8 papers · ranked by Valyu relevance
Daniel Danis, Julius O. B. Jacobsen, Alex H. Wagner, Tudor Groza + 15 more
'Martha A. Beckwith' 'Lauren Rekerle' 'Leigh C. Carmody' 'Justin Reese' 'Harshad Hegde' 'Markus S. Ladewig' 'Berthold Seitz' 'Monica Munoz-Torres' 'Nomi L. Harris' 'Jordi Rambla' 'Michael Baudis' 'Christopher J. Mungall' 'Melissa A. Haendel' 'Peter N. Robinson' 'Stephen R. Piccolo'] The Global Alliance for Genomics and…
Göksel Mısırlı, Pier Luigi Martelli
The libSBOLj3 library fully implements the SBOL3 data model. Some of the important library features are summarized below. The library handles information as a single SBOL document, which can be constructed using programmatic entities designed to represent information of interest, such as a Component entity to represent…
Göksel Mısırlı
The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBOLj3 to facilitate data exchange and provide interoperability between…
Pierre Pouchin, Rayan Zoghlami, Rémi Valarcher, Maxence Delannoy + 5 more
'Manon Carvalho' 'Clémence Belle' 'Marc Mongy' 'Sophie Desset' 'Frédéric Brau'] The Open Microscopy Environment Remote Objects (OMERO) is an open-source image manager used by many biologists to store, organize, view, and share microscopy images, while the open-source software ImageJ/Fiji is a very popular program used…
Diego Marcilio, Carlo A. Furia
When a method throws an exception- its exception precondition-is a crucial element of the method’s documentation that clients should know to properly use it. Unfortunately, exceptional behavior is often poorly documented, and sensitive to changes in a project’s implementation details that can be onerous to keep…
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche + 4 more
Mass spectrometry is a powerful technique for analyzing molecules in complex biological samples. However, inter- and intra-laboratory variability and bias can affect the data due to various factors, including sample handling and preparation, instrument calibration and performance, and data acquisition and processing.…
Michael R. Hoopmann, Christopher D. McGann, Christopher M. Rose, Devin K. Schweppe
Nova is a software library for the reading, writing, and management of mass spectrometry data natively in the C# language. It complements similar software libraries ubiquitously used in application development for C++, Python, and Java. Few software libraries and resources for mass spectrometry data analysis have been…
Jack D Huey, Nezar Abdennur, Jonathan Wren
Due to the limitations of the UCSC reference implementation, a number of alternative BBI software implementations have emerged in different languages, having varying levels of feature support and caveats [libBigWig and pyBigWig (, ), @gmod/bbi (), Big ([https://github.com/JetBrains-Research/big]()), bigwig-reader…