information management at vhir ueb using tiki-cms

InformationInformation Management (Management (andand more) at more) at

thethe StatisticsStatistics andand BioinformaticsBioinformatics Unit, Unit,

VallVall dd’’HebrHebróónn InstitutInstitut de Recerca (VHIR) de Recerca (VHIR)

withwith thethe WikiWiki--Tiki CMS Tiki CMS systemsystem

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

4

UEB services

Data analysisOMICS & STandard

Bioinformatics Training Consulting

•Microarrays,

• RTqPCR

•Methylation

•Metagenomics

•Exome sequencing

•Clinical / Epidemiological

• Web & Databasedevelopment

• HPC services

• Pipelines development

• Short Workshops

•Courses

•Official training (MSc)

•Sample size

•Experimental design

•GRANT review

•Statistical parts ofpapers

We provide support in …

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 Bazar (Version Control System)

• Different technologies

– R / Latex / Sweave(knitr)

– perl / shell programs

– Taverna / Galaxy

2. Controlling information flows

First wave

• Several systems

– Google • Docs, calendars

• Spreadsheets

– Dropbox

– MS-Acces databases

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

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

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

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 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