16 papers · ranked by Valyu relevance
Venus N. Sherathiya, Michael D. Schaid, Jillian L. Seiler, Gabriela C. Lopez + 1 more
Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be challenging for…
Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele
The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. There is a pressing requirement for a framework that allows for fast, efficient, manageable, and reproducible RNA-Seq analysis. We have developed a Python package, (pyrpipe), that…
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…
Matthew D. Blackledge, David J. Collins, Dow-Mu Koh, Martin O. Leach
We present pyOsiriX, a plugin built for the already popular dicom viewer OsiriX that provides users the ability to extend the functionality of OsiriX through simple Python scripts. This approach allows users to integrate the many cutting-edge scientific/image-processing libraries created for Python into a powerful…
Hugo Cornelis, Armando L. Rodriguez, Allan D. Coop, James M. Bower + 1 more
The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and…
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…
Eilif Muller, James A. Bednar, Markus Diesmann, Marc-Oliver Gewaltig + 2 more
'Michael Hines' 'Andrew P. Davison'] This Research Topic of Frontiers in Neuroinformatics is dedicated to the memory of Rolf Kötter (1961-2010), who was the Frontiers Associate Editor responsible for this Research Topic, and who gave us considerable support and encouragement during the process of conceiving and…
Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer, David R Stirling + 6 more
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or…
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…
Berk Ekmekci, Charles E. McAnany, Cameron Mura, Francis Ouellette
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware…
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.…
Andrew G. D. Rowley, Christian Brenninkmeijer, Simon Davidson, Donal Fellows + 6 more
SpiNNaker is a massively parallel distributed architecture primarily focused on real time simulation of spiking neural networks. The largest realization of the architecture consists of one million general purpose processors, making it the largest neuromorphic computing platform in the world at the present time.…
Felipe Machado, Norberto Malpica, Susana Borromeo, Talib Al-Ameri
Open source hardware for scientific equipment needs to provide source files and enough documentation to allow the study, replication and modification of the design. In addition, parametric modeling is encouraged in order to facilitate customization for other experiments. Parametric design using a solid modeling…
Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear + 5 more
'Justin M. Fear' 'Joseph Gerken' 'Xinlei Mi' 'Ali Ashrafi' 'Alison M. Morse' 'Lauren M. McIntyre'] Background Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic…
Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
The Keras deep learning library is used for producing the neural network architectures . The trained model is saved as an H5 file to simplify its distribution to different Galaxy instances (Galaxy, [RRID:SCR_006281]()). The file is an HDF5 store containing the weights of different layers of the neural network and their…
Marcel Friedrichs, Alban Shoshi, Piotr Jaroslaw Chmura, Jon Ison + 4 more
JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool…