Man. Comm. 3

Venue: skype conference call

Start: 10:00 BST

Duration: 2 hours

Meeting 3 : Draft Agenda [8 July 11]

  1. Apologies for absence
    Thierry Backeljau (Isa Van de Velde will deputise)
  2. Workpackage summaries [WP leaders]:
    1. Progress highlights;
    2. Milestones;
    3. Interdependencies with other WPs;
    4. Deviations from budget;
    5. Deviations from the Workplan.
  3. Project Co-ordinator's report
    A new standing agenda item for project-wide issues, matters from the strategic board and project invitations to meetings.
  4. Reporting
    6 month reports
  5. Special Clause 39
    Open Access publications.  We agreed to deposit an electronic copy of the published version or the final manuscript that relates to ViBRANT in an institutional or subject-based repository at the moment of publication.
  6. Outreach & publicity
    We have begun updating the public-facing website. We are keen to see ViBRANT products in the public domain. New leaflet is designed. Web page will use the 'chromosome' as core public navigation for which new topic pages will have to be written.
    We anticipate demonstrating Scratchpads2 at TDWG this year, so we need to start booking in training courses. Suggestions for venues are sought.
  7. Special publication
    We are suggesting a ViBRANT Special Issue to be published by Pensoft to be published before the Life & Literature conference.  Potential authors have been contacted directly.
  8. Travel funding for events outside Europe
    All partners are free to use their travel funds for any purpose associated with ViBRANT.  It is required that we alert the Commission to Conference travel outside Europe to ensure that the auditors don't reject the claim.  
  9. Associated grant proposals
    NHM & Oxford have recently submitted a proposal to the UK's BBSRC in conjunction with EBI.  If funded it will provide support for molecular data in Scratchpads.  There are potential benefits to WP5 and to WP6.
  10. Events calendar & training
    Events are now listed on the web site. This item is an opportunity to raise questions about ViBRANT's participation in up-coming events.
  11. External links
    Links to external projects are now on the web site. This item is an opportunity to discuss the appropriateness of including any particular link.
  12. Future meeting dates
    03 November 2011 from 12:00 to 04 November at 12:00
    18 January 2012 from 10:00 to 12:00
    18 April 2012 from 10:00 to 12:00
    18 July 2012 from 10:00 to 12:00
    17 October 2012 from 10:00 to 12:00 to 18 October at 12:00
    16 January 2013 from 10:00 to 12:00
    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

  13. Any other business



Vince Smith, Project Coordinator Dave Roberts, WP 1 Leader
Simon Rycroft, WP2 Leader Isa van de Velde, WP3 Deputy
Olaf Bánki & Wouter Loss, WP4 (only for part of the meeting) Neil Caithness, WP5 Leader
Lyubomir Penev, WP6 Leader David Morse, WP7 Leader
Christos Arvanitidis, WP8 Leader Lucy Reeve (Admin)


  1. Apologies
  2. Thierry Backeljau, WP3 (Isa Van De Velde deputising)

    Gemma Maldar, Finance manager

  3. Workpackage Summaries
    1. WP1 – Dave Roberts, NHM

    2. Nothing specific to report; all issues relating to WP1 are agenda items.

    3. WP2 – Simon Rycroft, NHM

    4. Good progress is being made on the upgrade to Scratchpads 2. The issue with the server has been resolved. Milestone 2.10 has been delivered, and 2.11 will be complete within the next 2-3 weeks. The server deliverable that is due at 12 months should be on time.

      There are no deviations from budget or workplan at the moment.

    5. WP 3 – Isa van de Velde, RBINS

    6. Ambassadors programme is making progress. No groups have been set up yet. Scratchpad usage data is being analysed to identify potential ambassadors.

      The Scratchpad questionnaire on helpdesk services and training is to be released next week.

      Outreach and Scratchpad studies’ preliminary results were presented at a symposium in June.

      WP3 are working on flyers.

      VS is following up with IV and Irina Brake re Scratchpads 2 and ambassadors. A slow build up is expected.

      There is currently no deviation from the workplan or budget.

    7. WP4 – Oláf Bánki & Wouter Los

    8. In the absence of OB and WL, DR provided an update. With OB moving to GBIF, WL will be taking over leadership of WP4, pending approval by the rest of WP4. OB will be looking after nodes in GBIF, which links directly to WP8 so OB is still likely to be involved in ViBRANT. This will result in stronger connections with GBIF and LifeWatch.

      OB and WL joined the meeting after the WP5 update.

      Milestone 4.10 has been completed this week and the entry on the website will be updated accordingly.

      BGBM is changing their workplan slightly and in August a new workplan will be delivered for WP4.

    9. WP5 – Neil Caithness, UOXF.

    10. NC has contacted Régine to get the 3TA package (3 Taxon Analysis) wrapped for Milestone 5.14, but this is not ready. There are other options such as BEAST.

      Action:  VS and NC to speak regarding ranking the different options

      Action:  Joint WP2 / WP5 meeting including Irina Brake to find a pool of users with the right requirements

      Phylogenetics – David Cunningham at Maryland – can possibly route jobs to their server but no contact has been made with him yet.

      OBOE – how to deliver – to be discussed at the WP2 / WP5 meeting.

      VS reminded all to be mindful that many users will only access these analytical services intermittently.

      Action:  Other WPs requiring computational intensive services should contact NC (e.g. literature markup)

      Milestone 5.15 has been completed.

      Currently investigating other parts that could be linked in for Milestone 5.16. The Windows cluster is problematic but there are other options, and there is no need at the moment. Once BEAST implemented we can then look at the supercomputer architecture.

