Bezrukov, I.

Schwab, R.

English

MPG.PuRe

1Atlassian Confluence as an ELN and shared resource system21.09.2021Ilja Bezrukov Rebecca SchwabMax Planck Institute for Developmental BiologyTübingen2MPI for (Developmental) Biology5 Departments (director + 2-5 groups) 7 research groups, 7 core facilitiesAdministrationWet lab biology (structural biology, molecular biology, genomics)+Computational biology(3) (4) (3) Confluence  (start: 2015)3ELN: how much flexibility is needed?• Flexible vs pre-defined structure• How flexible does an ELN need to be?• Balance computational focus with classical lab work• One system for everything vs specialized tools4What is Confluence?• Advertised as an enterprise collaboration system– Strong wiki functionality– Collaborative features (@tags, sharing, likes, commenting)• Large plug-in ecosystem• Can be run on-premises or as cloud instance• Proprietary, with access to source code available• Currently very generous licensing to non-profit organizations5Licensing• Self-hosted and cloud versions available• Proprietary, and expensive even for academic institutions• “Loop-hole” available: non-profit organizations get a free self-hosted license + generous cloud licensing• Future availability not guaranteed, which needs to be factored in the use decision• Our installation dates back to 2015, so far Atlassian has been forthcoming6Ecosystem• Large number of high quality plug-ins available• With a non-profit license, most can be used without license fees• Examples– Content formatting– External SQL database access– API for scripted page generation/editing– Encryption7Technical aspects• User directories can be imported from LDAP or active directory• Customization by template editing possible• Page version history is available• SQL database + Tomcat server stack• Our instance is restricted to the intranet• Access to Atlassian support available8Data model•9Data model10Confluence as ELN• Each page is versioned -> changes can be tracked• Structured notes with page templates• User-friendly editor with support for images (drag and drop), code blocks and attachments• No enforced structure -- a degree of user compliance is required• Fine-grained permissions system for sharing11Confluence as a shared resources platform• Data model with spaces and nested subpages supports multiple organizational units• User-friendly editor facilitates content creation• Well-accepted at the institute– Departments have their own spaces, usually restricted– Shared spaces for core services and general information12LIVE DEMO/ExamplesDocumentationInformation● Rather static● Maintained by few● Important for new people, new topics, new technologies + checking availability of stocks● Very dynamic● Used by many● Ideally interactive and collaborativeInstitute (including administration)Department/GroupsSubgroupsIndividuals2 main pillars and 4 levels of organization1314Confluence as ELN -- pro’s• Usability -- user-friendly without the need for extensive training (except permissions management)• Flexibility -- able to incorporate notebooks for lab and computational work• Robust social features: collaboration, comments and supervision possible15Confluence as ELN -- con’s• Does not work out-of-the box: Set up ELN workflows requires work and documentation• No specialized features for lab stock management • No ordering SAP ‘connection’• Flexibility can be a disadvantage if strict workflows need to be followed16Open-source vs. closed-source• Licensing model has danger of vendor lock-inhttps://martinfowler.com/articles/oss-lockin.html• Fall-back strategies– Content can be migrated to static HTML– A working version does not need to be updated ASAP, except for critical security fixes– Security fixes are provided for 2 years– Migration to a paid plan as last resort17Conclusion• Confluence can be used as an ELN for mixed computational/biology labs• User-friendly interface which facilitates information sharing and increases adoption• Flexibility, at a price: no enforced structure• Set up of ELN workflows requires work• No out-of-the box support for stock management• Vendor lock-in needs to be considered18Thank you for your attention!

Atlassian Confluence as an ELN and shared resource system

http://hdl.handle.net/21.11116/0000-000A-3332-4

Atlassian Confluence as an ELN and shared resource system

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