Man. Comm. 8


Venue: HCMR

Flight details
Name Flight Date Lands Flight Date Depart
Vince Smith A3 326 16 Oct 20:35 U2 8772 19 Oct 13:50
Dave Roberts A3 326 17 Oct 20:35 A3 301 19 Oct 06:30
Simon Rycroft A3 326 16 Oct 20:35 U2 8772 19 Oct 13:50
Thierry Backeljau A3 471 17 Oct 15:00 OA 501 19 Oct 06:00
Yde de Jong KL2860 17 Oct 20:20 KL2865 19 Oct 12:25
Neil Caithness A3 326 17 Oct 20:35 A3 301 19 Oct 06:30
Lyubo Penev A3 316
17 Oct
13:35 A3 317 19 Oct
David Morse A3 326 17 Oct 20:35 A3 301 19 Oct 06:30
Gemma Maldar U2 2351 17 Oct 13:05 U2 8772 19 Oct 13:50
Lucy Reeve A3 304 18 Oct 07:50 U2 8772 19 Oct 13:50
Training Course
Laurance Livermore ZB 702
16 Oct 18:55 U2 8772
18 Oct 13:00
Dimitris Koureas ZB 702 16 Oct 18:55 A3 301 18 Oct 06:30
Isa Van de Velde A3 326 16 Oct 20:35 - 18 Oct -
Best Western Your Memories Hotel,
Kato Gouves Pediados, 70014 - Heraklion Crete
Tel. +30 28970 41844; Fax:+30 28970 41791

Date: 18th October 2012

Start: 09:00 EEST

Duration: 8 hours

Meeting 8 : Agenda

  1. Apologies for absence

  2. Actions from last meeting

  3. Project Co-ordinator's report

  4. Workpackage summaries [WP leaders]:

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


  5. Budget report

  6. Technical workshops

  7. Topic Organiser Location Date Status
    Workshop on data visualization & mapping for biodiversity informatics Javier de la Torre Madrid November 12 Planning
    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


  8. Year 2 Report

  9. Final Project Meeting

  10. Travel plans

  11. 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. Biodiversity Informatics White Paper

  14. At the review meeting we were asked to engage with the preparation of a community vision for biodiversity informatics that has been initiated by Alex Hardisty (U. Cardiff) at the request of Carlos Morais Pires (Head of Sector for Scientific Data Infrastructures). The white paper is intended to form the basis of calls in Horizon 2020, the first drafts of which will appear in January 2013.

  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. 16 January 2013 from 10:00 to 12:00
    2. 17 April 2013 from 10:00 to 12:00
    3. 17 July 2013 from 10:00 to 12:00
    4. 16 October 2013 from 10:00 to 12:00 to 17 October at 12:00

  20. Any other business



Who Topic Action
CA Integration of Ecological analysis tools discuss with NC
YdJ BioVel Mailing list add CA and LP to mailing list.
All add text to future milestones Milestones should have some text to explain what the milestone is, not just the title. This is important for the review as the reviewers do check and ask questions.
CA Drop in COMBER users in Y2 provide a paragraph outlining the reasons for the drop in numbers for the annual review.
DM Bibliography of Life as a brand name. plan a significant launch mid-late 2013
LP uncertainty about D6.2 Liase with DR on interpretation and presentation
TB D3.2 changed description upload new description onto website
SR late completion of M2.16 Change deadline and Justification to be added to website
LR UOxf not getting admin e-mails check UOxf admin email address and ensure correct
LR Deadlines for financial reporting remind admin group of the deadlines (cc Management Committee)
DR & LR Potential to claim running costs Get a formal view of allowable costs
All Budget redistribution Ideas to be submitted to management team by 31 Oct 12
DR CartoDB extension e-mail Javier to export extending CartoDB
DR NPT Circulate url for startup page
LP PWT/BDJ promotion of March 2013 (at NHM?)
DM bibliographic services arrange a workshop
All integration and user services Put meeting together to attract people who wouldn’t otherwise use ontologies. Please all think of workshop ideas and contact wp contributors for ideas
DR Final meeting Circulate options to all partners



DR - Dave Roberts, WP 1 Leader SR - Simon Rycroft, WP2 Leader
TB - Thierry Backlejau, WP3 Leader 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
VS - Vince Smith, Project Coordinator LR - Lucy Reeve, Project Admin


  1. Apologies

  2. Gemma Maldar, Finance manager (GM)

  3. Actions from last meeting

    1. CA to contact TB about training for COMBER


    2. NC to contact Régine and Noël to clarify UdlR workplan. Statement received from Régine about what Noël is going to do

      Action – NC to post on website

    3. Bids for focused meetings (All WP leaders)


    4. NC to update milestones to support transfer of funds


    5. DM to set up SKYPE call between key people on joint meeting on core teaching module Discussions have taken place. The decision was made that a workshop is not the best way forward.

