Man. Comm. 10

Skype conference

Date: 17th April 2013

Start: 10:00 BST

Duration: 2 hours

Meeting 10: Agenda

  1. Apologies for absence

    Thierry Backeljau (replaced by Isa Van de Velde); Vince Smith

  2. Actions from last meeting

  3. Project Co-ordinator's report

    Follow-up on issues raised by the reviewers.

  4. Workpackage summaries [WP leaders]:

    1. Progress highlights;
    2. Milestones; highlighting new milestones & milestones overdue
    3. Interdependencies with other WPs; how are we managing (inevitable) changes to workplans and the knock-on changes that are entailed
    4. Deviations from budget;
    5. Deviations from the Workplan.

      Overdue Milestones to be addressed

      1. M1.35 - Second year financial reports [31/12/2012]
      2. M1.39 - Organise final meeting [31/03/2013]
      3. M3.13 - Recommendations to modify products [30/11/2012]
      4. M4.22 - BiolFlor Data as semantic web [28/02/2013]
      5. M4.32 - Integrating a wiki-glossary into the scratchpad [31/01/2013]
      6. M5.30 - Implement biodiversity indices tool [28/02/2013]
      7. M5.31 - Review of target applications and services (molecular identification) [31/03/2013]
      8. M5.36 – GBIF specimen records tool [31/03/2013]
      9. M6.17 - New open access data publishing journal [31/03/2013]
      10. M8.22 - Prototype version of a start-up portal for discovery of GBIF mediated data [01/03/2013]


  5. Budget report

    1. Allocation of funds to extend COMBER into Y3;
    2. Allocation of funds to promote BDJ;
    3. Relocation of Yde de Jong and the engagement of UvA;
    4. Orthopteran case study (WP2).


  6. Deliverable 2.3 - Sustainability

    1. Products to be sustained:
      • Scratchpads - NHM core funding
      • CDM - BGBM core funding
      • Biowikifarm - BGBM, SNSB & Plazi core funding
      • PWT & Scratchpad publication tool - Pensoft commercial funding
      • NPT - GBIF core funding
      • OBOE
      • RefBank
      • GoldenGate
      • Xper2
      • ...
    2. Service Level Agreements


  7. Final Project Meeting

    FAO, Rome 3 Sept - 6 Sept lunchtime to lunchtime

    Programme committee:

    • Eva Alonso - LifeWatch
    • Christos Arvanitidis - LifeWatch
    • Alberto Basset - LifeWatch
    • Palma Blonda - BioSOS
    • Donatella Castelli - iMarine
    • Frank Oliver Glöckner - Micro B3
    • Gregor Hagedorn - pro-iBiosphere
    • Alex Hardisty - BioVeL
    • Jörg Holetschek - OpenUp!
    • Jacco Konijn - Creative-B
    • Matthias Obst - BioVeL
    • Dave Roberts - ViBRANT
    • Soraya Sierra - pro-iBiosphere
    • Aaike De Wever - BioFresh
    • Anna-Maria Wremp - LifeWatch

    Funding: ViBRANT, LifeWatch, BioVeL, pro-iBiosphere

  8. Technical workshops

  9. Topic Organiser Location Date Status
    Workshop on RefBank/RefFinder Lyubo Penev Sofia Autumn 12/Spring 13
    Workshop on PWT/BDJ Lyubo Penev Sofia Autumn 12/Spring 13 Proposed
    Workshop on the nature and structure of the biodiversity research field Peter van den Besselaar ? ? Proposed
    Literature mining and markup using OBOE David Morse Oxford Winter 12 Proposed
    Text mining and markup with agINFRA and BioVeL David Morse Athens January 13 Proposed
    Workshop with JEMU on phylogenetics in Scratchpads Thierry Backeljau Brussels ? Proposed


  10. Travel plans

  11. TDWG will be in Florence (28 Oct – 1 Nov) and is expected to be the venue for ViBRANT participants to present their work. The ViBRANT final meeting will not have scope for all partners to present. Partners should be careful to keep travel funds for these two meetings.

