TeamStation AI System Report LATAM IT Salaries 2024
Information management at vhir ueb using tiki-cms
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)
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
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
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
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