A Survey of the Availability of Primary Bioinformatics Web Resources

Thireou, Trias; Spyrou, George M.; Atlamazoglou, Vassilis

doi:10.1016/s1672-0229(07)60017-5

Cited by 9 publications

(5 citation statements)

References 7 publications

(9 reference statements)

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“…Although appealing to users in principle for its unified bioinformatics portal, the IGD survived only 1 year, due to frequent updates and high cost of maintenance in response to the changes of source databases [5]. In bioinformatics, the sword of Damocles hangs over every Web 1.0 database/web server, due to the threat of loss of financial support [35,36]. With centralized updating of content, even a minor gap in funding support may hamstring and doom an otherwise cutting-edge Web 1.0 database, largely because in the Web 1.0 model, users are allowed only to retrieve information, but not to update it.…”

Section: Bringing Web 20 To Bioinformatics What Is Web 20?mentioning

confidence: 99%

Bringing Web 2.0 to bioinformatics

Zhang¹,

Cheung²,

Townsend³

2008

Briefings in Bioinformatics

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Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

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Section: Bringing Web 20 To Bioinformatics What Is Web 20?mentioning

confidence: 99%

Bringing Web 2.0 to bioinformatics

Zhang¹,

Cheung²,

Townsend³

2008

Briefings in Bioinformatics

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“…[85][86] Many times the aforementioned issues are interconnected trying to answer to complex questions such as: given the gene sequence that is responsible for a disease, is there a suitable drug that will stop the undesired action of the specified gene? A chain of bioinformatics actions strongly incorporating CI methods is necessary (but not always sufficient).…”

Section: Computational Intelligence In Biologymentioning

confidence: 99%

Computational Intelligence in Medicine and Biology: A Survey

Vasilakos¹,

Spyrou²

2008

Jnl of Comp & Theo Nano

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Modern Medicine and Biology are dependent on systems and methods for high throughput data acquisition and management, detailed analysis of huge amount of data, knowledge extraction and predictive ability. In other words, the life sciences do not simply need sufficient computers, they require computational intelligence. This paper describes the state of the art applications of computational intelligence in Medicine and Biology comprising a large part of the current research and applications in the fields of Medical Informatics and Bioinformatics as well.

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“…These numbers underline the tremendous popularity but show that scientific rigorousness must be assured for online implementations as well. It became a perception that computational biology resources lack persistence and usability ( 13 , 14 ). Following the study by Veretnik et al.…”

Section: Introductionmentioning

confidence: 99%

On the lifetime of bioinformatics web services

Kern

Fehlmann

Keller

2020

Nucleic Acids Research

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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.

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A Survey of the Availability of Primary Bioinformatics Web Resources

Cited by 9 publications

References 7 publications

Bringing Web 2.0 to bioinformatics

Bringing Web 2.0 to bioinformatics

Computational Intelligence in Medicine and Biology: A Survey

On the lifetime of bioinformatics web services

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