15 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…
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…
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…
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…
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…
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…
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…