Consolidated ViBRANT Project Final Review Presentations

9.30 Welcome and introduction of participants9.35 Overview of results & achievements, incl. a summary of budget & resources V. Smith

RESEARCH ACTIVITIES10.05 WP2: Technical architecture S. Rycroft (NHM)10.25 WP7: Biodiversity literature access and data mining D. Morse (OU)

NETWORKING ACTIVITIES10.45 WP3: Training, outreach and community support T. Backeljau (RBINS)11.05 COFFEE BREAK11.30 WP4: Standardisation Y. de Jong (RBINS)11.50 WP8: Ecological and conservation data mobilisation C. Arvanitidis (HCMR)

SERVICE ACTIVITIES12.10 WP5: Interaction and services N. Caithness (UOXF.E9)12.30 WP6: Scholarly publishing L. Penev (PENSOFT)12.50 LUNCH

MANAGEMENT & IMPACT14.00 ViBRANT impact and product sustainability V. Smith14.20 WP1: Management and Financial matters V. Smith14.50 Additional discussion (if necessary) All

15.10 Reviewers meeting with Project Officer Reviewers and PO15.30 Quick feedback from reviewers All15.45 Contingency (in case of over run)

End of review for the consortium16.00 Preparation of review report Reviewers and PO

Meeting agenda

Wednesday 29th Jan. 2014EC premises (Room 0/S5)Avenue de Beaulieu 25

1160 Brussels

ViBRANT Project Year 3/Final Review Meeting – Brussels 29-01-2014

Overview of results & achievements

Vincent SmithNatural History Museum London


Project coordinatorVincent Smith

WP Leaders1: Dave Roberts NHM, UK

2: Simon Rycroft NHM, UK

3: Thierry Backeljau RBINS, BE

4: Yde de Jong/Wouter Los RBINS, BE/UvA, NL

5: Neil Caithness UOXF.E9, UK

6: Lyubomir Penev Pensoft, BG

7: David Morse OU, UK

8: Christos Arvanitidis HMCR, GR

The Project ID


Project number: 261532

Start date: 01 Dec 2010

End date: 30 Nov 2013


Overview of results & chievements

17 partners in 9 countries(universities, museums & 2 SMEs)


Project’s concept and objectives


VisionConnecting the people, data & science of biodiversity

PositionOpen & sustainable development of a federated network of biodiversity informatics infrastructures

MissionFacilitate the mobilisation, sharing, reuse and publication of biodiversity data


1. provide sustainable services in data mobilisation, integration, publication, sharing, use and reuse to research communities and the European public

2. connect end users of biodiversity data to networks of primary producers

3. provide means to establish and document the state of the art in biodiversity research

4. identify research and development needs and gaps in the provision of support to biodiversity researchers

5. provide an information centre for biodiversity research results

6. defragment access to biodiversity data

Project’s concept and objectives




Interconnecting nodes in an federated network that retain operational autonomy


Our Products for


Promoting open access publishing and literature mining

Biodiversity data Journal

Pensoft Writing Tool

Bibliography of Life

Integrated online manuscript-authoring platform 50 manuscript submissions within first month

Novel open access journal for data publication 65,000 unique visits within three months

Freely accessible bibliographic citationsOver 215,000 references



Enabling data visualisation and computation

Our Products for

OBOE

CartoDB

GeoCAT

Ikey+ / Mkey+

Web-based platform for computing applications

13 computational tools

Rapid geospatial conservation assessments

1000 assessments in 2012

Online services for identification keys

Over 250 uses per month

Open source visualisation platform

26,000 subscribed users


Our Products for


efficient interoperability

Knowledge Organisation System

Platform for CybertaxonomyEffective links with Scratchpads for major European checklists

Controlled vocabularies for data mobilisation and aggregation


Our Products for


facilitating community support & participation

COMBER

Training and OutreachSupport and train users - enable community grow

38 training courses453 participants20 Scratchpad ambassadorsNew scratchpads.eu portal

Citizen science project for divers and snorkelers

5,650 marine species observations by citizen scientists


The ViBRANT Network hub


Enter, structure, curate, link and publish biodiversity data online

7000 active users in 630 vibrant communities

Over 260 citations in peer reviewed papers


Scratchpads case studies


Citizen ScienceAnimal Biodiversity

Plants Conservation

| 4 out of 630 communitiesSolanaceae source

Diatoms onlineAfrican Ichthyology Portal

Sampled Red List Index for Plants

Agriculture - Horticulture


Publications

62 scientific papers (59 open access)with a rate of c. 2 every month

Incl. Nature , PLoS One, BMC Informatics, BMC Ecology, ZooKeys & Biodiversity Data Journal

Selected publicationsThree special issuesZookeys vols 150, 209 & 365

The white paperHardisty, A., Roberts D. and The Biodiversity Informatics Community. “A Decadal View of Biodiversity Informatics: Challenges and Priorities.” BMC Ecology 13 (2013)



Conference presentations

105 conference presentationsreach out to more than 10,000 people (incl. researchers, policy makers and the public)

Meetings/workshops• Biodiversity Informatics Horizons 2013

in Rome, Italy• 96 workshops with more than 4,000

participants (incl. 38 Scratchpads training courses)



ViBRANT brochure

Presenting the major ViBRANT products Structured to address a wider audience32 pages full colour

Scratchpads brochure

Presenting Scratchpads functionality through several successful case studies by several biodiversity communities 24 pages full colour



Year 2 review feedback


Strengthen integration and clarify the main end products of the projectYear 3 was focused on integration activities and promoting main ViBRANT products

Attribute more emphasis on dissemination and hands-on training, including the organisation of final event and widening user communities. More training and dissemination activities than year 1 & 2. Online & on-site training, ambassadors activities, brochures

Prepare by 31st March 2013 a note outlining the activities and tasks to be accomplished in the last year, indicating the priority and time by which they are targeted to be achieved.Prepared and submitted

Prepare by 31st March 2013 a note summarising the changes brought to the DoW to date, and introduce subsequently a request for contract amendment, including contractual modifications and the updated DoW.Prepared and submitted

Deliverables should be more substantial content-wise and respect FP7 guidelines for project reports. In particular the final report should present clearly project results and their applicability, added value and impact.Included in the final report


D1.1 - Overall ManagementReport on the project overall management procedures

D2.3 - Financial sustainabilityProject’s financial sustainability model

D2.4 - Unit testingDistributed and automated unit testing mechanism for Scratchpad code

D3.3 - Community delivery and evaluationAssessment of a self supporting open source community for sustainable implementation

D4.3 - Design of robust servicesDevelop robust services, based on usage statistics and user feedback

D5.3 - Sustainable software servicesRefined and sustainable software services available for public use

D6.3 - Data publication workflowDescription of workflows and tools developed or upgraded by Pensoft in the course of the ViBRANT project

D7.3 - Literature searchDevelop the literature search software

D8.3 - A start-up portal for discovery of GBIF mediated dataDelivery of a Scratchpad based start-up portal for discovery of GBIF mediated data

Year 3 deliverables


all completed on time on line


Budget breakdown for the project


REDACTED



Type of Position (paid by the project positions) Number of people

Scientific Coordinator 1

Work package leaders 8

Experienced researchers 44

PhD Students 9

Technical staff 34


Sustainability outlook• 8,500 active users (7,000 in

Scratchpads)• 630 Scratchpads communities• More than 1.5 million unique visitors to

ViBRANT tools and services over the three-years (1.2 million to Scratchpad sites)

• NERC funding e-monocot• Marie Curie Grant (IIF) Starting mid-2014• US-NSF Grants• Major community databases to be

migrated to Scratchpads

Spin-off activitiesPromote links to EU projects BioVeL, agInfra, BioSOS, EU-BON, GIGESMED

Identify opportunities in H2020 to capitalise on current investments and minimise future redundant activities



WP2: Technical architectureSimon Rycroft

Natural History Museum London

Research activities


Description & Objectives

WP Description

WP Objectives

WP partners

Year three effort

To develop and deliver the technical architecture required to host, integrate and sustain the Scratchpad framework within the ViBRANT consortium. This moves the Scratchpad prototype into a sustainable open-source, enterprise-level system.

• Develop and deliver an enhanced technical framework for hosting the Scratchpad infrastructure.

• Distribute the Scratchpad server so that other institutions can independently host Scratchpads.

• Develop new functionality for Scratchpads, including human interfaces and APIs.

• Develop a financial model for sustainable delivery of service.

52.61 PM

WP2: Technical architecture

Research activities


Activities

Year three deliverables

D2.3 – Financial sustainability

Report on options for the ViBRANT financial sustainability model including selection of preferred model and accompanying Service Level Agreements (SLA's).


Research activities


Activities


Other year three activities

D2.4 – Unit testing

• Data search portal providing a single point of entry to all Scratchpad data• Report on the options for a biodiversity data citation metric• Additional module development as highlighted by M2.20• Integration of products from other WPs, including the PWT, OBOE, RefBank,

Vocabularies services, CDM and GeoCAT.

Distributed and automated unit testing mechanism for Scratchpad code completed and available. This will operate in conjunction with the Scratchpad Sandbox to ensure that the latest version of the software is available for testing.


Research activities


Description

Scratchpads

Scratchpads is an open source and free to use platform that enables you to work in a collaborative online environment. With a Scratchpad you can easily create your own website to structure, manage, link and publish biodiversity data.

WP2: Technical architectureForeground

Research activities


Follow up activities

Key Highlights• All Scratchpads 1 sites have now been migrated to Scratchpads 2• The Scratchpads are now hosted on a stable platform with failover and

mirroring capabilities• Completely redesigned Scratchpads homepage• Many new features have been added to the Scratchpads, including import from

Excel, export to DwC-A, content citation, integration with Lucid & BRAHMS, integration with the PWT…

Click to insert a related image Click to insert a related image


Research activities


KPI – Impact - Sustainability

• Numbers of users and sites is increasing at a consistent rate.• The number of views of Scratchpads data is increasing, although we only

started measuring the numbers of views in a reliable way within the last year.• The quantity of content is increasing, and if it were possible to measure the

quality of the content, that too is improving.

Scratchpads


Research activities



• Scratchpads integrating ViBRANT products with BioVeL (pilot project on killer-whales)

• Integration of agricultural VREs – agriDrupal in association with agInfra project and FAO

• Project proposal to integrate ISA Tools, BioVeL and Scratchpads into a single virtual research environment

• New projects to migrate existing online biodiversity databases to Scratchpads (e.g. H&M World’s Birds Checklist, Flora of Zimbabwe, MycoNet project)



WP7: Biodiversity literature access and data mining

David MorseOpen University

Research activities



WP Description

WP Objectives

WP partners

Year three effort

To facilitate the recovery of key content types (e.g. taxonomic names) and underpinning data from published documents, and the integration of those documents into the Scratchpad framework to meet the needs of Scratchpad users.

• Community contributed bibliography• Identification and mark-up of elements within documents• Disambiguation and annotation of mark-up• Web service for search and information retrieval 43.63 PM


Research activities


Activities



D7.3 - Literature search

• ViBRANT corpus, to support future NLP research

• RefConcile, to de-duplicate bibliographic references

• Support for• OBOE-Scratchpad integration• audience analysis

The deliverable is branded as ReFindit, which with RefBank achieves our goal of a Bibliography of Life.


Research activities


Description


A freely accessible bibliography of every taxonomic paper ever published.

Draws on references in Scratchpads and other targeted resources making it easier for researchers to produce accurate references for their citations.


Foreground

Research activities


RefBank

A network of servers to store, de-duplicate and parse bibliographic references into which users can load, edit and delete references, to provide a curated set of references.

ReFindit

A tool to discover and download bibliographic references from a wide range of open access on-line bibliographies, including RefBank.


Research activities



• More than 220,000 references loaded before launch 3Q 2013.

• All references loaded into Scratchpads are automatically harvested.

• Used seamlessly by authors in PWT when searching for references.

• Will be supported and used by Plazi and Pensoft after ViBRANT.

• The underlying tools are being adopted by the Global Names Architecture project, and being investigated by two EU FP7 projects, agINFRA and pro-iBiosphere.



Research activities



• Use of the Bibliography of Life within related projects.

• More RefBank nodes planned.• Take up of ViBRANT technology within the

Global Names Architecture project, including a reworked RefBank as BionomialBank.

• Continued collaboration between VU and OU analysing the audience of e infrastructure users.‑

• Project proposals submitted based on analysing content of RefBank.

• Project proposals submitted based on ViBRANT’s NLP tools used in preparing the Corpus, and extend to identify images.



WP3: Training, outreach and community support

Thierry BackeljauInstitut Royal des Sciences Naturelles de Belgique

Click to enter WP[x]: Title of WP Network activities

Year 3/Final Review Meeting – Brussels 29-01-2014


WP Description

WP Objectives

WP partners

Year three effort

Empower and enable biodiversity scientists to use ViBRANT tools to strengthen community collaboration. In particular to enhance the development of Scratchpads and to support and extend the user communities, leading to increased production of digital biodiversity information.

• Organisation and delivery of ViBRANT training courses• Implementation of network activities to extend the ViBRANT

community and to foster its long-term stability• Conducting user studies• Providing community support for the use of ViBRANT services

29.23 PM

WP3: Training, outreach & community support



Activities




D3.3 Community delivery and evaluation

• International training: on-site & online• Wiki-based documentation system• Open source bug/issues tracker• Global network of Ambassadors• ViBRANT’s audience classifier tool• Funder and output analysis tool

Structuring the necessary support mechanisms, crowdsourcing the support, maximizing its efficiency and assessment of the user base needs nurture a community based model and keep the open source community alive!




Foreground


Training

International training sessions, given online and on-site play an important role in assisting both new and existing Scratchpad users.

Support

A wiki-based documentation system and an open source bug/issues tracker play a vital role in connecting Scratchpads users with the Scratchpads developers.




Foreground


Ambassadors

A global network of experienced Scratchpads users support their local user community, linking the Scratchpads support team with the user base.

Sociological studies of use

In a series of studies, use and users were identified, in order to learn about impact and possible future actions to improve Scratchpads’ impact.




Description


Training, outreach & support

Large part of effort is invested in training. A mediawiki provides the basis for online and printed training manuals, a FAQ and videos. Redmine tracks all bug reports, feature requests and support queries from users. A worldwide Ambassadors network supports local Scratchpads communities and promotes Scratchpads use. Training organised by Ambassador in Lviv, May 2013




Description


Sociological studies

How can impact of Scratchpads be evaluated? What is the disciplinary landscape in which Scratchpads are and can be used? Who are the scholarly and non-scholarly users and does this change over time? Do Scratchpads create a new collaborative environment? What strategies may lead to a larger uptake? Co-author network of a Scratchpad

Knowledge flows in the journal citation network






• Over 450 participants have attended 38 international on-site & online training.

• A total of 2,907 issues submitted to the Redmine system have been tracked: > 2,500 have been successfully resolved.

• The help wiki has had 129,000 views since its creation in March 2012.

• Twenty users from 16 different countries signed up for the Ambassadors scheme.

• Training, support and outreach, along with sociological studies performed on the user-base, nurtured the creation of a community contribution business model that safeguards the long-term sustainability for most of the project’s products.

Training, outreach & support






Several publications are in different stages of finalisation. Some findings:• Increased use, main users in higher education

and research organizations. Small numbers of other user types suggest societal use (and possibilities for new outreach).

• Scratchpads membership also includes non-researchers, and generally members were previously not collaborating. So Scratchpads do organise taxonomists.

• Sustainability and impact may require strategies to involve communities in research infrastructures, next to individuals.

• Collaboration between different relevant disciplines is important.

Sociological studies






• Promotion of Scratchpads via the Distributed European School of Taxonomy• Scratchpads training is part of the DEST training curriculum• Training and support is sustained by NHM London• Continued Scratchpads promotion and support by Ambassadors• Use of Scratchpads as project website promoted in project proposals • Studies on use and users will be continued, leading to further insights in

strategies to involve researchers and research communities, including citizen scientists.

• Work on methods for measuring impact to be continued, also in related projects.



WP4: Standardisation

Yde de JongInstitut Royal des Sciences Naturelles de Belgique




WP Description

WP Objectives

WP partners

Year three effort

Ensure compatibility and interoperability of all data within ViBRANT and to other research and publishing infrastructures and services.

Enforce or facilitate the use of externally standardised ontologies or when no adequate standards exist, enable ViBRANT users to develop, document, and voluntarily share new ontologies.

• Facilitate integration and harmonisation of distributed data-sets.

• Provide management and dissemination facilities for the necessary ontologies by:o Providing access to external services based on these ontologies and APIs.o Developing APIs building on standard ontologies and protocols.

• Provide biologists with the necessary flexibility to express their knowledge regardless of whether the terminology has been standardised.

44.8 PM




Activities




D4.3 – Design of robust services

• Workflow optimised services on ViBRANT index

• KOS integration into Scratchpads• Xper2 and EDIT Platforms publishing

capability on Mediawiki• Xper2 (further) integration into CDM• Fauna Europaea data papers & migration• Global Names Europe H2020 preparations

Continuing improvements and extensions on establishing cross-platform integration and further 'Ontology Platform’ advancements.




Description


GBIF Knowledge Organization System (KOS)

Offers a set of Vocabulary Tools and Services providing routines and mechanisms to build, manage and exchange (controlled) vocabularies, including:• Term Forum (Semantic Media Wiki)• Term Browser• Vocabulary Server• Resource Repository




Description


EDIT Platform for Cybertaxonomy

• Offers a virtual common access point, optimising data exchange and management for taxonomists and supporting the treatment of descriptive data.

• Interoperate with the Scratchpads, KOS, Pensoft and Xper2 platforms.

• Hosts various taxonomic data sets and backbones (like CoL & PESI).




Foreground


ViBRANT index publishing platform

Offers a common searching index and access service for ViBRANT and CDM data, optimised for e-Science workflow application (via the BiodiversityCatalogue), using the CDM web-service layer.

ViBRANT Single Access Key Service

Offers a web service for biological key generation, based on the Xper2 platform features, helping building a consistent descriptive system for use in multi-access keys or descriptive items.




Foreground


KOS – Scratchpads integration module

Offers a feature replacing vocabularies in Scratchpads by controlled vocabularies from the GBIF Resources Repository, including (potential) updates of GBIF KOS terms.

Global Names Europe - assay

Offers a contribution to the Global Names Architecture preparations as a necessary component of Research Data e-Infrastructures: Framework for Action in H2020




Foreground


MediaWiki publishing platform

Offers enhancements on the publishing capability of the Semantic MediaWiki for use in KOS for vocabulary management.Also for the Xper2 and EDIT Platforms this Mediawiki features were investigated.

Pensoft publishing platform

Offers the preparation of data papers using the PWT following the launch of the BDJ as a next generation platform for publishing biodiversity science and data.ZooKeys special issue on Fauna Europaea.






• 67 Scratchpads harvested/published into the ViBRANT index, including 262,664 taxa.

• Two GBIF KOS vocabulary instances imported into the Scratchpads.

• CDM data set (Flora of Cyprus) imported into a (test) Scratchpad.

• Effective employment of the MediaWiki as a publishing platform for e-Taxonomy.

• TDWG VoMaG task group established for KOS governance.

• Active GN-EU outreach in initiatives like RDA, Coopeus, BIH/LifeWatch, TDWG, and EUDAT.

• 57 Fauna Europaea data papers manuscripts in preparation in the PWT.

• Xper² (full) integration into the CDM Taxonomic Editor.

ViBRANT WP4 products & services






• Import of additional KOS vocabularies into the Scratchpads.• Implementation of BDJ as a tool triggering community participation for

taxonomic indexing/editing and validation for taxonomic standardisation.• Further employment of CDM for the hosting and integrated access of

biodiversity data (EU BON) and descriptive data treatments (pro-iBiosphere).• Description of GN-EU as an European contribution to the Global Names

Architecture and the initiation of H2020 bids as part of a collaborative (LifeWatch) Taxonomic Roadmap plan.

• Continuation of VoMaG task group activities.