    ViBRANT can fund partners to travel outside Europe only if they are presenting. We need to apply to the Commission explicitly for permission. We expect all conferences for which ViBRANT funding is used to e listed on the web site. It will be used to build next year's annual report. Specifically, meetings need to be included under 'Presentations' under the 'outputs' tab.

  12. Follow-on grants

  13. Including comments on the H2020 meetings in March

  14. Biodiversity Informatics White Paper

  15. Associated projects

    1. eMonocot
    2. agINFRA
    3. BioVEL
    4. EU-BON
    5. pro-iBiosphere
    6. LifeWatch

  17. External links

  18. Links to external projects are now on the web site. This item is an opportunity to discuss the appropriateness of including any particular link.

  19. Future meeting dates

    1. 17 July 2013 from 10:00 to 12:00
    2. 16 October 2013 from 10:00 to 12:00 to 17 October at 12:00 - or should we defer this and meet at TDWG?

  20. Any other business




Who Topic Action
LP and DM Launch Bibliography of Life Liaise regarding suitable conference for launch
YdJ & DR Ontology workshops Discuss potential new audiences
LR Budget circulate the full budget before the end of April
YdJ, GH & DR Late delivery of milestone Discussion to take place to try and resolve issues
YdJ Collaboration with iMarine Discuss with CA the potential of downloading modules and modifying for separate use
NC & SR Integration of OBOE services with Scratchpads To resolve technical mechanism.
NC Sustainability Provide some text on the sustainability of OBOE to DR by 20 May 2013
LP & TB Launch of BDJ Discuss the preparation of promotional material
CA Hackathons Send details to DM
All Use of ViBRANT services by other projects Send details of uptake by other projects to DR & VS
All Sustainability Send DR details of any ViBRANT products missing from the list (Item 6 on the agenda) by 10th May
DR Final Project Meeting Add YdJ to programme committee
DR Final Project Meeting Circulate draft plan to WP leaders and start advertising
DM, YdJ & GH Final Project Meeting Evaluate the potential for a technical workshop
DM Sustainability Establish the status of agriDrupal (FAO)
DR Final Man Comm meeting Circulate request to WP leaders for consensus over venue



DR - Dave Roberts, WP 1 Leader SR - Simon Rycroft, WP2 Leader
IV - Isa Van de Velde, WP3 Deputy YdJ - Yde de Jong, WP4
NC - Neil Caithness, WP5 Leader LP - Lyubomir Penev, WP6 Leader
DM - David Morse, WP7 Leader CA - Christos Arvanitidis, WP8 Leader
LR - Lucy Reeve, Project Admin  



  1. Apologies

  2. Vince Smith, Project Coordinator (VS)
    Thierry Backeljau, WP3 Leader (TB) – Isa Van De Velde deputised

  3. Actions from last meeting

    1. Milestone listed on website - Add text before submission of the report to the reviewers on 24 January 2013 (All)


    2. Bibliography of Life - Plan launch in mid-late 2013 (DM)

      Discussions are ongoing. LP has a list of possible conferences.

      • Action – LP and DM to liaise regarding suitable conference for launch

    3. M2.16 - Add justification of change of deadline (SR)


    4. PWT/BDJ - Organise promotion events & timetable (LP & VS)


    5. bibliographic services workshop - Circulate workshop details to ViBRANT partners (DM)

      Not done yet due to continually changing landscape of bibliographic services. It was agreed that the final project meeting could host this workshop.

    6. Ontology workshops - Send YdJ any suggestions for audiences significantly outside the TDWG community (All)


      • Action – DR & YdJ to discuss potential new audiences

    7. Promotional Video - Consider outreach and product demos in video format (TB)

      Information was received from DM on Whistledown but it is really a radio company and specialises in audio.
      Pier Productions also do a lot on radio and comedy series for BBC. They work with the Open University on audio and visual interviews.
      Javier de la Torre sent info about two companies.

