1. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools Susanne Konermann skonerma@cebitec.uni-bielefeld.de Jan Krüger jkrueger@cebitec.uni-bielefeld.de IFB Retreat Loccum - 24.02.2011

2. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools Overview ● General Information ● BielefeldBioinformaticService ● History / Timeline ● User / Developer Support ● Statistics ● A short story about Persistence... ● Publishing on BiBiServ ● BiBiServ2

3. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools General Information – What is BiBiServ ? ● Bielefeld BioInformatics Service ● Provides a multitude of bioinformatics tools and online education courses for users worldwide via the Bielefeld BioInformatics Server ● Bielefeld BioInformatics Server ● A server for online publication of bioinformatics tools for researchers and developers at Bielefeld University ● Provides online access to the tools functionality ● Is currently hosting about 40 tools from different application areas, including Alignments, RNA, Genome Comparison, Primer Design and other areas

4. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools General Information – Timeline (1) 1996Started as part of AG „Praktische Informatik“ in 1996 with a hardware donation of SUN on a single server. BiBiServ serves a collection of loosely coupled bioinformatics tools. 2001Becomes the self-contained technology platform for the IFB of the CeBiTec with permanent staff 2002Redesign of the web appearance, consistent tool design 2003Because of a growing number of submissions a small compute grid is integrated into the server structure. Support for xmlrpc based webservices. 2004Member of HOBIT. Support for SOAP based webservices.

5. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools General Information – Timeline (2) 2006Development and Usage of XML specification for common bioinformatics data types to support workflow systems. 2007Ajax support for new/updated tools 2009Start rewriting complete server structure on top of J2EE for next generation BiBiServ 2010Integration of Semantic Web Technology

6. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools General Information - User Support ● Easy access to and usage of bioformatics tools via Browser and Web Services (API) ● Choice of different tools with same scope ● Download of binary and/or source version with basic support for usage ● 1 st level email support with average reaction time of one day ● Consistent user interface for all tools, allowing a simple reuse of learned access methods

7. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools General Information - Developer Support ● Proven and stable infrastructure ● Library of basic tools/databases for reuse ● Persistent long-term availability of tools ● Reliable support ● For tool publication and maintenance ● Introduction into development environment ● Individual requirement analysis and personal implementation help ● 'shielding' from 1 st level support questions ● Mercurial repository

8. Center for Biotechnology Bielefeld Bioinformatics Service BiBiServ – a platform for publication of bioinformatics tools General Information - Statistics ● About 15.000 tool usages per month (2010) ● About 5000 tool download per year (2010) ● Typical user runs Windows (60%) or MacOSX (30%) ● Monthly updated access statistic : http://bibiserv.cebitec.uni- bielefeld.de/statistics

9. Center for Biotechnology Bielefeld Bioinformatics Service 9 NATURE 24 ? ? ? ? ? http://.../DOWNL OAD http://.../SUBMIS SION + + WW W 404 BiBiServ – a platform for publication of bioinformatics tools Persistence (not only) in BioInformatics

10. Center for Biotechnology Bielefeld Bioinformatics Service 10 BiBiServ – a platform for publication of bioinformatics tools Persistence - BiBiServ ● Independence of concrete person and computer ● Stable (!) and well known citable location ● Continuos adaption to current technologies ● Example: Genefisher 1996, 2006, 2010

11. Center for Biotechnology Bielefeld Bioinformatics Service 11 BiBiServ – a platform for publication of bioinformatics tools Persistence – Tool Life Cycle on BiBiServ ● development/testing → URL unreachable, testing on local installation ● active (informal) → URL reachable BUT NOT linked ● active (formal) → URL reachable AND linked ● EOL → URL reachable, tool still online usable for limited period of time ● Archive → URL reachable, Tool/Paper available for download

12. Center for Biotechnology Bielefeld Bioinformatics Service 12 BiBiServ – a platform for publication of bioinformatics tools Publishing on BiBiServ – Think about ● Resources, Network bandwidth limits ● Theoretical and real runtime consideration ● Tool itself must be runable within BiBiServ environment ● Kind of publication : online usage (browser, webservice) / download ● Intended User audience ● (OS) License

13. Center for Biotechnology Bielefeld Bioinformatics Service 13 BiBiServ – a platform for publication of bioinformatics tools Publishing on BiBiServ – Needed informations ● Name, short and long description ● input/output data and format ● Parameter types, restrictions and dependencies (for online usage) ● (explained) example ● (detailed) manual ● Source code (→ long term persistence) ● archives for download (manual, example data)

14. Center for Biotechnology Bielefeld Bioinformatics Service 14 BiBiServ – a platform for publication of bioinformatics tools Publishing on BiBiServ Come early, Communicate often !

15. Center for Biotechnology Bielefeld Bioinformatics Service 15 BiBiServ – a platform for publication of bioinformatics tools Next Generation BiBiServ : current server structure problems ● Grown structure, outdated server technique ● Separate structure with different server approaches for web interface and webservice ● PERL/CGI on webserver ● J2EE on webserviceserver (=application server) ● Tool described within sourcecode ● Default Template based ● Tool based parameter and input/output validation

16. Center for Biotechnology Bielefeld Bioinformatics Service 16 BiBiServ – a platform for publication of bioinformatics tools Next Generation BiBiServ : BiBiServ 2 ● Tool description based approach (Wizard guided) ● Toolspecific Templates (including WI,WS,manual, download area) generated from description ● Automatic validation/conversion of data formats ● Increased usability (Interactive WI forms, On-The-Fly validation, Input Descriptions,...) ● Secured „MyBiBiServ“ area, user managment ● Statistics about tool usage, resource usage, used parameters,... ● Semantic Web techniques (type vs. format) ● http://bibiserv2.cebitec.uni-bielefeld.de (alpha/beta state!) http://bibiserv2.cebitec.uni-bielefeld.de

17. Center for Biotechnology Bielefeld Bioinformatics Service 17 BiBiServ – a platform for publication of bioinformatics tools Thanks for your attention!