26 papers · ranked by Valyu relevance
H. F. Stevance, Jack Leland, K. Smith
The Asteroid Terrestrial-impact Last Alert System (ATLAS) is an all-sky optical sky survey with a cadence of 24 to 48 hours (Tonry et al., 2018), and the ATLAS Transient Server (Smith et al., 2020) processes the alert stream to enable the discovery and follow-up of extra-galactic transients. The data from the ATLAS…
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…
Moshi Wei, Nima Shiri Harzevili, Alvine Boaye Belle, Junjie Wang + 3 more
'Lin Shi' 'Song Wang' 'Zhen Ming Jiang'] MOSHI WEI, York University, Canada NIMA SHIRI HARZEVILI, York University, Canada ALVINE BOAYE BELLE, York University, Canada JUNJIE WANG, Institute of Software Chinese Academy of Sciences, China LIN SHI, Institute of Software Chinese Academy of Sciences, China JINQIU YANG…
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…
Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck + 1 more
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management.…
James Martin, Jin Guo
Understanding the correct API usage sequences is one of the most important tasks for programmers when they work with unfamiliar libraries. However, programmers often encounter obstacles to finding the appropriate information due to either poor quality of API documentation or ineffective query-based searching strategy.…
Shuai Zhang, Guanping Xiao, Jun Wang, Huashan Lei + 3 more
'Yulei Sui' 'Zheng Zheng'] Abstract—In modern software development, Python thirdparty libraries have become crucial, particularly due to their widespread use in fields such as deep learning and scientific computing. However, the parameters of APIs in third-party libraries often change during evolution, causing…
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…
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve + 1 more
A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream processing of peptide-spectrum matches (PSMs) and PSM files. While standards exist to solve this problem, these are far from universally supported by search…
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…
Yintong Huo, Yuxin Su, Hongming Zhang, Michael R. Lyu
Online technical forums (e.g., StackOverflow) are popular platforms for developers to discuss technical problems such as how to use a specific Application Programming Interface (API), how to solve the programming tasks, or how to fix bugs in their code. These discussions can often provide auxiliary knowledge of how to…
Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang + 11 more
The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication, we identified the need for the development of an Application Programming Interface (API) that could promote biomedical data integration…
Authors not listed
The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions…
Antonios Saravanos, John Pazarzis, Stavros Zervoudakis, Dongnanzi Zheng
Python libraries often need to maintain a stable public API even as internal implementations evolve, gain new backends, or depend on heavy optional libraries. In Python, where internal objects are easy to inspect and import, users can come to rely on "reachable internals" that were never intended to be public, making…
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…
Akalanka Galappaththi, Sarah Nadi, Christoph Treude
Developers rely on third-party library Application Programming Interfaces (APIs) when developing software. However, libraries typically come with assumptions and API usage constraints, whose violation results in API misuse. API misuses may result in crashes or incorrect behavior. Even though API misuse is a…
Helle W. van den Maagdenberg, Martin Šícho, David Alencar Araripe, Sohvi Luukkonen + 9 more
Building reliable and robust quantitative structure-property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the number of available methods is continuously growing and evaluating different algorithms and methodologies can be arduous.…
Authors not listed
The widespread adoption of open-source cheminformatics toolkits remains constrained by technical implementation barriers, including complex installation procedures, dependency management, and integration challenges. Here, we present Cheminformatics Microservice V3, a significant update to the existing platform that…
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…
Sterling G. Baird, Taylor D. Sparks
Closed-loop Spectroscopy Lab: Light-mixing Demo (CLSLab:Light) is a teaching and prototyping platform for autonomous scientific discovery. It consists of a set of LEDs and a light sensor while encapsulating key principles for "self-driving" (i.e., autonomous) research laboratories, including sending commands, receiving…