      1. who produced GeoCAT & Protected planet. GeoCat cost less than €10k but it depends on complexity.
      2. riotcinema who made a video on GPS system for farmers, and one called Planet hunters about finding new planets. These videos involve real people, rather than animation, as the GeoCAT example. The budget for the GPS movie was around €7k.

    8. Sociology - Increase contact with Peter van den Besselaar to establish concrete work plan (TB)

      IV is confident that, with Henk Koerton appointed to replace Daphne Duin, work will make progress, although it remains an issue. Henk has been communicating with YdJ. There is a need for clear objectives in the next user survey. Before the next survey is launched it should be distributed to partners to comment on the questions.

    9. Training - Contact TB about training for products (All)


    10. Ontology integration - Discussions with WP2 to clarify allocation of tasks (YdJ)


    11. Ontology workshops - Contact Régine regarding engagement of communities with XPer2 (YdJ)


    12. Promotional Video - Send suggestions for and experience with video companies to Isa (All)

      Done - see (g) above

    13. Promotional Video - Pass details of WhistleDown to Isa (DM)

      Done - see (g) above

    14. LifeWatch - bring up the link between BDJ and LifeWatch at the March meeting (CA)


    15. Budget - Chase up delinquent financial reports (LR)


    16. Budget - Coordinate transfer of funds to support YdJ in RBINS (DR, LR, TB, YdJ)

      In progress. UVA have relinquished any claim to the remaining funds, which have been transferred to RBINS. The process is underway.

    17. Budget - Resolve spending plans with partners and establish sum for redistribution (LR)

      In progress. Awaiting the final few responses from partners.

      • Action – LR to circulate the full budget before the end of April.

    18. Workplans - Discuss with Alexander potential Y3 activities (DR)

      Done but not resolved

    19. Budget - Check VU & OU figures (LR)


    20. Workplans - Discuss with Noël potential Y3 activities (DR)

      Done but Noel has gone quiet since the discussions took place.

    21. Budget - Circulate final figures once budgets finalised (LR)

      See (q) above

    22. Y2 Review - Check sections and respond by Friday 18 January (WP leaders)


    23. Y2 Review - Make sure all partners have their list of presentations on the web site up to date and complete (WP leaders)


    24. Y2 Review - Review slides to be submitted to DR by Friday 1 February (WP leaders)


    25. Y2 Review - Print slides for reviewers (LR)


    26. Y2 Review - Send a few URLs for product demo to DR by Monday 4th Feb (SR, LP, NC, CA)


    27. Final meeting - Follow up with Alberto (CA & DR)

      Done, see main agenda item 7

    28. Final meeting - Work with Alberto and other project coordinators to agree date, plan programme and make logistical arrangements (DR)

      Done, see main agenda item 7

    29. Tech. Workshops - Contact proposers, establish timetables for proposed workshops (DR)

      Done, see main agenda item 8

    30. EU Bon meeting - Contact Anke Hoffmann regarding presenting ViBRANT (CA)


    31. EU Bon meeting - Ask Dimitris to coordinate slides and send to CA (VS)


  4. Project Coordinator’s report

  5. The formal response to the review has been done and the reviewers were happy with it. The Commission were keen to spread the due dates of the deliverables in the final year. It was agreed that ViBRANT would try and get drafts of the deliverables in early, with the deliverable dates remaining as set in the DoW.

  6. Workpackage Updates

  7. WP2: all Scratchpad 1 maintainers have been contacted to upgrade to Scratchpads 2. Scratchpad publication tool is completed and is being tested. Scratchpads 2 is now “stable” (i.e. no longer a beta release) and has moved to a fortnightly update schedule. The site has been improved. Katherine is working on NHM Scratchpad projects to improve sustainability. Khalid Almaini started at the NHM this week as Ben Scott’s replacement. An additional app server has been requested and should be up and running by the next Management Committee meeting.

