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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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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)

ueb services
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
ueb goals we aim at
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
ueb projects processes
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
1 accounting for quality in studies projects
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
2 controlling information flows
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
features 1 wiki pages
Features 1 - Wiki pages
  • Simple editor
    • Fonts, Lists, Headings
    • Links, Tables. Images
  • Markdown-like or wysiwig
  • Real time edit (no uploads)
features 2 wiki structures
Features 2 – Wiki structures
  • Facilities to manage page structures
    • Add pages easily
    • Structure layout
    • Table of contents
features 5 files
Features 5 - Files

Web folders from Tiki file galeries

Web Dav: direct access

from office apps

features 6 trackers
Features 6 - Trackers

Online databases

Form & database tightly integrated

Use it to “track” processes.

Easy to configure views

examples 6 ueb task trackers
Examples 6- UEB task trackers
  • Other UEB trackers
    • Studies,
    • Projects
    • Customers
    • Consultings
in summary
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
there is more than this
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
r in the web many tools no winner
R in the web: Many tools, no winner
  • Many tools
    • Recent
      • Shiny, Concert, rook, Rapache
    • Older
      • CGIwithR, Rphp,
  • Usually hard to implement
example basic pipe
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

in summary 2
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.
acknowledgments
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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