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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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Alex s nchez 1 2 xavier de pedro 2 ferran brians 2 1 departament d estad stica ub

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

Vall d’Hebron Research Institute


Unitat d alta tecnologia

Unitat d’Alta Tecnologia


Statistics and bioinformatics unit

Statistics and Bioinformatics Unit


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 resources we work with

UEB resources – We work with ...


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


The tiki wiki cms

The Tiki-Wiki CMS


Main features

Main Features


The wiki way

The wiki-way


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)


Ex 1 a simple wiki page

Ex. 1- A simple wiki page


Features 2 wiki structures

Features 2 – Wiki structures

  • Facilities to manage page structures

    • Add pages easily

    • Structure layout

    • Table of contents


Example 2 ueb page layout

Example 2- UEB page layout


Features 3 granular permissions system

Features 3 –Granular permissions system


Features 4 calendar events

Features 4 – Calendar & Events


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


Alltogether ueb vhir org public

Alltogether: ueb.vhir.org (public)


Alltogether ueb vhir org internal

Alltogether: ueb.vhir.org (internal)


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


Our choice tiki pluginr

Our choice (Tiki + pluginR)


Example ueb vhir org heatmaps

Example: ueb.vhir.org/heatmaps


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 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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