Date: 17th July 2013

Start: 09:00 BST

Duration: 2 hours

Meeting 11: Agenda

1. Apologies for absence

2. Actions from last meeting

3. Project Co-ordinator's report

   • Highlights from last 3 months (focus on integration)
   • Preparation for ViBRANT Final Report
   • ViBRANT Products Report (an appendix to the final report for public): develop and complete template
   • Products list: Scratchpads, PWT/BDJ, Platform for Cybertaxonomy, Biowikifarm, OBOE, Xper2, GeoCAT, RefBank and GoldenGATE(?), COMBER, CartoDB, GBIF NPT
   • Scratchpad case studies document (focus on exemplar communities using Scratchpads)

 

 

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.

    

5. Overdue Milestones to be addressed

    

   • M4.32 [due 31/01/2013] Integrating a wiki-glossary into the scratchpad
   • M4.22 [due 28/02/2013] BiolFlor Data as semantic web [NOTE deadline extended twice already]
   • M2.15 [due 31/05/2013] Biodiversity data citation metric [NOTE - pushed back one year to allow for further research and input from outside ViBRANT]
   • M2.19 [due 31/05/2013] Report on the options for a biodiversity data citation metric for data published through ViBRANT
   • M5.32 [due 30/06/2013] Tests and validation of the services in coordination with Workpackage 3

    

6. Budget report

7. Final Project Meeting

   Sapienza University, Rome : 3 Sept - 6 Sept

8. Follow-on grants

   • H2020 initial details, concept note and partner contribution form

 

 

9. Technical workshops

Topic	Organiser	Location	Date	Status
Workshop on RefBank/RefFinder	Lyubo Penev	Rome	Autumn 2013	Planned
Workshop on PWT/BDJ	Lyubo Penev	Sofia	Spring 2013 Sofia	Done
Workshop on the nature and structure of the biodiversity research field	Peter van den Besselaar	?	?	Proposed
Literature mining and markup using OBOE	David Morse	Rome	Winter 12	Will be part of September final project meeting
Text mining and markup with agINFRA and BioVeL	David Morse	Athens	January 13	Proposed

 

10. Travel plans

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 and we can present a clear case of benefit to the project. Travel is at teh discretion of the Project Coordinator. We expect all conferences for which ViBRANT funding is used to e listed on the web site. It will be used to build the annual report. Specifically, meetings need to be included under 'Presentations' under the 'outputs' tab.

11. Associated projects

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

 

12. 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.

13. Future meeting dates

    1. Sunday 27 October 2013 from 10:00 to 17:00 in Florence




14. Any other business

Actions

Delegates

Minutes

1. Apologies

None

2. Actions from last meeting

1. Liaise regarding suitable conference for launch of Bibliography of Life (LP & DM)

   Will be bundled with RefFinder and launched at TDWG or BIH2013.

2. Discuss potential new audiences for ontology workshops(YdJ & DR)

   Not done, carry forward.

   • Action – YdJ & DR to discuss potential new audiences for ontology workshops

3. Circulate budget (LR)

   Done

4. Discussion to resolve issues of late milestone delivery (YdJ, GH, DR)

   Done but ongoing issue complicated by GH moving to MfN.

5. Discuss with CA the potential of downloading modules and modifying for separate use (YdJ)

   Carried forward to next meeting

   • Action – YdJ & CA to discuss the potential of downloading modules and modifying for separate use

6. Resolve technical mechanism of integration of OBOE services with Scratchpads (NC & SR)

   In hand: NC meeting with Dauvit King to discuss.

7. Provide text on sustainability of OBOE to DR (NC)

   Done

8. Discuss preparation of promotional material for launch of BDJ (LP & TB)

   In hand. A flyer has been produced.

9. Send details of hackathon to DM (CA)

   Done

10. Send details of uptake of ViBRANT services by other projects to DR & VS (All)

    Nothing send so far.

    • Action – All to send details of uptake of ViBRANT services by other projects to DR & VS

11. Send DR details of any ViBRANT products missing from list for sustainability report (All)

    Done.

12. Add YdJ to final project meeting programme committee (DR)

    Done

13. Circulate draft final meeting plan to WP leaders and start advertising (DR)

    Done.

