Schultheiss bosc2010 persistance-web-services

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Schultheiss bosc2010 persistance-web-services

  1. 1. Persistence and availability of bioinformatics web services Sebastian J. Schultheiss BOSC 2010 <sebi@tue.mpg.de> Boston, July 9–10 TL-Stiftung Saturday, July 10, 2010 1
  2. 2. The Study S. J. Schultheiss et al. (2010) PLoS Comp Biol (under review) ‣ Curated data set: Nucleic Acids Research Web Server Issues 2003-2009 ‣ 927 web services ‣ 322 institutions ‣ 39 countries ‣ 827 corresponding authors (274 replies) Saturday, July 10, 2010 2
  3. 3. The Problem Veretnik et al. (2008) PLoS Comp Biol 4:e1000136 ‣ Original web address unreachable for 17% of services Saturday, July 10, 2010 3
  4. 4. The Problem ‣ Research is based on existing services ‣ Reproducibility, comparability ‣ Improving methods made difficult Saturday, July 10, 2010 4
  5. 5. Developments over Time ‣ More recent services are still reachable, have higher quality standards ‣ NAR publishing policies became stricter Saturday, July 10, 2010 5
  6. 6. Saturday, July 10, 2010 6
  7. 7. Long-Term Availability Score Saturday, July 10, 2010 7
  8. 8. Average Citations 43 S. J. Schultheiss et al. (2010) PLoS Comp Biol (under review) 40 Average Citations Reachable: Average Citations Unreachable: Average Citations 20% 19% % Unreachable 16% 13% 18 17 14 9% 12 12 11 9 8 9 7 7 7 4 2003 2004 2005 2006 2007 Saturday, July 10, 2010 8
  9. 9. Survey among NAR Authors S. J. Schultheiss et al. (2010) PLoS Comp Biol (under review) ‣ 64% of services used by researchers without computational background ‣ 58% of services developed by students only, difficult to maintain after graduation ‣ 24% of services will not be maintained Saturday, July 10, 2010 9
  10. 10. Web Service Problems # % Unreachable, web site down 132 48% No example datasets 110 40% No help text/documentation 109 40% Implausible arrangement of interface elements/not intuitive to use 99 36% Too stringent limitations (e.g. on file size, number of sequences, ...) 87 32% Processing/waiting time unreasonably long 77 28% No response upon personal e-mail or on mailing list, no support 66 24% Bad design choices (colors, size of edit fields, ...) 53 19% Missing contact information 24 9% Saturday, July 10, 2010 10
  11. 11. Ten Simple Rules S. J. Schultheiss (2010) PLoS Comp Biol (under review) 1. Consider a stand-alone version 2. Know your audience 3. Use an existing framework 4. Make it portable 5. Provide documentation and assistance Saturday, July 10, 2010 11
  12. 12. Ten Simple Rules S. J. Schultheiss (2010) PLoS Comp Biol (under review) 6. Assist users and involve the community 7. Be explicit about changes 8. Leave a forwarding address 9. Find someone else to do it 10. Plan the end of the service life cycle Saturday, July 10, 2010 12
  13. 13. Summary ‣ Available services cited 2.2x more often ‣ Authors: use persistent URLs (PURL, DOI, own domain, ...) and release source code ‣ Prepare to hand over responsibilities ‣ LT score predicts reliability of services for editors and reviewers Saturday, July 10, 2010 13
  14. 14. Poster Acknowledgements T5 ‣ Marc-Christian Münch and Gergana Andreeva ‣ Gunnar Rätsch and AG Rätsch/MLB at the FML ‣ Oliver Kohlbacher, WSI, University of Tübingen ‣ TL Foundation and its Board at University of Tübingen ‣ ISCB, DOE and NSF for a Travel Fellowship TL-Stiftung Saturday, July 10, 2010 14

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