Venue: Sofia

Start: 10:30 EEST

Duration: 1 day

Meeting 6 : Agenda [9 Feb 12; final 11 Apr 12]

1. Apologies for absence

2. Project Co-ordinator's report

3. First Annual Report

4. Workpackage summaries [WP leaders]:

   1. Progress highlights;
   2. Milestones; highlighting new milestones
   3. Task - milestone - deliverable mapping;Such a mapping was required of us by the reviewers.
   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. We should formally replace Annex 1 with a new workplan, so changes to tasks and descriptions are allowed here.

    

5. Budget adjustments
   The project reported a large underspend in year 1. We need to be confident that partners that underspent will be increasing activity in the year coming. This is tempered for the UK partners because the exchange rate has been unexpectedly strong against the UK pound.

6. Outreach & publicity
   The public-facing website has been updated and organised around tasks rather than workpackages per se. Notice of the new pages has been circulated and task leaders are encouraged to update and enhance their pages as part of the public outreach programme.

7. Travel plans
   This year's TDWG will be in China. 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.

8. Follow-on grants
   The final call for FP7 is likely to be very well funded. We should be aware of suitable opportunities for this successful consortium. At the time of writing (Feb 12) we have not yet seen the draft calls for Infrastructures. If anyone gets access, please circulate.

9. Biodiversity Informatics White Paper
   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.

10. Associated projects

    1. eMonocot
    2. agINFRA
    3. BioVEL
    4. EU-BON - submitted
    5. JRS Biodiversity Foundation - submitted




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

    1. 18 July 2012 from 10:00 to 12:00
    2. 17 October 2012 from 10:00 to 12:00 to 18 October at 12:00
    3. 16 January 2013 from 10:00 to 12:00
    4. 17 April 2013 from 10:00 to 12:00
    5. 17 July 2013 from 10:00 to 12:00
    6. 16 October 2013 from 10:00 to 12:00 to 17 October at 12:00





13. Any other business

1. Software for video conferencing.

We are investigating GoToMeeting and Adobe Connect as potentially better distance-meeting solutions compared with Skype. Both are paid-for services and we'll initiate trials (very short meetings just to look at the software).

2. Mid project meeting

We suggest that there would not be any benefit to the project from a mid-term meeting. We do consider that more small-group meetings (e.g. some or all of a workpackage) would be beneficial and propose directing the travel funds to that purpose.

3. A plan for developing a field course teaching exchange

 

4. Scratchpad training courses for project partners

 

Parallel Technical Workshop

Documented on ViBRANT wiki

Actions

Delegates;

Minutes

2. Apologies

   Gemma Maldar, Finance manager (GM)

2. Project Coordinator’s report

   The aim is to put in place sustainable activities for successor applications. ViBRANT is getting a lot of international recognition, e.g. invites to policy level discussions. DR is involved in White Paper to take forward the agenda of biodiversity informatics.

   From a user perspective the adoption of Scratchpads (SP) is growing extremely quickly. This is partly because of SP2, partly because of ViBRANT training activities and promotions. Promotional activity on SP site is being improved this year. SP are continuing to grow and new communities are engaging.
   There are three key areas to improve:

   Communication:

   The meeting agreed that the mid-term project meeting be abandoned and the funds redirected towards smaller focussed meetings organised by, but not restricted to, WPs (AOB item 2). These should be focussed on one topic, usually of a technical nature. Discussions on topics is expected to include more people. A new free “topic development” forum section was not generally supported. There is a feeling that partners who are not WP leaders are being left out. There should be more effort to engage these partners in relevant workshops and meetings.

   We also need to sell ViBRANT services more successfully. DR’s presentations are on the website and there are other resources on Slideshare. There is also a promotional video on the ViBRANT site, although its a large file.

   WP focus:

   Some of the WPs need to have more focus on their key mission in the project, or in some cases to identify a clear focus. The aim of ViBRANT was to be agile and the reviewers recognised this. Each WP should identify their key role as a thread for reporting at the next review. WP leaders should identify what each partner involved should be contributing and be thinking about “cross-fertilisation” with other projects e.g. AgINFRA, BioVel. EU-DAT is another new project developing workflow system for exposing datasets who are keen to work with ViBRANT.

