12 papers · ranked by Valyu relevance
Eytan Balken, Itai Ben-Nun, Amos Fellig, Daniel Khaykelson + 2 more
An upgrade to the D+ software is presented, simulating the 2D scattering pattern from structures with a single orientation or fibers. An upgraded independent D+ Python API is described, including structure factor, polydispersity and several other features.
Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian + 9 more
To meet the increased need of making biomedical resources more accessible and reusable, Web APIs or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological…
Matteo Valerio, Alessandro Inno, Stefania Gori
Python 36 was chosen as the programming language for pyBioPortal, given its growing popularity in bioinformatics and compatibility with all major operating systems. The version of Python used for development is 3.9, which ensures stability and support in the more recent versions of Python, as version 2 has not been…
Robert Vorbau, Gavin Poludniowski
Knowledge of the photon spectrum emitted from an x-ray tube is frequently needed in imaging and dosimetry contexts. As the spectrum characteristics are influenced by several parameters and routine measurement of a spectrum is often impractical, a variety of software programs have been developed over the decades for…
Nathan J. LeRoy, Oleksandr Khoroshevskyi, Aaron O’Brien, Rafał Stepień + 2 more
The PEPhub server is built with FastAPI, a web framework optimized for speed and high-performance. FastAPI is specifically designed for developing APIs. We chose FastAPI for its automatic data validation capabilities, built-in API documentation, and because using Python allows us to interface with existing Python…
Christoph Li, Josh Lawrimore, Dustin Moraczewski, Adam G. Thomas
labapi is a Python library that enables computational workflows to connect to LabArchives’ electronic lab notebook (ELN). Without an Application Programming Interface (API) connection, researchers must manually add workflow outputs through the LabArchives web interface, navigating to the appropriate page and uploading…
Erik Huckvale, Hunter N. B. Moseley
Background The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible…
Erik Huckvale, Hunter N.B. Moseley
The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and…
Erick Martins Ratamero, Kiya Govek, Julio Mateos Langerak, Fernando Cervantes Sanchez + 1 more
Many research laboratories need to manage, process, and analyze the increasingly large volumes and complexity of data being produced by state-of-the-art bioimaging platforms. OMERO is a popular open-source client-server application that provides a unified interface for managing and working with bioimages and their…
Rick P. Wierenga, Stefan Golas, Wilson Ho, Connor Coley + 1 more
'Kevin M. Esvelt'] Liquid handling robots are often limited by proprietary programming interfaces that are only compatible with a single type of robot and operating system, restricting method sharing and slowing development. Here we present PyLabRobot, an open-source, cross-platform Python interface capable of…
Tianze Cao, Qian Li, Yuexia Huang, Anshui Li
Background The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learning, Python is currently the most popular programming language. The…
Yajushi Khurana, Keisuke Ishihara
Three-dimensional biological morphologies encode functional and physiological state, yet the directional, orientational, and topological properties of these shapes are rarely captured by morphometric tools available for bioimage analysis. Minkowski tensors are mathematically rigorous tensor-valued measures that encode…