    WP3: Henk Koerten replaces Daphne Duin and will focus on user interviews. The idea is to have them connected to training session but also try to organize at the users' institution where there is a large group of Scratchpad users. These interviews should give info about the behavioural changes associated with the use of Scratchpads. A workshop is planned on mapping the field of biodiversity/taxonomy (item 8 below). Ten training sessions scheduled, in which the Ambassadors are involved. Training sessions are scheduled for Malaysia, Ukraine (2 sessions, one in English and one in Russian) and Cameroon. There is also likely to be one in Kenya. Pilot online Scratchpads training is scheduled. Three more Ambassadors have joined, one each from China, California and the Netherlands. This brings the total up to 20 Ambassadors in 16 countries. Some of the ambassadors are involved in the Scratchpads translation project and, as such, the Chinese ambassador is involved in the interface translation into Chinese. Furthermore, the Californian ambassadors has some funding for translating his Scratchpad into an Asian language. A one day WP3 workshop will be organized in June, entitled ‘ViBRANT tools for the DNA taxonomist’ and is meant for the Belgian Network of Barcoding of Life community.
    M3.13 is overdue PvdB has promised to complete it as soon as possible.
    M3.15 is postponed from April until July so the Malaysian and Ukraine training events outcomes can be included.
    A new milestone M3.18 has been added related the organization of a workshop in the usage of the Cybertaxonomy platform, responsible partners are BGBM and UPMC.

    WP4: The Fauna Europea server is being migrated to Berlin (MfN). Work with Pensoft on a special publication is ramping up. Testing is due to start on CDM. There are continuing delays in Gregor’s milestone delivery. YdJ attended a meeting of iMarine in Rome where there was interest in developing tools that ViBRANT can provide in the areas of biodiversity data management and vocabularies.

    • Action – Discussion to take place to try and resolve issues (DR, YdJ, GH)

    • Action – YdJ to discuss with CA the potential of downloading modules and modifying for own use (YdJ)

    WP5: M5.30 complete. M5.31 is in hand. There is a bottleneck so M5.36 has been delayed to 30 April 2013. A new server for NETi services was hoped for but the public site returns different results. This could be due to out-of-date code, so could be fixed by getting up-to-date code. NC awaiting a response. Integration of OBOE output with Scratchpads is still being actively developed. XML is being tried. NC suggested that Scratchpads offering a download link of zip file and PDF files might work. NC is trying to develop new services and boost interest in OBOE services. Currently there is a lack of sustainability which needs to be addressed. DR commented it is important for the sustainability report to try and bring together the fragility of integration. ViBRANT needs to convince the reviewers that OBOE is sustainable.

    • Action – Resolve technical mechanism for integration of OBOE services with Scratchpads (NC & SR)

    • Action – Provide some text on the sustainability of OBOE to DR by 20 May 2013 (NC)

    WP6: Ready to launch BDJ and PWT. The official launch has been postponed for final adjustments. First papers are expected to be published by the end of May. M6.17 is technically already complete but has yet to publish any papers. WP6 have been working with WP2 on the publication module. An eMonocot paper has been successfully submitted automatically and is now in review. Need a promotional “kick” for the launch of BDJ for which WP3 will need to be involved.