   “Killer deliverable”:

   The Zookeys special issue had an enormous impact on reviewers. What will be the equivalent talisman next year? The EU want to see linkage of services and a big punch can be made out of the links between services. Linkage with projects eg BioVeL and AgINFRA are key. ViBRANT is the first agile project within the EU and it is important to make it a success as it is an exemplar.

2. First annual report

   VS, DR, TB, SR, LR and Dave Remsen went to Brussels at end of January for the first year review. The review went extremely well and has been circulated. Overall it set an excellent tone for subsequent reviews. Carlos Morais-Pires represented the Commission instead of Krystyna Marek. Krystyna has subsequently moved to a different department so Carlos is ViBRANT’s interim Desk Officer until a replacement is identified.

   Two actions arose from the review: mapping of milestones to deliverables, and how changes to the workplan are managed. The reviewers were happy with the comments on the website on delays to milestones. WP1 will undertake the initial mapping, but WP leaders are reminded of the need to link to an identified deliverable when defining new milestones. Changes to the workplan will be managed through an increased communication effort. Ideally changes will be discussed on the forum which will act as a record of communication.

2. Workpackage summaries

   WP2

   SP2 was released slightly later than planned. So far the response has been very good. There are a number of testing sites that ambassadors have have been using and they are providing feedback – bugs are being fixed quite quickly. Next thing is the migration of SP1 sites which will start in April. Ed Baker (e-Monocot) has developed an e-Monocot-specific SP2 profile. GBIF are developing a profile for the GBIF nodes portal toolkit. EOL and AgINFRA SP profiles will be developed.

   WP2 relied heavily on Dw-C Archive for WP4. WP5 is making OBOE services accessible from SP. The initial module has been developed which is fully dynamic but hasn’t been integrated tightly into SP yet. WP2 has been working on publication module with WP6 which is awaiting stabilisation of the code base by WP6. The SP registry will be developed in conjunction with GBIF's registry and is due for delivery in May.

   e-Monocot is developing a specific portal tool to the CDM and, given the parallel nature of the two projects, we need to look at what BGBM are contributing to WP2 in the light of a changing landscape.

   WP3

   Training sessions for SP maintenance have been updated. Four basic courses and two advanced are planned for 2012. In addition, two Ambassadors training sessions are scheduled. Additional courses are planned on demand e.g. in Italy in 2013. SP2 released and Irina and Isa are testing. Content on basic and advanced courses and online help wiki pages is being updated. Screencasts are being developed on certain topics. There are currently 14 Ambassadors; more are being recruited and effort is being made to actively involve them, e.g. in testing.

   Sociological studies represented ViBRANT at a workshop and submitted paper with the OU (WP7) to PLoS ONE. Data from SP users database is being cleaned. The User Survey 2011 report is being written and User Survey 2012 is being prepared. A focus group introducing SP users is being developed to gain insight into content and expectations of users. ViBRANT is involved in barcoding conference (September 2012) with a demo showing what SP can do.

   More milestones, linked to deliverables, need to be developed as there are only two planed. D3.2 needs some clarification.

   There are interdependencies with WP2 for support services, beta testing and collection of user data, WP7 for developing alternative metrics and WP1 for website updates.

   In terms of outreach, the overall aims of ViBRANT need clarification, especially as the agile process modifies the workplan. Suggestions are sought about how these changes can be described for outreach purposes.

   Irina will be moving on from ViBRANT on 24 July. Laurence Livermore (e-Monocot) has been working on helping with SP2 transition, has very good knowledge, is dealing with issues in context of e-Monocot and running training programmes. He could potentially pick up on some of these. His contract doesn’t finish until April 2013. We need to enliven the training activity in the context of SP2 and how we make best use of Irina’s time whilst she is still with the project. There would still be funds in the RBINS budget to employ someone for two days per week for the remainder of the project. Ideally they would need to be based in NHM to work closely with WP2. Laurence would be quite well suited to inter-community training.

   WP4

   M4.19 is delayed by one month.

   BGBM continue to develop import/export routine linking the CDM with Scratchpads and e-Monocot. As partners in BioVeL, BGBM have an excellent opportunity to coordinate activity.

   YdJ to discuss with WP1 how Gregor Hagedorn's (GH) work with wikis and keys can be better harmonised within ViBRANT, specifically the connectivity within knowledge organisation community. GH is proposing work on mobile devices.

   GBIF are working on a set of tools for the development of vocabularies and they prefer to use repository rather than to store individual datasets. This would be a fixed version, with fixed URIs for terms. The use of wikis in this context raises issues of how to apply changes. They created a bioportal and they are evaluating user demand before developing further. Dave Remsen is going back to Woods Hole 25 April and retaining 25% commitment with GBIF. Dag will be taking over the ViBRANT work and will likely to need quite a lot of support. YdJ remarked there is no real leadership of Knowledge Organisation Systems (KOS) in GBIF.

   The landscape around vocabularies, thesauruses and ontologies is complicated, although attempts are being made to pull it together. FAO have made developments in KOS and have specialist Drupal modules that use agroVOC. GBIF are keen to talk to FAO. FAO has the leadership skills but not the developers.

   Action: Videoconference with YdJ, DR, VS, Donald to talk about leadership with KOS with view to arranging larger meeting to get a sense of the landscape. GH to be included in second meeting.

   The registry is a clear starting point: what have we got; how is it being used; and what is its potential? We need to make standard vocabularies easily accessible. Markup can use some vocabularies but we need the tools and to persuade people why it is important.

   At the Global Names meeting YdJ suggested, unsuccessfully, using SP to build proto-GSDs. Why not, what would help to make it possible?

   Action: Tangible, realistic milestones are required.

   WP5

   OBOE has its own front end website. Loosely coupled nature of using virtual machines to do computing and communication between OBOE web app and virtual machines via a Dropbox. Two years of new funding from Statoil have been secured for continuing the development of LEFT (to 30m resolution). Each service can get its own front page (e.g. LEFT). SP now also has link to submit OBOE jobs. It is necessary to advertise the services, e.g. by making the front pages pretty. This would be really good for outreach for GBIF – need to tell GBIF about this. NC demonstrated an OBOE task using LEFT to the meeting, which was very well-received.

   BioVeL are holding a workshop at which NC and Dauvit have been invited to speak about OBOE and LEFT (9 May, Gothenburg). VS invited NC to speak at a workshop at Kew on 28 May.

   IUCN won’t let UOxf use the distribution polygons of endangered species in a paid-for service so, UOxf is developing its own. There are a number of IP complications. Ecotrip and Ecofield are plans; Ecofield would be a phone app collecting species occurrences. It would show you maps of vegetation, ecoregions etc., and ask to take photo of places of interest. A potential IP complication exists in creating spin-off products from LEFT. There has been a lot of interest from the agricultural sector, so there is some overlap with FAO. Scaling issues are likely to come up very soon.

   It was noted that one way of funding sustainability of the project is through the private sector.

   BioVel, NERC application submitted and publication in Nature involving OBOE. A BBSRC application is to be submitted to continue development of OBOE.

   An Android app has been developed which was not anticipated at the start of the project.

   The main interdependency is with WP2.

   There are broader issues within WP5, specifically harmonising the work of UPMC, Vizzuality & JKI perhaps with a seminar workshop on batch or API-based services.

   Action: NC to arrange seminar before September.

   WP6

   Most of the resources are currently directed to creating the Pensoft writing tool (PWT). Other activities include an automatic export of metadata to Key Central and an exemplar paper converting text into DwC-A.

   LP demonstrated Pensoft writing tool to the meeting. Peer review can be conventional, open or public, defined by the journal and then by the type of paper or author’s choice. Plates as well as figures, audio, 3d images etc. can be added. Whole databases can be submitted. References are automatically marked up correctly. The tool, not specific to taxonomy, is to be finished in in May and will be tested before the official launch. After publication an export module will be created. There are plans to produce a gallery paper which describes a collection of images.

   M6.15 is going to be delayed. Additional milestones need to be added. Prototypes of XML queries have been made and implementation will start in May. Launch of a data journal is expected in Feb 2013 but might be able to be brought forward to autumn 2012.

