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On the lifetime of bioinformatics web services.

ABSTRACT: Web services are used through all disciplines in life sciences and the online landscape is growing by hundreds of novel servers annually. However, availability varies, and maintenance practices are largely inconsistent. We screened the availability of 2396 web tools published during the past 10 years. All servers were accessed over 133 days and 318 668 index files were stored in a local database. The number of accessible tools almost linearly increases in time with highest availability for 2019 and 2020 (?90%) and lowest for tools published in 2010 (?50%). In a 133-day test frame, 31% of tools were always working, 48.4% occasionally and 20.6% never. Consecutive downtimes were typically below 5 days with a median of 1 day, and unevenly distributed over the weekdays. A rescue experiment on 47 tools that were published from 2019 onwards but never accessible showed that 51.1% of the tools could be restored in due time. We found a positive association between the number of citations and the probability of a web server being reachable. We then determined common challenges and formulated categorical recommendations for researchers planning to develop web-based resources. As implication of our study, we propose to develop a repository for automatic API testing and sustainability indexing.

SUBMITTER: Kern F

PROVIDER: S-EPMC7736811 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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On the lifetime of bioinformatics web services.

Kern Fabian F Fehlmann Tobias T Keller Andreas A

Nucleic acids research 20201201 22

Web services are used through all disciplines in life sciences and the online landscape is growing by hundreds of novel servers annually. However, availability varies, and maintenance practices are largely inconsistent. We screened the availability of 2396 web tools published during the past 10 years. All servers were accessed over 133 days and 318 668 index files were stored in a local database. The number of accessible tools almost linearly increases in time with highest availability for 2019 ...[more]

PMID: 33270886

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Project description:Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

Dataset Information

On the lifetime of bioinformatics web services.

Publications

On the lifetime of bioinformatics web services.

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