Drupal at EMBL-EBI
What is EMBL-EBI?• Part of the EuropeanMolecular BiologyLaboratory• International, non-profitresearch institute• Europe’s ...
EMBL-EBI’s mission• Provide freely availabledata and bioinformaticsservices• Perform research inbioinformatics• Provide ad...
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• Frame...
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 Gen...
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.orgWh...
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.a...
What does Drupal do for us?Community portal• Membership• Training events• Blogswww.biotnet.orgwww.ebi.ac.uk/trainingwww.bi...
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 con...
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...
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://...
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-...
AknowledgmetsAt EBI• Brendan Vaughan, Peter Walter, Thomas Laurent, Jenny Cham, Francis Rowland, Liang Shen, Rodrigo Lopez...
Stay in touch!
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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 &amp; 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 &amp; Content types.
  • Content &amp; Content types
  • In some cases we can avoid the content creation process by pulling content from external sources.
  • Content &amp; 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

    1. 1. Drupal at EMBL-EBI
    2. 2. What is EMBL-EBI?• Part of the EuropeanMolecular BiologyLaboratory• International, non-profitresearch institute• Europe’s hub forbiological data servicesand research
    3. 3. EMBL-EBI’s mission• Provide freely availabledata and bioinformaticsservices• Perform research inbioinformatics• Provide advancedtraining• Help disseminatetechnologies to industry
    4. 4. Drupal
    5. 5. What is Drupal?• Content Management System• Free• Open sourcewww.drupal.org
    6. 6. Why Drupal?www.economist.comwww.whitehouse.govwww.greenpeace.org.uk/• High performance• SEO friendly• Big community• Framework• User management• Presentation // Content
    7. 7. The Drupal layers
    8. 8. Drupal EBI technology
    9. 9. EBI and Drupal
    10. 10. Drupal EBI websites in figures28 Drupal 65 Drupal 7_____________33 Drupal sites
    11. 11. What are we doing already with Drupal?EBI branded websites
    12. 12. What are we doing already with Drupal?EBI non branded websites
    13. 13. 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
    14. 14. What does Drupal do for us?Data distribution• Datasets• Studies• Catalogueswww.ebi.ac.uk/egawww.ebi.ac.uk/dgva
    15. 15. Data distribution• Search inventory engine• Query Bilder Interface• Return (cached) objects multi formatswww.pombase.orgWhat does Drupal do for us?
    16. 16. www.microme.euwww.1000genomes.orgWhat does Drupal do for us?Display information• Publications• Announcements
    17. 17. What does Drupal do for us?Documentation• Alfresco DMS• Download areawww.biomedbridges.euwww.ebi.ac.uk/Tools/docswww.ebi.ac.uk/training/online
    18. 18. What does Drupal do for us?Community portal• Membership• Training events• Blogswww.biotnet.orgwww.ebi.ac.uk/trainingwww.biomedbridges.eu
    19. 19. What does Drupal do for us?Project management• Work packages• Deliverables• Partnerswww.biomedbridges.eu
    20. 20. What does Drupal do for us?Drupal as a Service
    21. 21. The new EBI website
    22. 22. What is the story?
    23. 23. Evolution
    24. 24. Transition from old site to Drupal
    25. 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
    26. 26. Challenges• Assets• Content strategy• Development• Technology• Template• User management• UX design & testing• WYSIWYG
    27. 27. PeopleUX designersOutreachWeb team Web adminsDevelopersTarget usersContent authorsTeam leaders
    28. 28. Guidance for DesignLot of meetingsCollaborationWeb guidelinesStyleguideWeb guidelinescommitteeUX
    29. 29. The new EBI website in action
    30. 30. Changes• Static HTML• No users• Dreamweaver• Open roles• Web server• Scattered assets• Local/live deploymentCMSGroup-based CMWYSIWYGEditorial workflowLAMP + VMRepositoryDev/stage/prod environments
    31. 31. Content & Content types
    32. 32. Content & Content typesCreate GroupCreate Group
    33. 33. Content & Content typesCreate GroupCreate GroupMore content types…More content types
    34. 34. PublicationsBiblio Module:• Import PubMed, Bibtex…• Tied up to people/groups.• Link to www.europepmc.org
    35. 35. Content feeds< >XML as Data vector
    36. 36. Content feedsContrib: Views Xml BackendCustom: Staff FeedsContrib: Views data exportDrupal to DrupalRuntimeCron jobhttp://www…/file/system/…
    37. 37. Content feedsXMLExternal MySQLwww.ebi.ac.uk/dgvawww.ebi.ac.uk/egaNon Drupal to Drupal
    38. 38. Organize content and group workflow• Organic Group• Workflow, OG workflow• Revisioning, Rules
    39. 39. The Template• Grid based• HTML 5• CSS 3• Custom made Icon fonts
    40. 40. What’s next?• Improve the content authors’ experience• WYSIWYG• Testing Drupal 8• Responsive theme• Respond to feedback
    41. 41. Questions?
    42. 42. 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
    43. 43. 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
    44. 44. Stay in touch!

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