14. Evaluate the potential for a technical workshop at the final project meeting (DM, YdJ, GH)

    DM has done this, YdJ and GH haven’t.

15. Establish the status of agriDrupal (FAO) (DM)

    • Action – DM to prompt AgInfra on progress with agriDrupal & use of Scratchpad modules

16. Circulate request to WP leader for consensus over venue for final Man Comm meeting (DR)

    Done. The final Man Comm meeting will be held Sunday 27 October in Florence before TDWG starts.

3. Project Coordinator’s report

The focus of the BIH2013 is on integration and sustainability. The EU have asked that preparations be made for the next grant proposal.

ViBRANT is producing two public documents aimed at senior official audience, not technical experts. Two designers have been commissioned by NHM to produce these documents. One will be on ViBRANT products. The template will be circulated for text and images to be added. The second will be focused on Scratchpads and the user community and will be a case study document. Laurence Livermore is leading coordination to get the basic details. These documents will supplement the technical final report. The product list so far is:

• Scratchpads
• PWT/BDJ
• Platform for Cybertaxonomy
• Biowikifarm
• OBOE
• Xper2
• GeoCAT
• RefBank & GoldenGATE(?)
• COMBER
• CartoDB
• GBIF NPT

• Action – VS to circulate templates for booklet content.

• Action – All to send draft text when templates have been circulated

It will be challenging to produce the final report and periodic report due to DR's retirement and VS paternity leave. All are requested to draft text early to the report can be produced on time.

LR will email the deliverables to the Commission on 30 November 2013 so requests that the reports are not left until the last minute.

• Action – All to start preparing text for final report and deliverables

4. Workpackage Updates &

5. Overdue Milestones

WP2: Continued stable release of Scratchpads; improved process of releasing bug fixes, testing and updates. About 80% of Scratchpads 1 sites have been upgraded to Scratchpads 2, but still some large sites remain. NHM has a new, additional server, which is another step towards proper failover. Work on translation of Scratchpads is continuing, complete for Ukrainian and may be potential to translate into Thai.

M4.32 is out for testing. M2.15 and 2.19 are still overdue and need attacking. There is lots of overlap between these two milestones.

WP3: Training sessions are continuing with Ambassadors playing a crucial role. One has been held in Malaysia, two in Ukraine (one in Russian, one in English) and two are scheduled in Cameroon in September. Online training has also started.

Ambassadors are helping with translation of Scratchpads (e.g. Ukrainian).

ZooKeys special issue is in preparation, 15-20 papers.

Interviews with users are being held.

M3.15 will be delivered on time.

YdJ's contract is now sorted and he is employed by RBINS for the remainder of ViBRANT.

One slight budget deviation: Mac Mini server, capable of running the training sites without external internet, has been bought by NHM for Cameroon workshops.

WP4: DWC to CDM is done and is functional. Pipelines are in place. We need to show that we can use the pipeline to improve tools in CDM. Play day is planned to show how pipeline can be used.

ViBRANT index developing as index to search data between platforms. Also used to access different Scratchpads within the Scratchpads platform.

ZooKeys special issue will be a major outcome. 57 data papers of all major groups in Fauna Europea in BDJ which is very good news.

There is an issue with the development of the MediaWiki. Gregor Hagedorn has moved jobs so is slow in delivering. There is also an issue with MediaWiki and Scratchpad integration. Direct pipeline is not the direction that is being taken; a pipeline between CDM and MediaWiki instead.

YdJ is visiting Dauvit King to see to what extent can use text mining tools (ViBRANT/BioVeL interaction)

Number of users of CDM need to be increased before final report.

• Action – YdJ and DR to discuss issues with CDM & MediaWiki, and delayed milestones

WP5: Global names recognition and discovery service (GNRD) is running on OBOE. We want to package as services on OBOE and we need a use case for use of GNRD. The reason for running through OBOE is that the original form does not have ongoing funding.

• Action – NC to circulate request for feedback on uses for GNRD

M5.32 is in hand and will be complete by early August.

WP6: Peer review process is starting on BDJ, with 30 submitted manuscripts. This is reliant on ViBRANT participants to act as editors providing feedback on the system. To be finalised second half of August 2013, with the aim of publishing the first wave on 1 September 2013. ViBRANT consortium to help with reviewing.