ViBRANT WP4 working meeting, Berlin, 8-9 October 2012



WP8: Ecological and conservation data mobilisation

Christos ArvanitidisHellenic Centre for Marine Research




WP Description

WP Objectives

WP partners

Year three effort

The primary objective was to extend the capacity of the Scratchpads (in collaboration with WP2, WP4, and WP5) into ecology and conservation science. This has been proved to be particularly important for the sustainability of the project since its products are now being used by communities which are not traditionally included in the taxonomists

i. facilitate naturalist citizen scientists to contribute their observational information to the e-Infrastructure.

ii. improve data quality of information present in thematic and global biodiversity databases;iii. boost GBIF network expansion at national and regional scales;iv. integrate data from various biodiversity sources for ecological and biodiversity assessment and,v. facilitate the Red List assessment processes for endangered species by IUCN and other

stakeholders.

45.7 PM

WP8: Ecological & conservation data mobilisation



Activities




D8.3 - A start-up portal for discovery of GBIF mediated data

• Implementation (expansion of COMBER to the Aegean and Ionian Seas)

• Dissemination (e.g. IPC, Sydney, AU; BIH2020, Roma, IT)

• Impact and sustainability (GBIF NPT, COMBER, BICT, GeoCAT, CartoDB)

• Publication of pioneering scientific documents

Click icon to add picture

M8.18 - Scratchpads module for data recording (Citizen Science) - Alpha version

M8.23 - Integration of the 3D morphological and anatomical data in Scratchpads

M8.24 - Scientific document with the results from the COMBER data

M8.20 - Ecological and conservation applications implemented as a service

M8.21 - Integration of visualization applications with Scratchpads




Foreground


COMBER

COMBER is a citizen science project for divers and snorkelers to collect information on marine species and contribute to biodiversity monitoring. The software serves as a platform for similar citizen science projects.




Foreground


GeoCATGeoCAT simplifies the process of Red Listing and helps to identify threatened species. GeoCAT is an open source, browser-based tool that performs rapid geospatial analysis for Red List assessment.





Foreground


NPT Start-upThe Nodes Portal Toolkit start-up is an open source tool that provides biodiversity information web presence for GBIF Participants. The toolkit supports countries by highlighting the available national biodiversity species data for the benefit of science and society.


BICTThe Biological Index Calculation Tool (BICT) is an online tool available via OBOE. BICT calculates up to eleven different biodiversity indices on data submitted by the user and returns calculated data as well as a graphical report.



Description


COMBER

The module is now fully integrated in Scratchpads2 and consequently in the ViBRANT e-Infrastructure with a different, but fully functional and user-friendly, interface that can be searched in many ways. The philosophy for the Alpha version of the COMBER tool is that it is not restricted to fish species but can include any species found in the Mediterranean, even species detected for the first time in this regional sea. Furthermore, it is not directed exclusively to the SCUBA divers joining the diving clubs but can be operated by any diver or snorkeler throughout his/her diving/ snorkeling/ sailing activity. These features provide the tool with the potential to be adopted by many more user groups and applied in a more independent and automated way. It can also be readily customized to accommodate the needs of almost any citizen-scientists project.Finally, the data sets produced by the pilot have been analyzed and presented in a scientific document, testing a formal scientific hypothesis.






The COMBER module has already been adopted by three Consortia:i. EU BON, a recently started international

project, funded by the EU in the context of the 7th RTD FP3. The decision for the Greek study site (Amvrakikos) was made during the kick-off meeting of the project in Berlin, 12-14/02/2013.

ii. CIGESMED is a project which runs under the SeasERA ERAnet (EU funded) in the Mediterranean Sea.

iii. LifeWatchGreece, which is the national hub to the ESFRI Infrastructure.

COMBER




Description


GeoCAT

Over the past year, the tool GeoCAT was extended to make easier its integration with Scratchpads2. GeoCAT had already the possibility of opening files in various formats, created by Scratchpads, like for example CSV, but those formats did not contain semantics on the information content. Therefore, Scratchpads2 implemented the TDWG Standard Darwin Core Archives (DWC-A), so that an observation, or a specimen in a collection, could be exported under this format.







• GeoCAT has been further supported by one EU Consortium and a UK call for grants. The tool is maintained by the IUCN and is already part of the IUCN daily workflows for many scientists doing conservation assessments. The IUCN is also using GeoCAT in its training courses and maintaining the user community.

• For the continuation of GeoCAT’s development the EU project EU BON is extending functionality to support a larger amount of data and integration with other geospatial platforms.

• Finally NERC (UK Natural Environment Research Council) through the call on “Environmental Big Data Capital” call is funding in 2014 the development of additional functionality for GeoCAT to add multispecies support and deeper integration with CartoDB.

• GeoCAT has already had an impact on large user groups and this is reflected by the impressive number of users as well as by the number of citations GeoCAT is picking up in scientific peer-reviewed publications and the wider media.

