The document discusses EMBL-EBI's use of Drupal for their websites. EMBL-EBI is a European research institute that provides freely available biological data and bioinformatics services. They use Drupal to power over 30 of their websites, including those that distribute datasets, display publications and announcements, provide documentation, and act as community portals. Drupal allows EMBL-EBI to effectively manage and distribute data to users, while providing a consistent user experience across their many sites. Transitioning over 30 sites from static HTML to Drupal required significant effort related to content strategy, development, and user experience design.
2. What is EMBL-EBI?
• Part of the European
Molecular Biology
Laboratory
• International, non-profit
research institute
• Europe’s hub for
biological data services
and research
3. EMBL-EBI’s mission
• Provide freely available
data and bioinformatics
services
• Perform research in
bioinformatics
• Provide advanced
training
• Help disseminate
technologies to industry
11. What are we doing already with Drupal?
EBI branded websites
12. What are we doing already with Drupal?
EBI non branded websites
13. What does Drupal do for us?
Data distribution
• Datasets
• Studies
• Catalogues
www.ebi.ac.uk/ega
www.ebi.ac.uk/dgva
European Genome-phenome archive
Database of genomic variants
archive
14. What does Drupal do for us?
Data distribution
• Datasets
• Studies
• Catalogues
www.ebi.ac.uk/ega
www.ebi.ac.uk/dgva
15. Data distribution
• Search inventory engine
• Query Bilder Interface
• Return (cached) objects multi formats
www.pombase.org
What does Drupal do for us?
17. What does Drupal do for us?
Documentation
• Alfresco DMS
• Download area
www.biomedbridges.eu
www.ebi.ac.uk/Tools/docs
www.ebi.ac.uk/training/online
18. What does Drupal do for us?
Community portal
• Membership
• Training events
• Blogs
www.biotnet.org
www.ebi.ac.uk/training
www.biomedbridges.eu
19. What does Drupal do for us?
Project management
• Work packages
• Deliverables
• Partners
www.biomedbridges.eu
25. Transition from old site to Drupal
• Make things look better
• Help users find what they want
• Enable discovery
• Offer a consistent experience
• Transition phase
30. Changes
• Static HTML
• No users
• Dreamweaver
• Open roles
• Web server
• Scattered assets
• Local/live deployment
CMS
Group-based CM
WYSIWYG
Editorial workflow
LAMP + VM
Repository
Dev/stage/prod environments
43. Aknowledgmets
At EBI
• Brendan Vaughan, Peter Walter, Thomas Laurent, Jenny Cham, Francis Rowland, Liang Shen, Rodrigo Lopez (head
of Web Production team), the Webstyle Guidelines Committee members.
Sketchnotes by Francis Rowland
Slides of the content organization by Liang Shen
Images by
• Tkgd2007 (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via
Wikimedia Commons
• RRZEicons (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
• Bobarino [CC-BY-SA-2.5 (http://creativecommons.org/licenses/by-sa/2.5)], via Wikimedia Commons
• By The people from the Tango! project (The Tango! Desktop Project) [Public domain or Public domain], via Wikimedia Commons
• http://saa.dyndns.org/stewart [GFDL (www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via
Wikimedia Commons
• By nattu [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
• By Berdea (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
• Dries Buytaert for the Drupal logo
The EBI is based on the Wellcome Trust Genome Campus in Hinxton, which is near Cambridge in UK. The EBI is part of the European Molecular Biology Laboratory and as part of that, we’re a non-profit organisation.
EMBl-EBI’s mission is:to Provide freely available data and bioinformatics servicesContribute to the advancement of biology through researchProvide advanced bioinformatics trainingHelp disseminate cutting-edge technologies to industryCoordinate biological data provision throughout Europe
Drupal
Drupal is a Content Management System. It is free and open source. Drupal.org is the main site.
Why Drupal?Drupal is first choice when looking for a solution requiring as follows:High performance, Search Engine Optimization, a CMFramework, a user management system.Also, it has a wide community of developers updating, mantainig end extending the functionality of its core and contributed modules.
The Drupal layers build the architecture of the CMS. They are:Data layer, Modules layer, Blocks & Menus layer, the permissions and the template layers.
Drupal is written in PHP. Also, here is a list of requirements for Drupal to run: an OS, a web server,, and a DbMS.Additional and non mandatory technology can improve the quality of the Drupal experience, both on development and/or deployment.In our case we use Git as revision control and Memcached for enhancing the caching capabilities of Drupal.
EBI and Drupal
The EBI runs more than 30 Drupal installations, both on Drupal 6 and 7.
A list of EBI branded websites.
Another list of non-branded websites made in Drupal at the EBI.
Drupal helps data distribution by hooking it to external resources (Databases, data feeds)
By hooking Drupal to external data sources like the EGA or the DGVA repositories we can pull and display data like Datasets, Studies, Catalogues.
Like in the case of www.pombase.org we can build a custom search inventory engine or a Query builder interface to access data-sources like the Ensembl Genomes data set.
We can use Drupal to Display information through custom modules. In www.microme.eu we query the Citexplore literature search service by simply passing the publication ID (doi, Pmid, ISBN).
Drupal comes out-of-the-box with a set of features that enable document handling like in www.ebi.ac.uk/training/online. Also, Apart from having specific Drupal distributions addressing the problem of handling documents, Drupal can connect to Alfresco Documentation Management System to help building a doc-oriented application. It is helpful in project-management scenario like www.biomedbridges.eu.
Drupal can be used to build a community portal, involving users in the content creation, or through membership in a training programm or as a blogging platform.
Drupal can act as a Project Management System, enabling users to create Work packages, provide deliverables and manage
Through contrib or custom modules Drupal’s can create feeds for other resources/services to consume.
The EBI website redesign is a long-term and complex process. The inspiration for the design principle came from many sources. One for all: the BBC Global Visual Language.
The evolution has been a huge leap along the line of the web standards.
The transition implied one first simple change: going from static to dynamic.
The website redesign was not just about making things look better, but to help users find what they want, enable discovery and offer a consistent experience.The implementation is a two/phase process.
The team in charge of redesigning the site had to go through many challenges.
Several people were involved in the process. Each of them came with its own set of need, requirements and solutions.
The new EBI website in action
Here are just a few changes involved: from static to CMS; from no users to Group-based CM; from use of DM to a standard CMS WYSIWYG;
We can create diverseContent & Content types.
Content & Content types
In some cases we can avoid the content creation process by pulling content from external sources.
Content & Content types: Publication are created from Bibtex, Pubmed files. They can be tied up to specific groups and linked to the European PubMed Central Database.
Content feeds
Content feeds through Contrib modules:Views data export, Views Xml Backend and Custom module: Staff Feeds.
Content feeds. Drupal can connect external data-sources like an XML files or mapping a Database schema and import its data.
Organize content and group workflow
The EBI is based on the Wellcome Trust Genome Campus in Hinxton, which is near Cambridge in UK. The EBI is part of the European Molecular Biology Laboratory and as part of that, we’re a non-profit organisation.
The EBI is based on the Wellcome Trust Genome Campus in Hinxton, which is near Cambridge in UK. The EBI is part of the European Molecular Biology Laboratory and as part of that, we’re a non-profit organisation.
