TC conference call - 26. April 2016

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TC conference call - 26. April 2016
Title TC call
Location Google Hangout
Date Start
Date End


  • Reports from team on progress made during the last couple of weeks
  • Decision to adopt and follow guidelines for Releases and QA procedures
  • Preview of Collections Manager UI deployed at
  • ISC status report - please summarize team progress made since December 2015 in a couple of sentences
  • Any other business


Attending: James Macklin, Allan Jones, Nazir El-Kayssi (CAN), Thomas Stjernegaard Jeppesen (DEN), Rob Cubey (UK), Falko Glöckler (GER), Paul Morris (USA), Ingimar Erlingsson, Ida Li, Kevin Holston, Karin Karlsson, Carl Claesson (SWE).

Report from Sweden

Development progress is focused primarily on the Estonian taxonomy module integration and moving SeqDB into production for the Centre of Genetic Identification (CGI). Kessy has worked on the upload script for successful import of 93,000 DynTaxa records, which is a major step towards full integration with and dockerization of The Naturalist ( Parallel efforts to dockerize SeqDB in coordination with Satpal and Nazir will involve moving the local installation into the test environment next week.

Report from Canada

James mentioned that there will be more detailed discussion of the incoming funding and related decisions at the Berlin meeting. Metagenomics remains the next major step in SeqDB development, and a new version of the API is now available. This work will continue in coordination with Ingimar, and Satpal will be able to continue work with the SeqDB at end of May.

Report from Denmark

Andy Bentley from the Specify team in Kansas held a workshop in Copenhagen to train users from the seven Danish museums and ZMUC, which followed GNM (Gothenburg) training sessions by Andy during the previous week. There is more interest in evaluation of the new version of Specify 7 in an effort to expedite the migration process in Denmark. Servers have been ordered for installing Specify 7.1. A new developer has been hired into the Danish team and will attend the face-to-face TC meeting in Berlin.

Report from UK

Although local network stability is improving, database efforts are concentrated on BG-BASE without much time to allocated to work on Specify.

Discussions Points, from Team Reports

  • Paul Morris, Museum of Comparative Zoology (USA), has secured additional financial commitment (NSF) that allows him to work on the data model solutions within DINA. He will be able to attend the Berlin meeting, where the information model, developed in collaboration with James, will be examined in relation to DINA system components.
  • Thomas mentioned that his current project on fungi provides useful insights on Taxonomy module integration. He is using an alternative mechanism, which involves SOAP calls and jobs to synch data with DynTaxa rather than downloading static datasets. The Swedish team expressed their interest in these methods and referred to ongoing discussions with ArtDatabanken. These discussions have included similar procedures (i.e., the Delta protocol), emphasising the importance of coordination with the DynTaxa gatekeeper as well as clear prioritisation of synchronisation among the institutions involved. Paul suggested that maintaining lists could be considered a task beyond the scope of collections management, handled by system integration solutions.
  • Further development of the DDT will have to be reevaluated in the context of the recently available Specify 7 Workbench. Thomas mentioned that the use of Hibernate remains an issue in using the Specify Workbench, so perhaps DDT tree upload methods will be useful. This is related to memory handling, and Paul noted that the Workbench has limited capability to handle complex, large (>1000 records) datasets.

Guidelines for Releases and QA procedures

The decision to adopt and follow guidelines for Releases and QA procedures has been postponed until next meeting.

Preview of Collections Manager UI

Carl demonstrated the Collection Manager UI, which is now available to TC members ( with the caveat that it is a test system that will be unavailable periodically. The TC members agreed that the presentation is good ("very clean!") and were encouraged to contact Calle and Karin with feedback. Feedback forms provided in association with the most recent UI version are in Swedish, provided for the user group active in the ongoing sprint meetings. The renonymized test dataset currently in use will be improved with fabricated botany and zoology data.

ISC progress report

The ISC has requested reports on progress and issues from the TC for discussions during the next ISC meeting (18 May 2016).

Other business

Fredrik will lead the TC workshop in June at MfN, Berlin, with Falko as the host. A list of attendants has been compiled (see: The usual meeting equipment will be provided (e.g., white board, projector, WIFI, etc.) and two or three additional rooms will be reserved for break-out groups. Please contact Falko on issues related to visiting the MfN or meeting logistics.

Action points

  • The Quality Assurance guidelines will go through a final round of editing, which primarily involves contributions from Glen.
  • Each TC group will send a summary of progress to Markus S.
  • James will determine when Paul is available to discuss data model issues ("Complex Collection Objects").

Next meeting 17. May 2016, 13.00 UCT

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