    • Action – Discuss promotional material for the launch of BDJ (LP & TB)

    WP7: DM gave a presentation at the OU and David King gave an ad hoc presentation at pro-iBiosphere’s workshop in Leiden.
    Follow up from last year's three internal, cross-workpackage mini-workshops:

    • Wednesday 21 November 2012 at OeRC: Integration of GgWS, OBOE and Scratchpads 2.0 - Four sample GgWS facilities implemented in OBOE, with results available to Scratchpads. More GgWS facilities and other data mining facilities to follow.
    • Thursday 22 November 2012 at NHM: Integration of RefBank and Scratchpads 2.0 - Sample RefBank search routine delivered in Scratchpads sandbox. Full integration to be progressed in joint meeting with WP2.
    • Friday 23 November 2012 at NHM: Review of options for WP7 in Year Three, moving to LOD for data mobilisation - Continued review of the use of LoD including David King attending the EnviLOD project workshop on "Exploring the potential of Linked Open Data to Environmental Science" at the British Library. See mini-report for more details. Collaborating with agINRA project and their recent conversion of the AGRIS bibliographic database to RDF.

    A large amount of time and effort is being expended by WP7 to deliver the underlying environment to achieve ViBRANT's sustainability goals. In this reporting period this has included significant progress towards milestones M7.20 - Workpackage software documentation produced and M7.26 – Workpackage software packaged. Tangible output produced in this reporting period include two additional git repositories for our software, set up in conjunction with WP2. Exploring the long-term options for sustainability of RefBank and also a “back-up plan”. Working with Guido on GoldenGate. No overdue or late milestones. All existing milestones are on track to deliver on time.

    Interdependencies with other WPs/Partners:
    WP2 for RefBank integration in Scratchpads - Meeting scheduled for Monday 29 April.
    WP3 for publication of audience research paper - Meeting scheduled for Monday 22 April.
    WP5 for GgWS integration with OBOE - Additional services to be delivered through OBOE. Work in progress.
    WP6 for REFinder design and workflow integration with RefBank - Proposed meeting to follow pro-iBiosphere meeting 3 in Berlin at the end of May.

    Deviations from budget:
    Plan to absorb underspend at OU through secondment of developers.

    Deviations from the Workplan:
    No new deviations since those highlighted in Year One report and the re-shaping of WP7 from four to three deliverables.

    WP8: COMBER work is continuing and will be delivered by w/e 26 April 2013. A blue hackathon is taking place 1-2 July in Crete and a green hackathon is 27-30 June. Collaborating on ERANET project developing another service application for experienced divers who can take good photographs down to a depth of 70m. Tools produced by ViBRANT are being taken up and used in other new projects. Presentations of ViBRANT are taking place at the International Polychaete Conference in Australia and a MicroCT meeting in Brussels. M8.22 is mostly done; finalising some of the routines.

    • Action - Send details of hackathons to DM (CA)

    • Action - Send details to DR & VS of the projects in which ViBRANT products are being used (All)

  8. Budget report

  9. €27k has been transferred to HCMR to extend COMBER into Year 3.
    Approximately €17k has been set aside to promote BDJ. This is mainly for travel.
    The relocation of YdJ is in progress (see 2p); this has been agreed by RBINS and the bureaucracy is being negotiated at the moment.
    NHM intends to use €10k of its projected underspend in doing an Orthopteran case study collecting automated acoustic observations in the field. NHM is also planning on producing booklets for ViBRANT; one with case studies and another with ViBRANT products. These will be for general consumption, not specialist.
    LR is awaiting the audit of the finances to be complete and submission of the reports will follow. This will be done in the next week.
    Forecasts from all partners are being obtained to determine the likely budget situation at the end of the project and to determine if any more funds need to be transferred between partners. Once this is done the full budget sheets will be circulated to all partners and the Management Committee. (see action arising from item 2(q)

  10. Deliverable 2.3 - Sustainability

  11. Products to be sustained:

    • Scratchpads - NHM core funding
    • CDM - BGBM core funding
    • Biowikifarm - BGBM, SNSB & Plazi core funding
    • PWT & Scratchpad publication tool - Pensoft commercial funding
    • NPT - GBIF core funding
    • OBOE
    • RefBank
    • GoldenGate
    • Xper2

    Service Level Agreements are inappropriate for what ViBRANT is doing. We will have service level targets instead, for instance as detailed in the Scratchpad terms and conditions.

