1. Lab Service Wiki: a wiki-based data management solution for laboratories production services

• Antoni Hermoso Pulido , Michela Bertero, Silvia Speroni, Miriam Alloza and Guglielmo Roma
• [email_address]

2. Bioinformatics Core Facility, Protein Service - CRG

3. http://biocore.crg.cat 4.

Protein Service & Biocore @ CRG

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.

Elements of a protein service laboratory

Images from commons.wikimedia.org PCR HPLC Gel electrophoresis 6.

PDF Form for the service request

7. Email messages (submission, details, etc.) 8. Meetings 9. Multiple files in multiple disks not easily linked

Notetaking and reports (lab notebook, wordprocessors and spreadsheets)

Tasks before the wiki

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

Why Semantic MediaWiki?

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)

Wiki templates, properties and forms vs coding and database design

Why Semantic MediaWiki?

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.

Simplified workflow of a laboratory service

14.

Workflow of a laboratory service

Create study

Accept

Lab Member

Researcher

Access web interface

Fill form

Submit request

Reject

Review scientificinfo

Reviewstudy

Accept

Reject

Reject

Lab Manager

Assign study to core members

Finance Controller (ORDER MANAGEMENT SYSTEM)

Review financial Info?

Accept

Open study

Retrieve SOP

Perform all study steps

( quotation )

Reviewstudy results

Reject

Sign-off(?)

Request review

Prepare report

( order number )

Send results/report

( communication )

//

Retrieve results/report

Sign-off(?)

Accept

Meeting

Meeting

Meeting

Meeting

Meeting

Meeting

// ?

//

// ?

Receive invoice

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.

Conditional syntax

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.

Lists of tasks

28.

User Panel

Template(s) created when the user first registers. Modified NewUserMessage extension 29.

Current and upcoming development May 2010

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.

Test website

http://labservice.biocore.crg.cat 31. Bioinformatics Unit

Guglielmo Roma

32. Luca Cozzuto 33. Francesco Mancuso 34. Ernesto Lowy Acknowledgments Protein Service

Michela Bertero

35. Silvia Speroni 36. Miriam Alloza