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Alex Sánchez 1,2 , Xavier de Pedro 2 , Ferran Briansó 2 1 Departament d’Estadística UB PowerPoint PPT Presentation


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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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Alex Sánchez 1,2 , Xavier de Pedro 2 , Ferran Briansó 2 1 Departament d’Estadística UB

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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)


Vall d’Hebron Research Institute


Unitat d’Alta Tecnologia


Statistics and Bioinformatics Unit


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 resources – We work with ...


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

  • 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

  • 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

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


The Tiki-Wiki CMS


Main Features


The wiki-way


Features 1 - Wiki pages

  • Simple editor

    • Fonts, Lists, Headings

    • Links, Tables. Images

  • Markdown-like or wysiwig

  • Real time edit (no uploads)


Ex. 1- A simple wiki page


Features 2 – Wiki structures

  • Facilities to manage page structures

    • Add pages easily

    • Structure layout

    • Table of contents


Example 2- UEB page layout


Features 3 –Granular permissions system


Features 4 – Calendar & Events


Features 5 - Files

Web folders from Tiki file galeries

Web Dav: direct access

from office apps


Features 6 - Trackers

Online databases

Form & database tightly integrated

Use it to “track” processes.

Easy to configure views


Examples 6- UEB task trackers

  • Other UEB trackers

    • Studies,

    • Projects

    • Customers

    • Consultings


Alltogether: ueb.vhir.org (public)


Alltogether: ueb.vhir.org (internal)


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

  • 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

  • Many tools

    • Recent

      • Shiny, Concert, rook, Rapache

    • Older

      • CGIwithR, Rphp,

  • Usually hard to implement


Our choice (Tiki + pluginR)


Example: ueb.vhir.org/heatmaps


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)

  • 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

  • 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 MosqueraTiki 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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