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Alex Sánchez 1,2 , Xavier de Pedro 2 , Ferran Briansó 2 1 Departament d’Estadística UB

Information Management (and more) at the Statistics and Bioinformatics Unit , Vall d’Hebrón Institut de Recerca (VHIR) with the Wiki- Tiki CMS system. Alex Sánchez 1,2 , Xavier de Pedro 2 , Ferran Briansó 2 1 Departament d’Estadística UB 2 Statistics and Bioinformatics Unit (VHIR).

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Alex Sánchez 1,2 , Xavier de Pedro 2 , Ferran Briansó 2 1 Departament d’Estadística UB

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  1. Information Management (and more) at theStatistics and BioinformaticsUnit, Valld’HebrónInstitut de Recerca (VHIR) withthe Wiki-Tiki CMS system Alex Sánchez1,2, Xavier de Pedro2, Ferran Briansó2 1Departament d’Estadística UB 2Statistics and Bioinformatics Unit (VHIR)

  2. Vall d’Hebron Research Institute

  3. Unitat d’Alta Tecnologia

  4. Statistics and Bioinformatics Unit

  5. UEB services We provide support in … Data analysis OMICS & STandard Bioinformatics Training Consulting • Microarrays, • RTqPCR • Methylation • Metagenomics • Exome sequencing • Clinical / Epidemiological • Web & Database development • HPC services • Pipelines development • Short Workshops • Courses • Official training (MSc) • Sample size • Experimental design • GRANT review • Statistical parts of papers

  6. UEB resources – We work with ...

  7. UEB goals – We aim at... • We aim at providing high quality support • Services / Innovation / Teaching • How can we get to it? • We need highly qualified technicians • State of the art tools & resources (OS) • A profesional approach to service • Provide value for money • Produce well documented, reproducible, results • Manage projects and processes adequately • We are working to obtain ISO-9001

  8. UEB Projects & Processes • Main type of projects • Omics Data Analysis • Information management • Information flow • Meetings • Analysis/Reports/Results • Databases Customers/Studies • Process management • Documentation/Protocols

  9. 1. Accounting for quality in studies & projects • Create automatic & reproducible workflows. • Easy to use by different (expert) technicians • Possibility to reproduce • Identically for verification • With variations for process tuning • Maintained with Bazaar (Version Control System) • Different technologies • R / Latex / Sweave(knitr) • perl / shell programs • Taverna / Galaxy

  10. 2. Controlling information flows First wave Next wave (Tiki) One unique system Very good for Documentation File/Image sharing Event /Calendar management. Trackers for databases Tasks, projects Extra bonus! R web applications • Several systems • Google • Docs, calendars • Spreadsheets • Dropbox • MS-Acces databases

  11. The Tiki-Wiki CMS

  12. Main Features

  13. The wiki-way

  14. Features 1 - Wiki pages • Simple editor • Fonts, Lists, Headings • Links, Tables. Images • Markdown-like or wysiwig • Real time edit (no uploads)

  15. Ex. 1- A simple wiki page

  16. Features 2 – Wiki structures • Facilities to manage page structures • Add pages easily • Structure layout • Table of contents

  17. Example 2- UEB page layout

  18. Features 3 –Granular permissions system

  19. Features 4 – Calendar & Events

  20. Features 5 - Files Web folders from Tiki file galeries Web Dav: direct access from office apps

  21. Features 6 - Trackers Online databases Form & database tightly integrated Use it to “track” processes. Easy to configure views

  22. Examples 6- UEB task trackers • Other UEB trackers • Studies, • Projects • Customers • Consultings

  23. Alltogether: ueb.vhir.org (public)

  24. Alltogether: ueb.vhir.org (internal)

  25. In summary • Using the Tiki-Wiki CMS information flows happening in our unit can be managed. • Wiki pages for • Documentats & Protocols • Teaching materials • Trackers for • Studies & Customers databases • Project & Task management • Calendars & News for planning and informing • File & Image galleries for safestoring • All finely customized thanks to permissions

  26. There is more than this • A common important need is to be able to use R from the web • Internally: Create GUI to automate process • Call pipelines • Collect results • Externally • Provide common-use tools to users • Increase visibility • Saves us from repeating monotonous tasks • E.g. Post exploiting results

  27. R in the web: Many tools, no winner • Many tools • Recent • Shiny, Concert, rook, Rapache • Older • CGIwithR, Rphp, • Usually hard to implement

  28. Our choice (Tiki + pluginR)

  29. Example: ueb.vhir.org/heatmaps

  30. R/Sweave Covers all steps for a MDA Start with a (long) parameters file Run R/Sweave Output Results Tables Figures Report HTML browser Use trackers/forms to Build parameters file Control execution/iteration Use File/Image galleries to Store results, plots Use wiki page to present Report Give access to results Example: Basic Pipe Current version Web version

  31. In summary (2) • The Wiki-Tiki CMS has interesting capabilities to empower efficient work at all levels. • In a context where it can be necessary to create web pages implementing R programs, combining Tiki with R through pluginR is a powerful approach.

  32. Acknowledgments • The members of the Unitat d’Estadística i Bioinformàtica of the VHIR https://ueb.vhir.org • Xavi de Pedro – Tiki developer • Ferran B. • J.L Mosquera Tiki testers/users • Ricardo Gonzalo • Unitat d’alta tecnologia at VHIR https://uat.tiki.org • Grup de Recerca en Estadística i Bioinformàtica (UB) https://eib.stat.ub.edu

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