      Using GBIF specimen locality data. Obtained permission from GBIF to take a local copy of the data. Awaiting Oxford University Legal Services to do data sharing agreement then will copy all the data onto a local machine.

      Working on spatial analyses. Looking at what potential users want from this. SR and Ben Scott are also working on mapping with Scratchpads, and ViBRNT is producing a tool in conjunction with Kew for the Red List.

      Action:  NC to discuss with Javier de la Torre, SR and Ben Scott

      VS reminded everyone that if something is developed with ViBRANT money it must be branded. This is an EU requirement. Links should also be posted onto the ViBRANT website. The branding should be subtle and not normally dominant.

    11. WP6, Lyubomir Penev, PENSOFT.

    12. Milestone 6.11 is ready already – developing an extended version agreed by ZooRecord. Same process with IPNI. Has also talked with Paul Kirk re. Index Fungorum.

      Workflow guidelines have been published.

      Automated harvesting from CITEBANK to Mendeley.

      Published paper and workflow of automated export to Wiki.

      Automated harvesting by PLAZI.

      Automated dissemination workflow in advanced stage.

      Currently working on rewriting publications module and facilitating integration into Phytokeys and Mycokeys.

      HTML forms for ZooRecord have been created and will be linked to the input system for manuscript submission .

      Goal is to produce the right forms.

      There is no need for WP2 to work on publication module yet.

      We have had agreement from Dryad to integrate our system with theirs. From Dryad data can flow to other appropriate repositories such as TreeBASE. Dryad has an agreement with GenBank and seems to be growing in importance as a major dataset portal.

      GBIF data publication format has been decided; guidelines are available

    13. WP7, David Morse, OU.

    14. Overdue milestones are in progress. Updates are available on the Scratchpad Wiki and outstanding work should be finished by the end of July.

      The WP 6/7 meeting at the beginning of June highlighted the overlap with old literature and new literature requirements. Opportunity to share/copy code between WPs to avoid duplication of effort.

      Plan is to open up GoldenGate to create parts as a web service to integrate into other apps. API is working and working towards extracting bibliographies from legacy documents. Progress is being made towards segmenting documents automatically. Identifying bibliographies is not as far on as splitting them.

      Action:  VS & DM to speak to identify testers of bibliosplitting tool

      Action:  DM & NC to arrange meeting re services to run computer-intensive parts

      The WP7 product 'Bibliography of Life' is looking at CiteBank to be the preferred host for pushing information out.

      Chris Freeland has NSF grant to further develop CiteBank. CiteBank has been reluctant to put effort in to taking metadata of marked up reference lists as well as new publications due to lack of funding. If funding is now in place this should not be an issue.

      WP6 to expand export to CiteBank.

    15. WP8, Christos Arvanitidis, HCMR (written report received after the

    16. CA received no news from MfN on milestone M8.11. Alex was in the WP8 meeting in Crete and he agreed to deliver this on time. CA will contact him as soon as he is back to Crete.

      The pilot project ( is already up and running with good feedback from all kinds of interested users. We have an automated counter on the front page that shows the number of observations uploaded in our system and the number of dives.

      There are no deviations from budget or workplan at the moment.

  4. Coordinators report

  5. We are negotiating publication of a special issue with Pensoft in ZooKeys. Partners and users of ViBRANT have been contacted and all those contacted are willing to contribute manuscripts. Additional requests to contribute have also been received. An email will be sent at the end of the week regarding this.

    Manuscripts deadline is 26 September, to be published before the Life & Literature conference in Chicago. This will be directly useful for the annual report.

    There are lots of copies of Scratchpads and ViBRANT leaflets. The website is being updated with links to these.

    There is a need to brainstorm re services for NC service centre.

    ViBRANT needs to know about grant applications where there is overlap with ViBRANT; this is an impact indicator. A pre-proposal has been submitted by DR. Information on grant applications needs to be kept confidential so website is being worked on to accommodate this.

    VS congratulated the team for the progress made so far.

  6. Reporting

  7. Almost all the 6-month reports have been received. Most of the next tranche of payments have been released with the remainder to follow once the reports have been received.

    The same process will be followed next year as it is easier to gather the data in this manner.


    Action:  DR to make reports available to WP leaders confidentially

  8. Special Clause 39

  9. DR reminded all about Special Clause 39; Open Access publications.  We agreed to deposit an electronic copy of the published version or the final manuscript that relates to ViBRANT in an institutional or subject-based repository within a year of publication. Publications should be listed on the ViBRANT site and a link to the open access copy given there.

  10. Outreach & publicity

  11. Leaflets will be available on the website soon.

    SR and Ben Scott are attending TDWG and plan to demonstrate Scratchpads 2.

    Action:  DR to circulate list of TDWG participants

  12. Special publications

  13. VS covered in the Coordinator’s report.

  14. Travel funding for events outside Europe

  15. All partners are free to use their travel funds for any purpose associated with ViBRANT.  It is required that we alert the Commission to conference travel outside Europe to ensure that the auditors don't reject the claim.

  16. Associated grant proposals

  17. VS covered in Coordinator’s report

  18. Events calendar and training

  19. These are on the website. The bibliography is up as are talks and presentations. The information has been taken from the reports. The dissemination table will be taken from submissions. Not quite complete.

  20. External links

  21. Links to external projects are now on the web site.

  22. Future meeting dates

  23. Action:  DR to repost dates of next meeting taking place at NHM.

    NB this has been done and teh meeting is now scheduled for 3rd + 4th November 2011.

    The next meeting will be preparation for the review, taking place possibly early February. Desk Officer will confirm who is to attend the review; likely to be VS and a few others, not all WP leaders. To be confirmed.

  24. AOB

  25. Flyers will be available when they have been printed.