    • Action - Send DR details of any ViBRANT products missing from the list by 10th May (All)

  12. Final project meeting

  13. FAO, Rome 3 Sept - 6 Sept lunchtime to lunchtime. We are waiting confirmation from their accommodation office that the room is available. No budget has been set for the meeting yet. A virtual meeting of the programme committee will be held before the end of the month.

    Funding: ViBRANT, LifeWatch, BioVeL, pro-iBiosphere, EUBrazil:OpenBio

    • Action - Add YdJ to programme committee (DR)

    • Action - Circulate draft plan to WP leaders and start advertising (DR)

  14. Technical workshops

  15. Workshops on RefBank/RefFinder and on PWT/BDJ have taken place.
    Workshop on the nature and structure of the biodiversity research field (PvdB) is still intended
    Literature mining and markup using OBOE and workshop text mining and markup with agINFRA and BioVeL will be simplified and made part of September final project meeting. AgroTagger uses FAO ontologies to tag publications using KEA. Should be possible to use ontologies to build custom versions of KEA for biodiversity publication tagging through OBOE.
    Workshop with JEMU on phylogenetics in Scratchpads is still under consideration

    • Action - Follow up with YdJ and GH on potential of running a separate technical workshop (DM)

    • Action - Establish the status of agriDrupal (FAO) (DM)

  16. Travel plans

  17. TDWG will be in Florence (28 Oct – 1 Nov) and is expected to be the venue for ViBRANT participants to present their work. The ViBRANT final meeting will not have scope for all partners to present. Partners should be careful to keep travel funds for these two meetings.
    ViBRANT can fund partners to travel outside Europe only if they are presentation. The rules have recently changed and permission does not need to be sought from the Commission. Requests must still come to the Coordinator for approval. All conferences for which ViBRANT funding is used must be listed on the website so they can be include in the annual report.

  18. Follow-on grants

  19. The final meeting will be an opportunity to form consortia and work together. The budget is estimated to be 20% down on the original H2020 budget, but this is still an increase on FP7. This increase in funding along with the reduction in Commission staff means that the Commission is likely to fund larger grants.
    A UK call has gone out for infrastructure grants (known as BBR). Deadline 16 May 2013. We will revise a proposal that failed on a technicality last year to incorporate molecular data in Scratchpads with a workflow to submit the data to EBI. Scratchpads group has distributed the call to Scratchpads maintainers to establish slevel of demand.

  20. Biodiversity Informatics White Paper

  21. Incorrect proof published by BMC Ecology on Monday 15 April 2013. It seems that the first proof, on which corrections were, sent was published instead of the corrected version. The authorship and copyright are both incorrect on the published version. They have been informed and will fix it.

  22. Associated projects

    1. eMonocot – no update available
    2. agINFRA – project meeting scheduled for May 2013. Services will start to become more visible.
    3. BioVEL – workflows being published
    4. EU-BON – Kickoff meeting has taken place. Focusing on producing services that can channel data that GeoBON needs. Mainly terrestrial. Workshop is taking place on data standards in Trondheim. DR and VS can’t go so Dimitris may be going.
    5. LifeWatch – Website updated. First signatures for the long-awaited ERIC (the formal contractual agreement) are expected by the end of summer
    6. Pro iBiosphere – GH and LP are involved. Three people from the NHM team will attend the meeting in Berlin in July.

  23. External links

  24. DR was invited to give a presentation to a Masters course at Oxford and now has links with BioFresh. Paul Jessop also contacted NC regarding development of an OBOE service.

  25. Future meeting dates

  26. Next meeting 17 July 2013 10:00 BST.
    Final Management Committee meeting is scheduled for 16-17 October 2013. It was suggested that the meeting be held during TDWG instead.

    • Action - DR to circulate request to WP leaders for consensus over final Management Committee meeting (DR)

  27. AOB

  28. None