Information management at vhir ueb using tiki-cms

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II Jornades de Consultoria Estadística i Software - Octubre 2013

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Information management at vhir ueb using tiki-cms

  1. 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. 2. Vall d’Hebron Research Institute
  3. 3. Unitat d’Alta Tecnologia
  4. 4. Statistics and Bioinformatics Unit 4
  5. 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. 6. UEB resources – We work with ...
  7. 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. 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. 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. 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. 11. The Tiki-Wiki CMS
  12. 12. Main Features
  13. 13. The wiki-way
  14. 14. Features 1 - Wiki pages • Simple editor – Fonts, Lists, Headings – Links, Tables. Images • Markdown-like or wysiwig • Real time edit (no uploads)
  15. 15. Ex. 1- A simple wiki page
  16. 16. Features 2 – Wiki structures • Facilities to manage page structures – Add pages easily – Structure layout – Table of contents
  17. 17. Example 2- UEB page layout
  18. 18. Features 3 –Granular permissions system
  19. 19. Features 4 – Calendar & Events
  20. 20. Features 5 - Files Web folders from Tiki file galeries Web Dav: direct access from office apps
  21. 21. Features 6 - Trackers Online databases Form & database tightly integrated Use it to “track” processes. Easy to configure views
  22. 22. Examples 6- UEB task trackers • Other UEB trackers - Studies, - Projects - Customers - Consultings
  23. 23. Alltogether: ueb.vhir.org (public)
  24. 24. Alltogether: ueb.vhir.org (internal)
  25. 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. 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. 27. R in the web: Many tools, no winner • Many tools – Recent • Shiny, Concert, rook, Rapache – Older • CGIwithR, Rphp, • Usually hard to implement
  28. 28. Our choice (Tiki + pluginR)
  29. 29. Example: ueb.vhir.org/heatmaps
  30. 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. 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. 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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