GeoCAT




Description


NPT Start-up

The tool helps GBIF Participants to set up a national biodiversity information website that includes an initial species country checklist and static maps of species occurrence data published through GBIF. It also provides species contents (descriptions, functional traits, images and videos) from the Encyclopedia of Life, as well as basic features to run the website as a communication portal. The product helps establish the Node’s identity on the web, manage biodiversity information at the country/thematic level and engage local and global communities with the relevance of biodiversity information.NPT Start-up was developed in Drupal because this content management system has a very strong open source community behind it. There are numerous biodiversity information related projects that make use of Drupal as a development framework, so extensive functionality relevant to biodiversity information is already available and this is likely to be maintained and extended in the future.






A review of the first version of the NPT Start-up was conducted from 9 April to 20 May 2013 amongst all GBIF Node Managers and Nodes staff. Fifty percent of the forty GBIF Participant Nodes responding to the questionnaire indicated an interest in using the first version of the NPT Start-up in its current form. The majority of the responding Nodes considered the first version of the NPT Start-up as either “very useful” or “extremely useful”. Half of the respondents (20 GBIF Participant Nodes) of the NPT start-up review indicated the desire to use the tool in its initial form.TaiBIF has contributed by translating the installation procedure in traditional Chinese. GBIF Participant Nodes in Argentina, ASEAN Centre for Biodiversity, Belgium, Chinese Taipei, Costa Rica, Indonesia, Kenya, Madagascar, Norway, Portugal, and South Africa have tried installing the tool and have provided invaluable suggestions to the development and the documentation. Currently, a group of around 10 GBIF Participant Nodes have indicated the interest in becoming part of an early adoption program.

NPT Start-up




Description


BICT

The indices calculated by the module are those most frequently used in ecological, conservation and environmental health assessment studies. The three last indices, BQI, AMBI and BENTIX, are largely used during the implementation of the EU Water Framework Directive (WFD) and in the context of the Marine Strategy Framework Directive (MSFD).






i. The BICT module has already been adopted by EMBOS (European Marine Biodiversity Information System), a Consortium developing a network of permanent marine biodiversity monitoring stations from the Arctic to the Mediterranean and the Black Seas, as their main tool for the assessment of the benthic quality. EMBOS is funded by the EU COST instrument and it's running for four years: 2011-2015. This issue was discussed during the last meeting of the Consortium in Riga 15-17/10/2013.

ii. BICT will be further developed and made available in the context of the LifeWatchGreece (ESFRI) Infrastructure.

BICT






• LifeWatch will make available most of the products developed by ViBRANT (WP8)

• Some EU projects and Consortia have already adopted the services of the project as part of their hard-core operational system (e.g. EMBOS, MAPMED, EU BON, CIGESMED)

• There has been a growing interest in communities for the services and products of ViBRANT, which has overcome any of the initial anticipation or assessment, especially in the cases of GeoCAT, CartoDB, and NPT start-up

• Some of these products have already initiated the development of spin-off schemes (Vizzuality)

• The WP8 is well involved in the proposals under development in the context of the HORIZONS 2020




Our mottos: (a) team work; (b) just DO IT!



WP5: Interaction and services

Neil CaithnessUniversity of Oxford

Service activities



WP Description

WP Objectives

WP partners

Year three effort

To provide seamless integration of relevant external computing services for biodiversity researchers and Scratchpad users

• Stable middle-ware and backend infrastructure• Clean and attractive web-based user interface• Extensible palette of services with server-side post processing• Fully documented machine API for task submission• Loosely coupled architecture for maximum maintainability• Usage tracking by number of tasks, users, and location

37 PM

WP5: Data Interaction and Services

Service activities


Activities



D5.3

• IKey+ MKey+ (UPMC, ULR, JKI)

• CartoDB (VIZZ)

Click to enter a related to the activities image

Refined and sustainable software services available for public use with mechanisms to measure usage rates


Service activities


Foreground

OBOE

The purpose of OBOE is to provide easy access to computing services.


Service activities


Foreground

IKey+ / Mkey+

Single- and multi-access identification keys, delivered on-demand, via web-services.


Service activities


Foreground

CartoDB

A cloud based mapping, analysis and visualization engine that lets users build spatial applications for mobile devices and the web.


Service activities


Description

OBOE

OBOE is a science gateway to research computing:

• new methods for developers to deploy their applications in the cloud

• easy access for users with no need for technical knowledge of cloud computing


Service activities



• ~200 users• ~1000 tasks• Still growing …• … unsolicited new users• Links with Manchester HTC centre

(anticipated soon)

• Support from Microsoft Research • Migration to Windows Azure

OBOE


Service activities


Description

IKey+ / MKey+

Online services for identification using structured descriptive data (SDD)

• single-access keys (IKey+) • multi-access keys (MKey+)


Service activities



Recently introduced services that are expected to grow quickly:

• >350 IKey+ keys in Oct & Nov 2013• >150 MKey+ keys in Oct & Nov 2013

IKey+ / MKey+


Service activities


Description

CartoDB

CartoDB was launched in April 2012, version 2.0 was released in Nov 2012.The platform is already being used by major news organizations, research institutions, non-profits, and geospatial application developers the world throughout.


Service activities



The latest CartoDB release allows anyone to create geo-temporal maps directly from their browser. To make this possible, the CartoDB team has been quietly perfecting a new technology over the past few months. CartoDB is already being used by the UN, US National Park Service, Twitter, The Guardian and the World Resources Institute.