      Action – NC & DM to brainstorm to see if can create a grant proposal

    6. DM to update milestones and add links to completed milestones on website


    7. LR to request Yr 2 spend forecast from all partners


    8. Contact TDWG committee for decision on location of 2013 meeting (YdJ)

      Done; will probably be in Florence

  4. Project Coordinator’s report

  5. The Biodiversity Data Journal (BDJ) is building up a collection of editors and support.

    The key issues for final year for everyone are integration and users. We need to show how the WP leaders are working together across WPs to bring the project together as a whole. Some parts may struggle to attract user base (e.g. Berlin, RefBank).

    More effort needs to be put in to integrate ViBRANT with other projects.

    SR is now employed by the NHM – demonstrating that Scratchpads is sustainable beyond the grant. Need to weave sustainability into the story of ViBRANT.

    ViBRANT has a new desk officer (Antonios Barbas) who is more pro-active and giving a lot of attention to the project.

    DR will be writing a sustainability report and will be asking WP leaders for input next year.

    N.B. Sustainability doesn’t mean permanence.

    ViBRANT is a project name that will die at the end of the project. The name is in the entities that have been created e.g. Scratchpads, RefBank

  6. Workpackage Updates

  7. WP8: COMBER expanded this year (website demonstrated) with Cretaquarium link.

    Mini workshop planned for all divers in HCMR to be trained so they can start reporting.

    Update on the COMBER site (to Drupal 7)

    24 tools & services were studied and reported on (classification) analysed with 2 factors in mind (tools from same provider and same function).

    To improve ViBRANT services need to take into account services already available.

    This could be a paper if more time is spent on it. There is a gap in the market for a review into the services available.

    Ecological analysis tools: BENTIX and BQI have been launched . BQI suffered in samples with few species. How can we integrate these into ViBRANT? Possibly develop APIs but need help as specific requirements. (In BENTIX is there a specific table that it gets data from)

    Action: - CA to discuss with NC

    Meeting on taxonomic services for BioVel in Copenhagen in December

    Action: – YdJ to add CA and LP to mailing list.

    Problem with MS8.16, 8.21 – CA will chase Javier again and make a decision on how to proceed with the milestone (delay or mark as complete).

    Action: – all to add text to future milestones. Milestones should have some text to explain what the milestone is, not just the title. This is important for the review as the reviewers do check and ask questions.

    SCRATCHPAD module for data recording needs more time.

    CA to upload publications to website

    Some concerns that COMBER is not pulling in sufficient numbers this year. CA advised this was mainly due to the nature of the tourists this year.

    Action: - CA to provide a paragraph outlining the reasons for the drop in numbers for the annual review.

    Repeat users potentially interesting sociologically (WP3).

    Potential to take the COMBER site and repackage it for other groups to use.

    WP7: See Summary report

    1st going live of REFinder is at TDWG. Do need reference editing interface in RefBank but not essential to search. Fits D7.3 – can be the key deliverable.

    Need to think about branding. Bibliography of Life is a potential brand name. Product of ViBRANT with contributing partners and data sources.

    Workshop to finalise and lift out.

    Action: - Need to plan a significant launch mid-late 2013 (DM)

    BioStore and RefBank could combine.

    Extend search on BioStore

    WP6: Potential integration of Pensoft writing tool with REFinder is being investigated.

    INSDC-type arrangement between bibliographic providers (RefBank, CiteBank & Mendeley) should be developed.

    There is some uncertainty about D6.2 – Automatic export of information from papers published by Pensoft to various sources.Action: - LP to liaise with DR over interpretation of the deliverable

    Lots of activity targeted at peer review. Concentrate on feedback.

    Some of the milestones will be reordered to a sequence that makes more sense.

    Mirroring of ZooBank at NHM won’t be tied into ViBRANT.

