Status reports

2017 January

See the changelog and roadmap

ACTIONS

See roadmap :

  • tweak search behaviour to address most critical issues from https://biotools.sifterapp.com/issues/274
  • drop mandatory requirement for email or URL in credits (non-breaking change for 2.1.0)
  • clarify what is meant by “beta”, maybe change label to “This entry has not been manually verified”
  • set up access to repo for Kenzo et al.

2016 December

Actions (November)

  • Technical developments

    • stable schema biotoolsSchema 2.0.0 released. It will define the scope and potential functionality of bio.tools for years to come. Future versions will follow the MAJOR.MINOR.PATCH pattern (http://semver.org), with major changes that could break bio.tools API dependencies restricted to once/year.
    • EDAM_1.16 released and available on BioPortal and OLS.

  • Documentation

Plans (December)

  • Technical work towards the Dec release, see roadmap of registry software developments
  • Various content additions listed on sifterapp
  • WP 1 / ELIXIR-DK partners telcon 10AM UK, Fri Dec 2

2016 October

Actions (October)

Plans (November)

  • Technical work towards the Dec release, see roadmap of registry software developments
  • import of SEQwiki (see sifterapp issue.)
  • EDAM 1.16 including requests via GitHub and addition of data format concepts

2016 September

Actions (September)

  • Major recent work highlights
    • finished rewrite of registry software (see https://dev.bio.tools)
    • major revision of underlying data model (biotoolsXSD) producing candidate stable schema (https://github.com/bio-tools/biotoolsxsd/)
    • Deliverable D1.1 submitted on time
    • Presentation of work at ISMB, ECCB and DKBC
    • improved & extended bio.tools docs
    • detailed roadmap for registry software developments
    • paper submitted “ReGaTE, Registration of Galaxy Tools in Elixir” Olivia Doppelt-Azeroual, Ph.D.; Fabien Mareuil, Ph.D.; Eric Deveaud; Matus Kalas, Ph.D.; Nicola Soranzo; Marius van den Beek, Ph.D.; Björn Grüning; Jon Ison; Hervé Ménager

Plans (October)

2016 June

Actions (June)

  • Content
  • Outreach actions
    • ASMS/IMSC conference - Magnus Palmblad (LUMC, NL) et al - member of registry-core - submitted a poster on workflow composition using EDAM / bio.tools annotations.
    • ISMB - Prepare 5 posters (ELIXIR & ELIXIR-DK, ELIXIR EXCELERATE WP1, bio.tools, EDAM, biotoolsXSD, computerome) - Booth preparations (freebies, dressing etc.) & logistics
    • Meeting with representatives of The Open Microscopy Environment and Euro-BioImaging (including Gloabl-BioImaging) scope technical for collaboration with bio.tools. See https://biotools.sifterapp.com/issues/166.
  • Technical specification documents
    • “Tool types and relations” (1st draft) to inform biotoolsXSD 2.0 development and support re-use of tool descriptions, and reduce duplications and inconsistencies in bio.tools.
  • Technical developments
    • ~750 automated unit tests
    • new and improved grid view
    • ‘my profile’ page, with account information and list of tools registered by this account
    • admin / curation interface (work ongoing)
    • Continue bio.tools rewrite to pay off technical debt, with a focus on user interfaces and unit tests
    • Curation admin interface (content edition) (beta)
    • General admin interface (account management, password change, reset etc)
  • Tasks not completed
    • Prepare new slide deck for Tech Track including software demo

Plans (July)

  • Technical developments
    • migrating and consolidating the content from the production database to the new system
    • testing improvements to the search (so that it returns more relevant results)
    • quality of life improvements to the registration interface (error handling)
    • work towards release new system for testing by registry-core
  • Outreach actions
    • ISMB
  • Technical specification documents
    • Settle these in prep for EXCELERATE WP1 D1.1 - API specs - Tool types and relations - Content ownership model - Improved tool annotator mock-up

Notes

The “Tools, Workflows and Workbenches” hackathon (Institut Pasteur, May 18-20) was co-organized by the French and Danish ELIXIR nodes. The event brought together over 40 representatives from 21 academic institutions and companies, with projects including Galaxy, bio.tools, Common Workflow Language, biotoolsXSD, EDAM, Debian Med, BioShadock and more. The delegates enjoyed a series of talks, lively discussions and breakout hacking sessions including bio.tools entry relationships, Galaxy to bio.tools publishing, CWL specification, workflow specification interoperability, and training workflows. In addition to concrete outcomes including various technical documents, new CWL bindings and enabling support for EDAM annotations in Galaxy, the hackathon provided a boost to various ongoing collaborations between the projects and institutes. We look forward to a re-run soon!

2016 May

Actions (May)

  • Outreach actions (see https://bio.tools/events)

    • At ISMB, ELIXIR-DK will have a booth a give a technology track presentation
    • The “Tools, Workflows and Workbenches” hackathon (Institut Pasteur, May 18-20) was attended by over 40 people. See tinyurl.com/registryhackathon8 and the summary (below).

  • Development of the improved tool annotator is being led by Hans-Ioan Ienasescu, based on the mockup

  • Content

    • EDAM 1.15 is out
      It includes new community-requested concepts and terms, including for metagenomics and biodiversity, structural improvements and fixes (synonyms clean-ups etc.), format updates, and implification of some concepts. See the Change log. Browse EDAM on BioPortal and in the new OLS.

  • bio.tools rewrite to pay off technical debt . Features done but not yet in production:

    • back-end development
      • robust validation of incoming tool descriptions
      • new URL / persistent ID scheme
      • unit tests for EDAM topics, operations, data types and formats
    • front-end development
      • ongoing work on the admin / curator interface
      • ongoing work on the improved grid view

Plans (June)

  • Outreach actions
    • ISMB - Prepare 5 posters (computerome, ELIXIR-DK, bio.tools, EDAM, biotoolsXSD) - Prepare new slide deck for Tech Track - Booth preparations (freebies, dressing etc.) - Plan logistics
    • Meeting with representatives of The Open Microscopy Environment and Euro-BioImaging to scope out technical collaboration with bio.tools.
  • Technical specification documents
    • “Tool types and relations” (1st draft) to inform biotoolsXSD 2.0 development and support re-use of tool descriptions, and reduce duplications and inconsistencies in bio.tools.
  • Technical developments
    • Continue bio.tools rewrite to pay off technical debt, with a focus on user interfaces and unit tests
    • Curation admin interface (content edition) (beta)
    • General admin interface (account management, password change, reset etc)
  • Tasks not completed in May
    • General admin interface (account management, password change, reset etc) - postponed for now

2016 April

Actions (April)

Plans (May)

  • Tasks not completed in April

    • Preparations for ISMB 2016
    • Release of EDAM 1.15 addressing multiple requests logged on GitHub

2016 March

Actions (March)

Plans (April)