Physical TC meeting 2015

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Physical TC meeting 2015
Title Physical TC meeting
Location Copenhagen, Denmark
Date Start 2015/11/02
Date End 2015/11/06
TC Meeting Copenhagen 2015.jpg


DINA Technical workshop 2-6 Nov 2015 Copenhagen

The workshop will be held in the Zoological Museum, Universitetsparken 15 in the meeting room.

The meeting will start with the lunch at 12:00 on Monday, which will be held in August Krogh Institute (Universitetsparken 13, next door to the musem). If you're early and/or want to drop off suitcases etc, go to the Museum main entry. The museum does not have a reception, but the staff in the museum shop will be informed about the meeting and can show you the way to the meeting room.

Communication package - presentation of the participants

Monday 12.00-16.30

  • 12.00-13.00 Lunch

Overview - progress reports from all parties:

  • 13.00-13.30 - Welcome! DINA introduction (Fredrik Ronquist)
  • 13.30-14.00 - DK (Nikolaj Scharff/Thomas Stjernegaard Jeppesen)
  • 14.00-14.30 - EE (Urmas Kõljag)
  • 14.30-15.00 Coffee break
  • 15.00-15.30 - DE (Falko Glöckler)
  • 15.30-16.00 - CA (James Macklin)
  • 16.00-16.30 - SE (Markus Skyttner)

Tuesday 09.00-16.30

DINA Road Map

  • 09.00-12.00 Discussion: Module map, API blueprints, Milestones/Feature sets
  • 12.00-13.00 Lunch
  • 13.00-16.30 Continuing discussion/breakout sessions: Module map, API blueprints, Milestones/Feature sets

Wednesday 09.00-11.00

Conclusion: DINA Road map

  • Wednesday 9.00-10.00 Conclusion: DINA Road map (Fredrik Ronquist)

Presentation GBIF

  • Wednesday 10.00-11.00 Presentation GBIF (Tim Robertson)

Wednesday 11.00-16.30 - hackathons/coding sessions


  • APIs discussion - comparison of APIs visavi Pluto-F, Specify 7 and identifying overlaps/unique differentiators and formulating DINA-Specify specific needs.
  • Hackathon: API blueprints: “Apiary” (Markus Skyttner)

User module

  • User module/user rights/Specify resource management for the DINA-Web collection manager (Markus Skyttner and Ida Li)
  • Hackathon: get the bare bones metal DINA-Web box up and running (Markus Skyttner)

Thursday 09.00-16.30 - hackathons/coding sessions

DINA Data Tool

  • Hackathon: Integration of DDT – vagrant file using Bitnami node JS stack (Markus Skyttner and Thomas Stjernegaard Jeppesen)
  • Support installation of the DINA Data Tool on other partners' servers (Thomas Stjernegaard Jeppesen)

Accessibility and Security

  • Accessibility tools and guidelines/Security tools overview and guidelines – (Glen Newton)
  • Run security tools on the existing web applications (Glen Newton)
  • Run accessibility tools on the existing web applications (Glen Newton)
  • Hackathon - security review of DINA packaging at system level (Glen Newton)

DNA module

  • SeqDB – voucher data, integration with DINA collection manager (Satpal Bilkhu)
  • SeqDB web service examples (Satpal Bilkhu)

Friday 09.00-12.00

  • 09.00-12.00 Concluding discussion - next steps
  • 12.00-13.00 Lunch - Meeting ends


Working groups

During the week we worked in parallel groups, making progress on the taxonomy module, the user module, the core collection management data model, user roles, and a communication strategy. We will continue these working groups after the workshop, also inviting DINA collaborators who were not able to attend the meeting this time to participate.

Working documents from the different groups on Google Drive (read only)

Data model group

The data model group currently consists of James Macklin, Paul Morris, Martin Stein, Markus Englund, Kevin Holston and Falko Glöckler, with Satpal and Thomas as contributors. It would be nice to have someone from Edinburgh (Rob?) and someone from Tartu (Kessy and/or Urmas?) participate in this group. The group is making good progress, and you can follow their work in the Data Model folder on Google Drive. The revision of the data model will happen in several steps. The first step, for feature set 1, will have to be completed by the end of this year, so that version 1 of the new core collection management data model and its associated REST API. This first revision is going to be relatively modest but it will contain some of the more critical changes we want to see. In the spring, the group can continue with the next revision, for feature set 2, which can be more substantial.

During the workshop the data model group made some progress on user roles in the DINA system. There is a text document and a spreadsheet on the Drive in the folder User Roles summarizing the proposal, which is not complete yet. However, we have suggested that we focus on just two user roles for the initial feature set, so we will only need the permissions details for those two groups to start with.

User module

The user module group currently consists of Ida Li, Markus Skyttner and Al Jones. This group discussed technical solutions for single sign on and permissions associated with users and user roles. During the workshop the group was able to test-implement support for some simple use cases that will be common in DINA Web using keycloak and some other software components.

Taxonomy module group

The taxonomy module group currently consists of Ingimar Erlingsson, Satpal Bilkhu and Thomas Stjernegaard Jeppesen. the group made good progress during the workshop, and part of their work is documented on Google Drive.

It is still uncertain whether the Estonian group can release more than the taxonomy module backend under an open-source license in the near future. It is also difficult for the Tartu team to isolate the front end code for the taxonomy module from the rest of the Pluto-F code. Therefore, we will have to modify or redevelop the front end code for the taxonomy module (the taxon editor), a task that we will probably have to take on in Stockholm, hopefully with assistance from the Tartu team. Similarly, we hope for assistance from Canada in developing an initial DNA sequence editor for the collection manager, connecting SeqDB to the taxonomy module.

With respect to reference taxonomies, we are currently thinking that a good strategy might be to take them from the GBIF API, after hearing Tim Robertson say that all the relevant reference taxonomies are available from there under a uniform API. Thomas quickly examined the GBIF API for DynTaxa and it looked quite promising. With this solution, we would not have to upload the reference taxonomies to the DINA taxonomy module, or if we wish to do this for performance reasons, at least we can upload the relevant reference taxonomies from a single place using a standard API.

Communication group

The communication group currently consists of Falko Glöckler and Karin Karlsson. They were hoping that Elspeth would be interested in joining the group, and others would be welcome too. They are developing a draft communication policy for the DINA project, and will be presenting their proposal for the rest of the group at a future TC meeting.

Next DINA Technical workshop

More news from the workshop will follow at the coming DINA ISC and DINA TC meetings. We are already planning for the next TC workshop, which will be in Berlin (at MfN) in June.

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