    WP5: 111 users of OBOE now, a large number of which are real users. Mostly doing LEFT jobs. Some are BEAST jobs which take a lot of time. Useful having real users to provide real usage data – useful for negotiating times with supercomputing centre.

    £1200-£2k per year requested for virtual machine to run web application. NC was advised that the indirect costs are intended for this purpose, so additional funds would not be granted. This is part of the institutional infrastructure and therefore should be funded by the overheads.

    Need to calibrate services according to what HTML you want.

    All due milestones have been completed.

    New milestones are all on ecological spatial analysis.

    Working on a phone app to go with the land cover classification tool. Data gathered from this and accumulated at OXF.

    Threatened species tool. Extracting species from IUCN list and data from GBIF and producing a combined map of threatened species.

    Also alpha and beta diversity tools

    There may be potential to extend these tools to marine, not just terrestrial.

    NC informed the Committee that LEFT is still paid for under Statoil contract, but they don’t want to pay for it any more. They want it entirely in zoology, don’t want it part of OBOE. LEFT will run until end of 2012.

    NC confirmed that Milo has done no work on LEFT, he has only been working on OBOE.

    There was confusion about whether LEFT was being marketed as a ViBRANT product. NC clarified that LEFT was a demonstration of a type of product that could be provided by OBOE, and not the actual product.

    Services that allow ecological assessment tools to be delivered are being developed. The same generic framework is to be provided to other partners.

    Needs to be better integration with GeoCat. Standardise way we’re doing the mapping. This will be pursued at a workshop in Madrid.

    Loss of efficiency in multiple workflows; ultimately users will judge which is best.

    Other people can write services for OBOE. agINFRA have grid resources so potential to link up.

    Attention needs to be given to scalability and sustainability issues.

    Need to be able to demonstrate the end-to-end services to the reviewers in Feb 2013

    Sustainability: access to OSC will ultimately have to be paid for. Working on authentication process

    WP4: M4.15 now at BGBM

    M4.19 canvassing potential contributors

    27 Audubon core term list

    Semantic wiki forum for terms – intended to be a replacement for the GBIF vocabulary server

    M4.18 and M4.24 done, working towards an integrated search index, i.e. a full text search across all ViBRANT-supported resources.

    There will be a subgroup meeting during the GBIF meeting

    GBIF want to continue doing this work.

    Lots of discussions have been going on about governance of vocabs. GBIF solution is TDWG VolMac vocab management group. Is this outsourcing the work ViBRANT is paying them for?

    Semantic mediawiki is quite limited at the moment as isn’t known widely. This seems to be an ongoing issue from previous projects and still failing to deliver users.

    Depends on ease with which users can access and use a vocabulary – needs to be built into a system.

    There were concerns about integration between the systems.

    Status on ViBRANT index with respect to GBIF’s registry which covers the same ground. The Scratchpads to GBIF registry is automatic whilst users have to manually export to the CDM to be in the ViBRANT index.

    CDM is a potential repository for sources of information. We now have methods of searching across Scratchpads. One advantage of CDM is you can add other resources e.g. Xper2.

    Need to look at automation of harvesting DwCA, and marketing to increase visibility.

    Milestones for WP4 are linked to deliverables which are already complete. They need to be mapped to deliverables in other WPs. WP5 will be able to catch most of them.

    WP3: 2 extra basic training sessions (NHM and HCMR). This year 10 courses that have served >100 people

    Training schedule for 2013 will be drafted soon

    Dimitris Koureas replaces Irina on support and training

    Help wiki developed, 13 video tutorials so far on Scratchpads2 online. More are being developed.

    17 Ambassadors who have been helping with outreach, doing training, promoting to the media, testing Scratchpads2

    Also taught as part of MSc course at NHM (not funded by ViBRANT) – further promoting ViBRANT by using ViBRANT products e.g. on eMonocot.

    PlosOne article prepared.

    New Scratchpad survey finished for non-maintainer users and will go out once NHM has given the go ahead

    Scratchpad maintainer survey 2011 results are available in a report

    Waiting for user feedback data from NHM. Uncertain whether we have all the data or the time that may be required to extract the data.

    New training material being developed.

