23 papers · ranked by Valyu relevance
Gustave Monce, Thomas Couturou, Yasmine Hamdaoui, Thomas Degueule + 1 more
'Jean‐Rémy Falleri'] Designing an effective API is essential for library developers as it is the lens through which clients will judge its usability and benefits, as well as the main friction point when the library evolves. Despite its importance, defining the boundaries of an API is a challenging task, mainly due to…
Maria Paasivaara, Philippe Kruchten, Saeid Heshmatisafa, Marko Seppänen
'Marko Seppänen'] Many companies have followed the trend toward exposing their business assets through open (i.e., Web) application programming interfaces (APIs). However, these firms appear to have adopted API technology largely to meet their customers’ needs and demands. The pressures on industries to develop…
Rediana Koçi, Xavier Franch, Petar Jovanović, Alberto Abelló
A Web API (WAPI) is a type of API whose interaction with its consumers is done through the Internet. While being accessed through the Internet can be challenging, mostly when WAPIs evolve, it gives providers the possibility to monitor their usage, and understand and analyze consumers' behavior. Currently, WAPI usage is…
Aziz Khan, Anthony Mathelier
JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to…
Nicolas Harrand, Amine Benelallam, César Soto-Valero, François Bettega + 2 more
'François Bettega' 'Olivier Barais' 'Benoît Baudry'] Abstract—This paper addresses the following question: does a small, essential, core set of API members emerges from the actual usage of the API by client applications? To investigate this question, we study the 99 most popular libraries available in Maven Central and…
Xiaodong Gu, Hongyu Zhang, Dongmei Zhang, Sunghun Kim
Developers often wonder how to implement a certain functionality (e.g., how to parse XML files) using APIs. Obtaining an API usage sequence based on an API-related natural language query is very helpful in this regard. Given a query, existing approaches utilize information retrieval models to search for matching API…
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…
Chunlei Wu, Adam Mark, Andrew I. Su
Biomedical knowledge is often represented as annotations of biological entities such as genes, genetic variants, diseases, and drugs. For gene annotations, they are fragmented across data repositories like NCBI Entrez, Ensembl, UniProt, and hundreds (or more) of other specialized databases. While the volume and breadth…
Anne Kiirikki, Hanne Antila, Lara Bort, Pavel Buslaev + 17 more
Anne Kiirikki 1 , Hanne Antila 3 , Lara Bort 4 , Pavel Buslaev 5 , Favela Fernando 6 , Tiago Mendes Ferreira 7 , Patrick Fuchs 8 , Rebeca Garcia-Fandino 9 , Ivan Gushchin, Batuhan Kav 10 , Norbert Kučerka 15 , Patrik Kula 13 , Milla Kurki 14 , Alexander Kuzmin, Jesper Madsen 11 , Markus Miettinen 2 , Ricky Nencini 1 …
Frederik Buelthoff, Maria Maleshkova
Recent developments in the world of services on the Web show that both the number of available Web APIs as well as the applications built on top is constantly increasing. This trend is commonly attributed to the wide adoption of the REST architectural principles [1]. Still, the development of Web APIs is rather…
Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner + 3 more
HTTP defines a set of verbs that can be applied to an endpoint to change the action performed. The most commonly used are ‘GET’ to transfer a current representation of the resource from an endpoint. ‘POST’, ‘PUT’, ‘PATCH’, and ‘DELETE’ (so-called unsafe methods) perform a processing operation, which could be…
Stephen K Woody, David Burdick, Hilmar Lapp, Erich S. Huang
Storing very large amounts of data and delivering them to researchers in an efficient, verifiable, and compliant manner, is one of the major challenges faced by health care providers and researchers in the life sciences. The electronic health record (EHR) at a hospital or clinic currently functions as a silo, and…
George Jones, Amanda E. Wakefield, Jeff Triplett, Kojo Idrissa + 3 more
'James Goebel' 'Dima Kozakov' 'Sandor Vajda'] Within the last few decades, increases in computational resources have contributed enormously to the progress of science and engineering (S & E). To continue making rapid advancements, the S & E community must be able to access computing resources. One way to provide such…
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…
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…
Bishwa Ghimire, Nicholas Booth, Tapio Lönnberg, Tero Aittokallio + 1 more
Nextflow’s command-line interface has the optional flag -with-trace, which generates an execution tracing file trace.txt for a single pipeline run. Alternatively, Nextflow’s configuration file option (‘trace.enabled = true’) generates the execution tracing file for all pipeline runs as well. The file contains task…
Marc Chakiachvili, Anne-Muriel Arigon Chifolleau, Vincent Lefort
WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely…
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.…
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…
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.…
Max Mathijssen, Michiel Overeem, Slinger Jansen
API Management is the design, publication, and deployment of APIs by an organization for (external) developers to consume. API Management encompasses capabilities such as controlling API lifecycles, access and authentication to APIs, monitoring, throttling and analyzing API usage, as well as providing security and…
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…
Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara + 3 more
Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common data format offers significant advantages, that…