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Presentation in SemWiki2010 workshop in Extended Semantic Web Conference 2010 in Crete.
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3. http://biocore.crg.cat 4.
CRG @ PRBB (Barcelona) International-based research center in PRBB Biopark Protein Service Internal CRG service thatproducesandpurifiesproteins for researchers in CRG. Other analyses in the future, such asmutagenesis .Bioinformatics Core Facility Provide researchers at CRG, PRBB, and other external institutions with services of consultation, data analysis and management, software development, and access to computing resources. 5.
Images from commons.wikimedia.org PCR HPLC Gel electrophoresis 6.
7. Email messages (submission, details, etc.) 8. Meetings 9. Multiple files in multiple disks not easily linked
10. Allows efficient collaboration between different users Group roles specific permissions Researchers , lab members, lab managers, administrators Well-know interface.All people should have edited Wikipedia once! Notetaking in wiki for future consultation
11. Users can be both humans and robot script applications Refined and specific queries Possibility of logic connection with other semantic empowered software Easy set up of new environments (high level programming)
12. Users roles S ubmit requests to the service using pre-defined templates, view the status of his/her requests at any time, and retrieve the study reports when experiments are complete Can add, edit experimental data, cannot create or delete experiments. Can create, edit, delete new experiments, associated to submitted requests, using pre-defined templates C reation of new templates, users management and their training 13.
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Design: Guglielmo Roma 15. Permissions & security Login & role permissions.Done automatically or via administrator Namespaces specific permissions:Experiment:: (only lab members/managers) Template:: (only administrators) Page specific permissions By using user and parse functions extensions with Semantic properties MediaWiki Image authorizationNetwork, LDAP, etc. 16. Request Form Thanks toExtension:Semantic Forms 17. Request Form 18. Request result page 19. User specific request access 20. Enable experiment 21. Follow associated experiments 22. Experiment form 23. Experiment form 24. Experiment form fine-grained control Emailing linked to change of properties. ModifiedSemantic Tasks extension . 25. Experiment form - restrictions Logical input Restrictions. Data Type linked 26.
Enable certain experiment sections if asked by the researcher or lab manager Input value restriction at the form level Example: Only nucleotides allowed inPrimer sequences. Regular expressions. 27.
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Template(s) created when the user first registers. Modified NewUserMessage extension 29.
Better look and feel for the wiki Detailed image (semantic) annotation To study:http://commons.wikimedia.org/wiki/Help:Gadget-ImageAnnotator Semantic properties coupled to image permissions http://www.mediawiki.org/wiki/Manual:Image_Authorization Integration with popular biological services Study or search for a common ontology for laboratory services Import biological ontologies (e.g. Gene Ontology) 30.
http://labservice.biocore.crg.cat 31. Bioinformatics Unit
32. Luca Cozzuto 33. Francesco Mancuso 34. Ernesto Lowy Acknowledgments Protein Service
35. Silvia Speroni 36. Miriam Alloza