CartoDB


Service activities



IEEE/ACM CCGrid 201414th IEEE/ACM International Symposium on Cluster, Cloud and Grid ComputingMay 26-29, 2014 -- Chicago, IL, USA


Microsoft Research Awards~40K


WP6: Scholarly publishing

Lyubomir PenevPensoft Publishers

Service activities



WP Description

WP Objectives

WP partners

Year three effort

Develop novel tools and workflows to streamline the publication process at all stages, starting from authoring, through peer-review and editing, to publishing and dissemination. Develop and promote XML tagging and semantic Web publishing in the biodiversity domain. Establish a novel data publishing platform.

• Automated submission, review and publication from Scratchpads and GBIF

• New methods of XML tagging• Streamline the scholarly publication process• Automated deposition of taxon descriptions• Highly automated data publishing workflow• Semantic enhancements to biodiversity publications

14.6 PM

WP6: Scholarly Publishing

Service activities


Activities



D6.3 Data publication workflow

• ReFindit tool• Bibliography of Life, RefBank and ReFindit

interface design• Five research papers• ViBRANT special issue published• Another ViBRANT special issue assembled

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Biodiversity Data Journal and Pensoft Writing Tool:• a next-generation, narrative (text) and data integrated, publishing workflow• authoring, peer review and publication within a single platform, for the first time• community peer review


http://www.pensoft.net/journals/bdj

http://www.pwt.pensoft.net/

Service activities


Foreground

Pensoft Writing Tool (PWT)

An entirely XML-based, manuscript authoring, online, collaborative platform, integrated with peer-review, editorial, publishing and dissemination tools.

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Biodiversity Data Journal (BDJ)

Novel, community peer-reviewed, open-access journal, launched to accelerate mobilisation, dissemination and sharing of biodiversity-related data through the act of scholarly publishing.


Service activities


Description

Pensoft Writing Tool (PWT)

•Full article life cycle, from writing to publication and dissemination

•Upfront XML markup •Submit at the click of a button• Import Darwin Core and other data into text•Automated import of manuscripts generated

in various platforms•A set of pre-defined article templates•Easy online collaborative editing by co-

authors and peers•No layout stage, reduced publication costs!


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http://rs.tdwg.org/dwc/2009-02-20/terms/guides/text/index.htm

Service activities


Description

Biodiversity Data Journal (BDJ)

•Making “small” data “big”!•No lower/upper limit of manuscript size•Articles structured and stored as DATA•Community ownership of data•Download data straight from the text•A novel community-based peer-review•Easy online collaborative revisions•Post-publication peer-review•Free to publish for now•Low page charges in future affordable by all

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Service activities



• Innovative, XML-based publishing workflows, proven successful; currently a model for other publishers to follow

• Increased dissemination and re-use of published content

• “Small” data publishing in BDJ: a globally unique and viable data mobilisation tool

• Educational and sociological impact of data publishing and sharing

• Low production costs will ensure reduced page charges and facilitate sustainability

• The PWT/BDJ workflow has potential to expand in other domains

Flying start and increasing usage of PWT/BDJ Workflow


1/13

2/13

3/13

4/13

5/13

6/13

7/13

8/13

9/13

10/13

11/13

12/13

1/14

0200400600800

100012001400

PWT Usage Monthly StatsAuthorships Manuscripts

9/2013 10/2013 11/2013 12/2013 1/20140

20

40

60

80

100

120

140

BDJ Usage Monthly StatsAuthors Papers

Service activities



• Expansion of the PWT/BDJ workflow in other domains, in first place Genomics, Biomedicine, Agricuture, etc.

• Launch of industry standard, XML-based data publishing platform as a service for other journals or publishers

• Further promotion and increased number of users of PWT/BDJ• Adoption of XML markup and semantic enhancements by other journals• Further automation of input and output data publishing formats • Closer integration with Scratchpads, GBIF, and other data suppliers• Possible solution for the “dark” taxa problem• Re-publishing and databasing of historical literature


Service activities

ViBRANT Project Year 3/Final Review Meeting – Brussels 29-01-2014ViBRANT Project Year 3/Final Review Meeting – Brussels 29-01-2014


Welcome aboard!


ViBRANT Impact and Product Sustainability

Vincent SmithNatural History Museum London


Product Usage

Scratchpads 7,000 active users - 1.5m* visitors

OBOE 1,000 job submissions

BDJ/PWT 22,000 unique visitors/3 months47 articles since launch

GeoCAT 1,000 assessments5 official IUCN assessments

COMBER 409 activities - 5,600 observations

Ikey+/Mkey+ 500 keys produced

KPIs / Scientific Impact

Impact and Product Sustainability

* 1.2m during ViBRANT

Scratchpads visitors


62 Scientific publications in 20 international scientific journals from 97 different authors

Three special issues (one more in preparation)Zookeys v.150: e-Infrastructures for data publishing in biodiversity scienceZookeys v.209: No specimen left behind: mass digitization of natural history collectionsZookeys v.365: DNA barcoding: a practical tool for fundamental and applied biodiversity research

Selected publications:• Hardisty A., Roberts D & The Biodiversity Informatics Community.

