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Updated: Nov 27, 2025
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
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On the lifetime of bioinformatics web services
Fabian Kern1,2, Tobias Fehlmann1,2, Andreas Keller1,2,3
1Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany.
Nucleic Acids Research
|December 3, 2020
Summary
Most life science web tools are available, but consistency varies. Newer tools show higher uptime, and citation counts correlate with accessibility, suggesting a need for better maintenance and testing resources.
Area of Science:
- Life sciences
- Bioinformatics
- Computational biology
Background:
- Web services are crucial in life sciences, with numerous new servers emerging annually.
- Inconsistent maintenance and varying availability of these online resources pose challenges for researchers.
Purpose of the Study:
- To assess the long-term availability and reliability of web-based tools in the life sciences.
- To identify factors influencing web tool accessibility and provide recommendations for sustainable development.
Main Methods:
- Systematic screening of 2396 web tools over 133 days, storing 318,668 index files.
- Analysis of tool accessibility trends over a decade, including downtime duration and frequency.
- A "rescue experiment" to test the recoverability of inaccessible tools published from 2019 onwards.
Main Results:
- Tool accessibility generally increased over time, with ~90% availability for 2019-2020 tools vs. ~50% for 2010 tools.
- Over the test period, 31% of tools were always accessible, 48.4% occasionally, and 20.6% were never accessible.
- A positive correlation was found between the number of citations and web server reachability; 51.1% of inaccessible recent tools were restorable.
Conclusions:
- While web tool availability has improved, significant inconsistencies persist, impacting research reproducibility.
- Developing a repository for automatic API testing and sustainability indexing is proposed to enhance resource reliability.
- Recommendations are formulated for researchers to improve the development and maintenance of web-based life science resources.
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