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)

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 & Database development

• HPC services

• Pipelines development

• Short Workshops

• Courses

• Official training (MSc)

• Sample size

• Experimental design

• GRANT review

• Statistical parts of papers

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 Bazaar (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 VHIRhttps://ueb.vhir.org Xavi de Pedro – Tiki developer Ferran B. J.L Mosquera Tiki testers/users Ricardo Gonzalo

Unitat d’alta tecnologia at VHIRhttps://uat.tiki.org

Grup de Recerca en Estadística i Bioinformàtica (UB)

https://eib.stat.ub.edu