Abstract:
:Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Pazos F,Chagoyen Mdoi
10.1093/bib/bby001subject
Has Abstractpub_date
2019-07-19 00:00:00pages
1329-1336issue
4eissn
1467-5463issn
1477-4054pii
4812639journal_volume
20pub_type
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
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更新日期:2020-11-03 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2019-11-27 00:00:00
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pub_type: 杂志文章
doi:10.1093/bib/bbz028
更新日期:2020-05-21 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa285
更新日期:2020-11-14 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa349
更新日期:2020-12-30 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx097
更新日期:2019-01-18 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs074
更新日期:2014-07-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbu016
更新日期:2015-05-01 00:00:00
abstract::Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-inc...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa322
更新日期:2020-12-18 00:00:00
abstract::Effectively representing Medical Subject Headings (MeSH) headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. In this paper, we converted the MeSH tree ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa037
更新日期:2020-03-31 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-06-10 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2017-01-01 00:00:00
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更新日期:2011-05-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz090
更新日期:2020-09-25 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbv109
更新日期:2016-11-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbq086
更新日期:2011-11-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbr076
更新日期:2012-09-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2013-09-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-08-14 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2000-09-01 00:00:00
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更新日期:2017-03-01 00:00:00