The RefFinder Tool is already functioning, with the preliminary workflow to be completed mid-August. Design of Bibliography of Life (BoL), including RefFinder and RefBank, will be demoed in BIH2013 and BoL launched at TDWG.

Extra funds for promotion of BDJ will be used.

• Action – VS & LP to coordinate publication and promotion of BDJ

WP7: RefBank has now over 200,000 references. Working on robustness and sustainability. The source code is available in the Scratchpad git repository . Nodes are being set up throughout Europe.

Conferences are being attended to promote RefBank and other products.

We are looking into integration with Scratchpads.

A joint bid with Peter van den Besselaar (PvdB) “digging into data” call is in preparation.

Usage of RefBank is currently rather low, probably because it isn’t very visible.

• Action – DM to provide information on usage of RefBank

WP8: M8.21 and 8.23 are delayed; both need collaboration with WP2.

M8.18 is basically done. The webpage needs more work and final testing is being done.

M8.20 is being worked on with EMBOS (Herman Hamill coordinating). This will have big usage but need to test stability and robustness of indices.

Alex Kroupa has promised an app for citizen science recordings by 1 September

• Action – CA to follow up with Alex Kroupa

Five Israeli people have been diving collecting data on assemblages. They are keen to take up COMBER protocol to implement in dives in Cyprus and will use in Israeli citizen science.

Paper has been submitted to BDJ and is going through the review process. 80+ students are taking part in a course (MSc level) as part of another project. A paper arising from this will be submitted to the BDJ.

• Action – CA to provide an itemised list of WP8 products

SR was aware of M8.18 but not the others.

• Action – CA & SR to liaise re milestones M8.21 and 8.23

6. Budget report

Form Cs to sign were received from Commission and circulated to partners 16 July 2013.

• Action – WP leaders to chase partners for return of signed copies

Budget updates and forecast requests will be circulated so Management Committee have an accurate view before the final Management Meeting.

• Action – LR to circulate updated budgets and requests for end of project forecasts

7. Final project meeting

Venue has been finalised: Sapienza University, Rome..

All slots have been filled apart from the slot on ecological modelling, as all the speakers approached were unavailable.

The purpose of the final meeting is to bring people together to develop consortia to bid for funds for H2020. Based on sight of a confidential draft, the focus will be on “big data” i.e. the Grid, e.g. integration of trait-based information with molecular information..

8. Follow-on grants

A BBI proposal with EBI Cambridge has been submitted by NHM. There is a relationship with SYNTHESYS 3 which starts 1 September 2013 (NHM coordinating).

A very early draft of the call details for DG-CNECT has been received. The focus is on big data and high performance computing.

• Action – VS to circulate in early August a concept note with themes of how ViBRANT would fit in as an online form. To be discussed at BIH2013

There may be place for ViBRANT in Research Infrastructure #5: Community Data Services (call in 2015), or topic #10, which seems to be a mirror of where currently at. There is likely to be a call in 2014 with a preliminary budget of around €20m.

It will be necessary to identify potential partners outside the ViBRANT consortium who are well-linked to grid etc..

There may be scope for smaller projects in certain areas for modest amounts.

9. Technical workshops

These workshops have been pending for a long time now so unless informed otherwise they will be removed from the list and any ringfenced budget will be redistributed.

• Action – All to find out if any of these workshops are going ahead and inform DR.

10. Travel plans

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 funds partners to travel outside Europe only if they are presenting and we can present a clear case of benefit to the project. Travel is at the discretion of the Project Coordinator. We expect all conferences for which ViBRANT funding is used to be listed on the website. It will be used to build the annual report. Specifically, meeting need to be included under ‘Presentations’ under the ‘outputs’ tab.

All requests for travel outside Europe should be sent to LR with details of the event, what presenting, estimated costs and the benefit to ViBRANT.

11. Associated projects

Updates were not given as time was running short.

1. eMonocot
2. agINFRA
3. BioVEL – solid collaboration as Alex Hardisty and DR organised BIH2013
4. EU-BON
5. LifeWatch
6. Pro iBiosphere

12. External links

Links to external projects are now on the website.

13. Future meeting dates

Sunday, 27 October 2013 from 10:00-17:00 in Florence

14. AOB

VS advised the Committee that the final review meeting will require all WPs to be represented. The final meeting will be in January 2014 (details to follow later).