    D3.2 has changed description (title also changed but kept the same as not substantial enough a change to warrant amending Annex 1)

    Action: : TB to upload new description onto website

    M3.17 (suggestions for potential new user groups) should be clarified - when identify new user group what service are we giving them and how will we attract them? E.g. through academic societies, mailing lists, websites etc

    Leave with TB for the moment, maybe bring in the big guns later if not delivering.

    Deviations from budget – VU – problems with last year Form C not submitted

    Deviations from schedule – training and survey planning adapted according to upgrade of Scratchpads

    Daphne is leaving VU in mid-Dec. Peter is trying to get a replacement from his department

    Planning to produce special Zookeys volume

    Scratchpads workshop 2013 for JEMU community

    WP2: 2 new developers – Alice working on Scratchpads (claiming from ViBRANT), Katherine, working on NHM-based projects which integrate with Scratchpads, initially focussing on porting the Solanaceae Source to Scratchpads, which means interfacing with a Brahms database. redesign coding is complete, content needs to be finished. Should be live by early November.

    1st Scratchpads1 site converted to Scratchpads2 and old site discarded. A number of other sites are being reviewed (upgraded but keeping Scratchpads1 site while the new one is being checked).

    Users outside ViBRANT completely are adapting and building on the infrastructure tools.

    eMonocot is also bringing in new users and new content.

    Planning meeting in a fortnight to discuss milestones

    M2.16 likely to be late – tied in with deliverable at end of the project and no work has been done on it so far.

    Action: Justification to be added to website

    M2.15 moved to D6.3

    M2.19 moved to D6.3

    M2.17 moved to D5.3

    M2.18 moved to D5.3

    M2.20 moved to D5.3

    17 and 20 are the same but a year apart, dependant on getting feedback from WP3.

    No deviations from workplan or budget

  8. Budget update

  9. Year 1 report approved and partner payments have been made.

    Signed Form C’s not received from UOxf, VU and KNAW – adjustments to be made in Year 2.

    BGBM and UdlR are not receiving a payment as they are estimated to have underspent based on the funds they have already received.

    VU/KNAW will not be receiving a payment as they did not submit a Form C

    UOxf will only be getting the additional funds for NC’s extra time input.

    Action: : LR to check UOxf admin email address and ensure correct

    Based on the forecasted figures received from partners there is 43% of the total budget remaining in the final year. This is subject to change.

    Most partners are on track with their spending; concerns with UOXF and VU due to the lack of Form C returned in Year 1, OU as no forecast was received in time for the meeting, MfN as their forecast spend is only 40% at the end of Year 2, and Vizz and GBIF who have spent over 90% of their allocation.

    Partners will be responsible for adding their own financial information to the NEF this year. LR will advise when the NEF is open.

    Draft figures added to the NEF and finalised by 4 January 2013, to enable enough time to check and feedback.

    Final adjustments to the Explanation of Resources to be complete by Friday 22 January

    Deadline for electronic submissions is 29 January. Once the Commission have checked the claims they will email a pdf of the final Form C’s for signature and returning to the Commission.

    Action: : LR to inform admin group of the deadlines (cc Management Committee)

    There may be some unallocated budget available resulting from the differences in overhead rates/reimbursement rates after transferring budget between partners. Options for the spend are:

    1. WP8 for COMBER
    2. Pensoft for promotion of BDJ
    3. Supporting Laurence Livermore (at NHM)
    4. Vizz to migrate GeoCat with CartoDB

    NC requested some more funds for OBOE. Want to see better integration and what happens beyond ViBRANT. Note that OBOE funding is expected to be supported by the overheads paid to UOXF because it will be using existing infrastructure. It was considered unlikely that such a charge would be an allowable cost, but we would check.

    Action: : DR & LR to get a view of allowable costs

    YdJ requested some more funds to support his time input. Cost estimates and justification are required. This was considered unnecessary given the low spend made by UvA to date.

    Action: : ideas for budgets and how to spend to be submitted to NHMMT by 31 October 2012

    DR informed the Committee that GM will be leaving the NHM at the end of November. LR will be taking over ViBRANT administration.

  10. Technical workshops

  11. Workshop on data visualisation and mapping for biodiversity informatics will be going ahead in November.

    Action - DR to e-mail Javier re CartoDB work and

    Action - DR circulate http - //

    Workshop on RefBank/RefFinder won’t be taking place in Autumn 2012 due to BDJ commitments. Planned for Spring 2013

    LP and DM to keep in contact re workshops

    It was considered that a workshop on PWT/BDJ would not be the best method.

