19 papers · ranked by Valyu relevance
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…
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…
Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross + 2 more
'Cecilia Arighi' 'Cathy H Wu'] Title: Abstract iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and…
Juan Cabral, Ehsan Kourkchi, M. Beroiz, Erik Peterson + 1 more
In this paper we present PyCF3, a python client for the cosmological distancevelocity calculator CosmicFlow-3. The project has a cache and retry system designed with the objective of reducing the stress on the server and mitigating the waiting times of the users in the calculations. We also address Quality Assurance…
Yury V. Zaytsev, Abigail Morrison
NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, [11]). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., [1]). The introduction of…
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.…
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…
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.…
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…
Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard van Westen
This manuscript describes the development and architecture of the GenUI software platform for integration of molecular generators. The source code for the components of the platform is available in the following repositories: https://github.com/martin-sicho/genui https://github.com/martin-sicho/genui-gui…
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…
Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner + 3 more
Authentication is the process of identifying a client when the server is provided with a login and password (credentials) that match an authorised individual’s information within an authentication service. We encourage API developers to use common authentication methods such as OAuth 2.0 , JsonWebToken , and Basic…
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…
D. M. Faes
The use of Python is noticeably growing among the scientific community, and Astronomy is not an exception. The power of Python consists of being an extremely versatile high-level language, easy to program that combines both traditional programming and data reduction and analysis tools. Here I make a brief introduction…