Drupal at-embl-ebi gmod
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  • Drupal @ EMBL-EBI
  • 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.

Drupal at-embl-ebi gmod Drupal at-embl-ebi gmod Presentation Transcript

  • Drupal at EMBL-EBI
  • What is EMBL-EBI?• Part of the EuropeanMolecular BiologyLaboratory• International, non-profitresearch institute• Europe’s hub forbiological data servicesand research
  • EMBL-EBI’s mission• Provide freely availabledata and bioinformaticsservices• Perform research inbioinformatics• Provide advancedtraining• Help disseminatetechnologies to industry
  • Drupal
  • What is Drupal?• Content Management System• Free• Open sourcewww.drupal.org
  • Why Drupal?www.economist.comwww.whitehouse.govwww.greenpeace.org.uk/• High performance• SEO friendly• Big community• Framework• User management• Presentation // Content
  • The Drupal layers
  • Drupal EBI technology
  • EBI and Drupal
  • Drupal EBI websites in figures28 Drupal 65 Drupal 7_____________33 Drupal sites
  • What are we doing already with Drupal?EBI branded websites
  • What are we doing already with Drupal?EBI non branded websites
  • What does Drupal do for us?Data distribution• Datasets• Studies• Catalogueswww.ebi.ac.uk/egawww.ebi.ac.uk/dgvaEuropean Genome-phenome archiveDatabase of genomic variantsarchive
  • What does Drupal do for us?Data distribution• Datasets• Studies• Catalogueswww.ebi.ac.uk/egawww.ebi.ac.uk/dgva
  • Data distribution• Search inventory engine• Query Bilder Interface• Return (cached) objects multi formatswww.pombase.orgWhat does Drupal do for us?
  • www.microme.euwww.1000genomes.orgWhat does Drupal do for us?Display information• Publications• Announcements
  • What does Drupal do for us?Documentation• Alfresco DMS• Download areawww.biomedbridges.euwww.ebi.ac.uk/Tools/docswww.ebi.ac.uk/training/online
  • What does Drupal do for us?Community portal• Membership• Training events• Blogswww.biotnet.orgwww.ebi.ac.uk/trainingwww.biomedbridges.eu
  • What does Drupal do for us?Project management• Work packages• Deliverables• Partnerswww.biomedbridges.eu
  • What does Drupal do for us?Drupal as a Service
  • The new EBI website
  • What is the story?
  • Evolution
  • Transition from old site to Drupal
  • Transition from old site to Drupal• Make things look better• Help users find what they want• Enable discovery• Offer a consistent experience• Transition phase
  • Challenges• Assets• Content strategy• Development• Technology• Template• User management• UX design & testing• WYSIWYG
  • PeopleUX designersOutreachWeb team Web adminsDevelopersTarget usersContent authorsTeam leaders
  • Guidance for DesignLot of meetingsCollaborationWeb guidelinesStyleguideWeb guidelinescommitteeUX
  • The new EBI website in action
  • Changes• Static HTML• No users• Dreamweaver• Open roles• Web server• Scattered assets• Local/live deploymentCMSGroup-based CMWYSIWYGEditorial workflowLAMP + VMRepositoryDev/stage/prod environments
  • Content & Content types
  • Content & Content typesCreate GroupCreate Group
  • Content & Content typesCreate GroupCreate GroupMore content types…More content types
  • PublicationsBiblio Module:• Import PubMed, Bibtex…• Tied up to people/groups.• Link to www.europepmc.org
  • Content feeds< >XML as Data vector
  • Content feedsContrib: Views Xml BackendCustom: Staff FeedsContrib: Views data exportDrupal to DrupalRuntimeCron jobhttp://www…/file/system/…
  • Content feedsXMLExternal MySQLwww.ebi.ac.uk/dgvawww.ebi.ac.uk/egaNon Drupal to Drupal
  • Organize content and group workflow• Organic Group• Workflow, OG workflow• Revisioning, Rules
  • The Template• Grid based• HTML 5• CSS 3• Custom made Icon fonts
  • What’s next?• Improve the content authors’ experience• WYSIWYG• Testing Drupal 8• Responsive theme• Respond to feedback
  • Questions?
  • Thank youSlides athttps://dl.dropbox.com/u/2914319/Drupal-at-EMBL-EBI_GMOD.pptxhttps://dl.dropbox.com/u/2914319/Drupal-at-EMBL-EBI_GMOD.pdfSketchnote athttps://dl.dropbox.com/u/2914319/Drupal-at-EMBL-EBI-sketchnotes-JosephRossetto.pdf
  • AknowledgmetsAt EBI• Brendan Vaughan, Peter Walter, Thomas Laurent, Jenny Cham, Francis Rowland, Liang Shen, Rodrigo Lopez (headof Web Production team), the Webstyle Guidelines Committee members.Sketchnotes by Francis RowlandSlides of the content organization by Liang ShenImages 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)], viaWikimedia 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)], viaWikimedia 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
  • Stay in touch!