A decadal view of biodiversity informatics: challenges and priorities. BMC Ecology 13 (2013)

• Duin D. et al. Identifying audiences of e-infrastructures – Tools for measuring impact. PLoS ONE 7 (2012)

• Smith et al. Collaborative electronic infrastructures to accelerate taxonomic research. ZooKeys 150 (2011)

• Harfoot M, Roberts D. Data would help ecosystem models. Nature (2014)



95%

5%

OA not OA


Impact of Scratchpad communities to the wider scientific community

Average of > 100 citations per year (2012) in scientific Journals to Scratchpads communities and the Scratchpads project



Citations to Scratchpad communities

Citations to the Scratchpad project


105 Conference presentations in 23 countries (Europe, America, Asia, Africa & Oceania)

96 workshops and training courses in 24 Countries

Marie Curie fellowship (IIF) – ViBRANT-BioVeL

Biodiversity Informatics Horizons 2013, Rome200 participants – 6 organising, 17 participating EU FP7 projectsSpin-off: h2020.myspecies.info for coalescing community activities and support future joined actions




D2.3: Financial Sustainability


A federated network of compatible services with no single point of failure

A service will be considered sustainable if it is both available and continues to be used on an open-ended basis


Scratchpads Status: secure

Platform for Cybertaxonomy Status: secure

Biowikifarm Status: secure

PWT & Scratchpad publication tool Status: secure

Nodes Portal Toolkit Startup Status: secure

OBOE Status: uncertain

RefBank Status: reasonably secure

GoldenGATE Status: reasonably secure

Xper2 Status: secure

GeoCAT Status: secure

CartoDB Status: secure

COMBER Status: reasonably secure

Impact and Product SustainabilityD2.3 Financial Sustainability


Marketing

Anchoring to core funding• Generate compelling use cases to enable

support by associated institutions• Develop towards mutually established goals

(e.g. ESFRI objectives, EU objectives)

Investment in Crowdsourcing• Nurture a community based

sustainability model• Minimise support and development

costs by outsourcing to the end user communities


+

A successful hybrid sustainability model

Confidence

Agility

Society

Community

Institution

D2.3 Financial Sustainability



Drupal CMS

git repository

Modularity

Ambassadors scheme

Co-learning environment

Self-learning (e.g. sandbox)

Scratchpads portal

Issues queue

Wiki based documentation

Train the trainers effort



Identifying common goals

Investigation of the interaction area with other EU funded projects, tools and services


BIH 2013 Conference200 participants – 17 supporting projects

The White paper"A decadal view of biodiversity informatics: challenges and priorities." BMC ecology (2013)

Interactions withBioVeL, agInfra, ISA-tools, CIGESMED, EU-BON


135 registered users from 28 countries


• Sustain the existing tools and services

• Capitalise on ViBRANT’s successful products

and promote Innovation for future scientific

application scenarios

• Identify potential convergence with other EU

initiatives

Work towards supporting

the data to model the Biosphere

Future plans



WP1: Management and Financial Matters

Vincent Smith / Dave RobertsNatural History Museum London

Service activities



WP Description

WP Objectives

WP partners

Year three effort

The logos of the partners will be included at the final stage of merging all the presentations – Do not fill this in

Workpackage 1 provides the consortium financial management required by the Commission and integration of the activities undertaken within the consortium

• Project management• Consortium coordination• Financial administration

WP1: Management & Financial Matters


D1.1: Overall management

Agile Management

• More efficient and responsive management model

• Re-direction of some aspects of project to better integrate with the other elements and create a better product (e.g. WP7)

• Our user-centric focus required a easily adaptable management model


Properties of Agile management

ViBRANT Project Year 3/Final Review Meeting – Brussels 29-01-2014ViBRANT Project Year 3/Final Review Meeting – Brussels 29-01-2014


Year 3Integration

Year 2Operation

Year 1Prototyping

Project agile management


Project management elements

Management committee

Project Reporting

Management of resources

Advisory Board

Consortium members

Interactions with other projects




Project structureDoW and modifications

Deadline monitoring

Project outputsScientific papers, Deliverables & Milestones, Presentations, Reports

Effective communicationForums for WP, Administration and Researchers with more than 1100 registered posts

Open accessScratchpads based website

Digital Project management


Outputs

23 Deliverables all completed on time164 Milestones3 Annual consolidated reports1 Final report



Management Committee• 12 meetings (7 through

teleconferencing)• Open proceedings (Agenda & Minutes)• Management by consensus (no voting

necessary)

Project reporting

• In each annual review new milestones for the next year

• Single narrative reports drafted• All reporting documents online



Year 3 financial breakdown



Budgeted spend


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Project financial breakdown


Budgeted spend

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Community Contribution

REDACTED

Wednesday 29th January 2014EC premises (Room 0/S5)Avenue de Beaulieu 25

1160 Brussels

Final review meeting

Consolidated ViBRANT Project Final Review Presentations

Technology

Transcript of Consolidated ViBRANT Project Final Review Presentations