    Action - LP to put forward something for promotion of PWT/BDJ (at NHM?) March 2013

    Literature mining and mark-up using OBOE has already taken place.

    Workshop on the nature and structure of the biodiversity research field (PvdB) was not accepted.

    Text mining and mark-up with agINFRA and BioVeL was approved to go ahead in January 2013. ViBRANT will only fund people from ViBRANT.

    Action - DM to arrange a workshop on bibliographic services

    It was suggested that some funding be directed to family-friendly policies, e.g. funding for parents to attend meetings towards cost of child care etc..

    Workshop with JIMU in phylogenetics early 2013. Training and promotion.

    It was suggested that NC proposes a workshop on ecological tools Spring 2013.

    Action - WP leaders to think about integration and user services. Put meeting together to attract people who wouldn’t otherwise use ontologies. Please all think of workshop ideas and contact wp contributors for ideas

    Consumables money can be vired into travel for workshops if necessary.

  12. Year 2 report

  13. Same mechanism as last year. DR will put together report based on submitted milestones. Focus on integration and users.

    1st week of December deadline for WP leaders to submit their report, focusing on integration and users.

    Review will probably be on 7 February 2013. (5, 19 and 21 have also been suggested).

    It was proposed YdJ, LP, TB, CA, plus DR, VS, LR, SR to represent the project.

    Action - Will need presentation of no more than 5 slides on highlights of previous year to present from every WP leader

  14. Final project meeting

  15. Needs to be Sep/Oct so all finances are resolved by the end of the Project. We could have special session in TDWG (Florence) but that will probably be hard to organise at this early date. Such a session could not be titled VIBRANT. We'd have to call it something about open data or open services.

    TDWG likely dates are 7-11 or 23-28 October.

    Offers from RBINS , KIT (Karlsruhe), Pensoft (Sofia) and HCMR (Crete) to host the meeting.

    We will get a better audience by running back-to-back with another meeting, such as the 8-11 Oct meeting in BGBM Pro-iBioSphere.

    Potential to combine with other projects. Cut off date late November for thinking about potential

    Action - DR circulate to researchers put forward invitations received and any other suggestions welcome but want to do this in conjunction with LifeWatch & other supporting projects, i.e. BioVel, ENVRI, Creative-B for feedback by end of November. Decision by beginning Jan.

  16. Travel plans

  17. 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 be 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.

  18. Follow-on grants

  19. Bid put in to BBSRC building on services making data submission easy. Failed at second stage due to administrative issues withdrawn on a technicality. Lobbying at the moment.

    There were 2 opportunities for EU funding deadline Oct but there was not enough time.

    One in Jan which is a potential to put in a bid on ICT framework. Paul Wilkin (Kew) is keen.

    Doesn’t look like H2020 money will be available early 2014 so there will be a gap between VIBRANT and any successor.

  20. Biodiversity Informatics White Paper

  21. Version 4 is being edited. Version 3 has not been circulated as an external editor who didn’t understand the domain so in edit at the moment. Will be circulated as soon as it is done.

    BMC Ecology has been approached to publish the paper.

  22. Associated projects

    1. eMonocot: Workshop in SA and one coming up in Brazil helping with outreach of VIBRANT projects. Portal integrates a lot of VIBRANT content.
    2. agINFRA: Nothing to add from earlier. One problem is it needs to talk to its user community and get away from the grid focus.
    3. BioVEL: Struggling with workflows. There is a danger the project may end with three or four pipelines which are too customised for general use.
    4. EU-BON: Monitoring data integration and publishing citizen science.
    5. Pro-iBiosphere: 2 yr project 6 partners, Naturalis coordinating. About linking legacy data to prospective publishing and creating basis for knowledge base for biodiversity informatics. 6 important pilots.
    6. LifeWatch: Speaking to Wouter 2 Nov.
  23. External links

  24. External links are now public

  25. Future meeting dates

  26. 16 January 2013 from 10:00 to 12:00 – final report draft discussion

    17 April 2013 from 10:00 to 12:00

    17 July 2013 from 10:00 to 12:00

    16 October 2013 from 10:00 to 12:00 to 17 October at 12:00 –included in final meeting

  27. AOB

  28. None