II Jornades de Consultoria Estadística i Software - Octubre 2013

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