at massive rates and will require significant improvements in analysis techniques to reach their promised levels of performance in a routine manner. Until these techniques are fully developed, productivity and accessibility in scientific programming environments will…
Benjamin M. Gyori, Charles Tapley Hoyt
Understanding the complex molecular processes governing how cells respond to external stimuli crucially relies on prior knowledge about signaling, regulatory, and metabolic pathways. Standardized representations are necessary to exchange such pathway knowledge and allow interoperability between tools. BioPAX () is a…
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R. Thomas + 3 more
The rapid development of high-throughput sequencing (HTS) techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for…
Kirill Zinovjev, Marc W. van der Kamp
Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained…
Kirill Zinovjev, Marc W. van der Kamp
X-ray crystallography allows detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. However, crystal structures provide little more than a static picture of proteinligand interactions, whereas dynamical…
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…
Manuel Garcia-Albornoz, Subazini Thankaswamy-Kosalai, Avlant Nilsson, Leif Väremo + 2 more
'Leif Väremo' 'Intawat Nookaew' 'Jens Nielsen'] Analysis of large data sets using computational and mathematical tools have become a central part of biological sciences. Large amounts of data are being generated each year from different biological research fields leading to a constant development of software and…
John L Moreland, Apostol Gramada, Oleksandr V Buzko, Qing Zhang + 1 more
'Philip E Bourne'] Background The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as…