   There are plans for many more developments, e.g. DwC-A viewer.

   WP7

   There are links with WP3 treating logs of SP data as data to be mined and with WP6 on increasing connections in RefBank. BHL's decision to re-purpose CiteBank meant that RefBank was developed on a very short time-frame. It currently holds over 80k references but reference loading has stopped temporarily to concentrate on milestones.

   Milestones: 7.21 done. Some milestones need to be re-prioritised as the mark-up milestones are behind schedule. These will be pushed back and RefBank milestones will be brought forward. Need to re-evaluate the markup milestones to see if they are still relevant. AgINFRA is looking at taking old text and passing to supercomputer to do extraction. If they succeed markup milestones will be redundant. There is an opportunity to have a meeting about markups.

   There is a need to work more closely with WP2 over how to integrate different bits of RefBank and markup into SPs. There is a wiki page that all partners involve need to update regularly so that we know where we are with references. It is crucial to keep re-evaluating. It is essential that we link to Mendeley, which has become the largest assemblage of references. We need to think more about the interface that RefBank is using. Within the workflow we need to have some more direct user service. How might people use the resource?

   Still don’t have the CiteBank dump so need to chase Chris Freeland.

   WP8

   The reviewers were very impressed with COMBER and also that there was activity outside the training areas. Most time this year has been spent on scaling. This summer the owners of diving classes are going to be trained and they will try and sell out as a service, which is essential for sustainability. If successful it will link to another proposal to link on a national scale. One of the next products will be to test whether the data is meaningful and can be used. There is an issue with training courses for next year’s dive schools. The training budget will pick up on this (Action: CA to contact TB).

   Some milestones have been postponed as lots of jobs have to be done in collaboration with WP2 and WP5, COMBER and APIs to link indices with WP5 and provide calculations to ViBRANT portal. Can some of the analysis tools be picked up and integrated to make them available within the context of the COMBER framework?

   A paper was published showing a change in the way species are being described with the aid of micro CT tomography, which we would like to develop as a resource.

   WP8 overspent during Yr1 and likely to overspend in Yr2. This was forecast and will be managed by a reduced Y3 spend.

   Olaf will be taking over the GBIF WP8 tasks.

2. Budget adjustments

   HMCR will overspend in Yr 2 but this will managed in Yr 3 due to decreasing COMBER staff.

   RBINS have reported low spend on travel in Yr 1 which will pick up in subsequent years.

   MfN only had one milestone and have completed it so need to decide what will happen to their remaining allocation.

   UvA have an underspend due to travel. This will be picked up with the organisation of meetings and workshops.

   OU have underspent due to ill health. It is planned they will recruit a short-term post commencing at the end of July 2012.

   BGBM have an underspend. 11 person months have been transferred to UPMC but still only spent 16% on their direct costs. Need to obtain their plans in writing.

   Action: YdJ to negotiate with BGBM using financial details supplied by LR

   Action: NC to clarify UdlR's workplan.

   €17k were originally allocated for a Yr 2 general meeting and there is €10k per year for general travel. Bids are being accepted for travel funds beyond standard allocations.

   Around €300k remains unallocated. It was emphasised that no partner will lose money but unspent funds will be reallocated. It is preferable that this goes outside the UK as ViBRANT is very close to the UK limit of 40% total spend. Suggestions of identifying new products that would make a difference. There is potential to allocate some staff time to assist Guido with help on some issues particularly if located with Pensoft. CA advised the tomogram could be developed and linked to the WP6 work by embedding in a PDF a link to the gallery so full contact with the product there.

   Action: WP leaders to estimate meeting costs

   Action: DM and LP to cost person time for developing RefBank and publishing of tomograms.

   NC remarked that spinout services that WP5 wants to develop are unfunded. He would like to up his time to spend on these services. This was complicated by being UK based, so needed to be found with the UK portion of the budget.

   Action: NC to provide WP1 with estimated costs.

