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Information management at vhir ueb using tiki-cms

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II Jornades de Consultoria Estadística i Software - Octubre 2013

II Jornades de Consultoria Estadística i Software - Octubre 2013

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  • 1. Information Management (and more) at the Statistics and Bioinformatics Unit, Vall d’Hebrón Institut de Recerca (VHIR) with the 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 4
  • 5. UEB services We provide support in … Data analysis OMICS & STandard Bioinformatics • Microarrays, • Web & Database development • RTqPCR • Pipelines development Consulting • HPC services • Methylation Training • Exome sequencing • Clinical / Epidemiological • Sample size • Courses • Metagenomics • Short Workshops • Experimental design • Official training (MSc) • 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 Bazar (Version Control System) • Different technologies – R / Latex / Sweave(knitr) – perl / shell programs – Taverna / Galaxy
  • 10. 2. Controlling information flows First wave Next wave (Tiki) • Several systems • One unique system – Google • Docs, calendars • Spreadsheets – Dropbox – MS-Acces databases – Very good for • Documentation • File/Image sharing • Event /Calendar management. – Trackers for • databases • Tasks, projects – Extra bonus! • R web applications
  • 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. Example: Basic Pipe Current version Web version • R/Sweave • Covers all steps for a MDA • Start with a (long) parameters file • Run R/Sweave • Output • Use trackers/forms to – Results • Tables • Figures – Report – HTML browser – Build parameters file – Control execution/iteration • Use File/Image galleries to – Store results, plots • Use wiki page to present – Report – Give access to results
  • 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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