   Action: WP leaders to disseminate information to their WP

   Action: Bids no longer than one side of A4 with budget and concept to be submitted to DR

   NC would like to develop a teaching exchange programme consisting of a field course in conservation management. This would be a repeating course structuring around more modern bioinformatics tools. The course would repeat each year so data would be obtained. This is related to WP3. The framework of the teaching course could be run in other places. It was commented that there may be a problem with it being outside the EU. There would be issues with the amount of time input required. The proposal would need to go through the Desk Officer. There was significant support for this idea, based around a core infrastructure and specific content components. Interest was expressed by CA and DM. This is also known to be an interest in agINFRA, so DM will proposa a joint workshop to explore how the idea might be realised.

   Action: DM to liaise with agINFRA for a joint meeting, possibly in Athens.

2. Outreach and publicity

   Isa and DR have put together chromosome diagram on a webpage which has topics on it rather than WPs. Most people have had access apart from WP7. Once text has been approved it will be the new front page. Each page has a key resources block in top right and key outputs as well e.g. chapters from Vol 150 as PDF links.

   Action: All to check with people who are represented on the pages.

   SP.eu will be getting a revamp this year.

2. Travel plans

   WP2 plan to send two people to TDWG. A list of who is intending on going is to be coordinated. The contract is still not signed, but likely to be in China. Dates are 22-26 October provisionally but need to be confirmed. Note that many partners bid to attend TDWG meetings and already have budget.

   All were reminded that all non-EU trips must go through the Desk Officer. Permission is likely to be denied if not presenting.

   Action – bids to DR for TDWG and any other travel that is out of the ordinary or outside EU

2. Follow-on grants

   FP7 have spent this year’s budget for DG Research & Infrastructures. There will be a call for ICT but no realistic opportunity for ViBRANT is evident in the draft. We expect to get a draft of Horizon 2020 call in early 2013. The White Paper (item 9) is designed to influence the structure of that call. SUbmission is expected to be early summer with funding available from Jan 2014

   NHM expect to submit a bid to a UK Research Council with Oxford and EBI on molecular data workflows.

2. Biodiversity informatics white paper

   An item of correspondence has been accepted into Nature (proofs have gone back). Set up date for public meeting in Brussels on 17 July. Ecological community don’t understand the language being used. Complication is GBIF have organised their own review of biodiversity informatics (GBIC) on 2-4 July in Copenhagen. Paddy has organised session in IUBS (China 5-7 July) on virtually the same thing. (Note added after the meeting: this has been cancelled).

   Danger is GBIC and IUBS are closed meetings with rather different objectives. If the message is different from these than community-wide paper then the whole field will be damaged. No reason why it should as white paper is completely public. We need to encourage all partners to participate and get ViBRANT view expressed strongly.

2. Associated projects

   e-Monocot – overlapping activities that we need to monitor. Keys and portal issues are the big things. e-Monocot building network of monocot based communities and formed around one portal.

   agINFRA – 6 month progress meeting next week in Madrid. Main issues of interest are FAOs data, vocabularies (agroVOC), AGRIS (bibliographic data relating to agriculture) and AgriDrupal.

   BioVeL – next event in Gothenburg ViBRANT giving presentation. Taverna has released a Taverna server that can be installed on local machine, but we're waiting for next version. They can provide same dynamic service we do in SPs; any workflow that is in BioVeL repository can be dynamically called up and run via OBOE. Look at milestones in a few months and evaluate linking together. BioVeL want exposure to user base from ViBRANT to see what services are in demand. One of the services they were talking about is data cleaning.

   JRS biodiversity foundation – won’t be funded as was too expensive.

2. External links

   External links are currently private – BioVeL makes some public so ViBRANT could consider having some public.

   Action – DR to create new view that is public

2. Future meeting dates

   Doodle poll to be done nearer the July meeting as some people will be in Brussels so may be the possibility of having face-to-face if all people are going to be in Brussels.

   The committee gratefully accepted CA’s offer that the October meeting will be in Heraklion.

2. AOB

   CBOL use a software product called go-to-meeting and we have some experience with Adobe Connect. Not too expensive. There are some free options but they have problems with bandwidth. Flashmeeting is a free one, but is push-to-talk so you can’t all talk at the same time. All feedback gratefully received.

   SP training courses for project partners.

   Partners developing tools for use with SPs are encouraged to use the GIT repository to install a local development server. If these are to be maintained and made public, tell WP2 so that you can get the updates.