2013.12 Activity Report

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This Activity Report captures the activities performed in December 2013:

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

Activity was focused on exchanges with the EC Project Officer to obtain concensus on the modifications to be included in the Description of Work. Exchanges were also made with the representatives of NEAFC to develop a sub-contracting agreement within WP6.

The proposal for the new activity T3.4 Formalization of Business and Sustainability Intentions could not be finalized with the Steering Board before the end of year break. In January, the PO requested a 5 month project extension, whereas we had been working on a 4 month request.

  • A proposal was received for undertaking the newly proposed T3.4.
  • A subcontract with NEAFC was developed, under review by signatories.
  • Project Officer approves the project's request for extension of the project duration.

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

  • Finalization of the scientific part of the project extension proposal;
  • Organization and chairing of the monthly SB meetings (14.12 and 20.12)
  • Organization, chairing and minutes preparation of the monthly PEB meeting (17.11);
  • Establishment of new exploratory liaisons (e.g. LTER, HCMR);
  • Supervision of scientific and technical activities (including the participation of the TD in teleconferences dedicated to coordinate specific community-driven activities);

No major deviation.

  • Monthly SB and PEB meetings;
  • Specification of the modifications to be applied to Part B of the amended DoW
  • New Liaisons

WP3: Governance and Policy Development


T3.1 Activities User Community Mediation

  • Trendylyzer was promoted at the OBIS steering group meeting and Caribbean Marine Atlas meeting
  • iMarine was present at the FAO project proposal for the GEF funded ABNJ/deep sea project. iMarine infrastructure (and data from OBIS) for the identification of VMEs among other topics.
  • Board operations such as meeting preparations and liaison with individual members continued, including monitoring of H2020 calls.

T3.2 Activities Governance Mechanisms, Policies and Guidelines Development

  • Continued refining the iMarine policy for data access and sharing
  • continued developing best practices and guidelines
  • Continued contributing to Business Model development (ToR's and workplan)
  • Discussed OBIS data policy and terms of use at the OBIS Steering Group meeting, where iMarine may assist in aligning data and policies.

T3.3 Activities Harmonisation of Metadata, Semantics and Technologies

FAO activities include:

  • BiOnym development
  • VME-DB development
  • Interaction with NEAFC on DataExchange; the components to connect to the NEAFC database, and make the semestral reports available to ICES for further analysis;
  • Liaise with the VME-DB team to facilitate the exchange of data between the iMarine and VME-DB (Oracle) database;
  • Continue development of cotrix.
  • Proposal for StatBase migration (Ticket 2425) (Y.Laurent)
  • SmartFish service for FLOD content

FORTH Activities include

  • Ontological analysis of the iMarine sources (FISHBASE, ECOSCOPE, WoRMS, FLOD and DBpedia)
  • Designing and Implementing MarineTLO Version 4.0.0
  • Extending the design of Mapping and Transformation rules between MarineTLO and iMarine sources

UNESCO activities included:

  • Data preparation for Trendylyzer and discussions with Gianpaolo Coro and Tom Webb on several steps forward to categorizing species according to conservation status
  • Harvesting data form 12 OBIS nodes: OBIS Canada | South Western Pacific OBIS | OBIS-SEAMAP | EurOBIS | OBIS Japan | WSA-OBIS | AntOBIS | AfrOBIS | ArOBIS | MicrOBIS | FishBase OBIS | ESP-OBIS. Currently harmonizing, standardizing, integrating, quality controlling and indexing these data for publication. Lots of new and improved quality data will be available to iMarine by end of December/early January 2014

The major issues faced in the reporting period and the identified corrective actions should be reported here

  • NEAFC Sub-contract details forwarded to ERCIM for preparation
  • VME-DB first test version reviewed

WP4: Communication, Dissemination and Training

WP Leader: TRUST-IT - Participants: CNR, NKUA, FAO

The WP leader should report here a summary of the activities performed in the reporting period

  • Events:
  • The Fifteenth International Conference on Grey Literature, 2-3 December, 2013 Bratislava, Slovak Republic The iMarine poster "A Social Networking Research Environment for Scientific Data Sharing: The D4Science Offering" has been presented. The social portal facilities have been presented to a new community.
  • NKUA gave an iMarine presentation @ SEMAGROW and agINFRA stakeholder meeting, Dec. 12, at NCSR "Demokritos"
  • Courses on the iMarine e-infrastructure for students in France

5-6 / 12-13 December, 2013-Paris, France: The first course took place on 5-6 December 2013 at the UPMC - Sorbonne Université in Paris. The 4 lessons, each lasting three hours, focus on “Using the iMarine infrastructure: In Theory and In Practice”.

The second course took place the following week, 12-13 December 2013 at the Observatoire Océanologique de Villefranche sur mer, Villefranche sur mer: “Using the iMarine infrastructure: In Theory and In Practice” with 2 lessons, each lasting 6 hours. Both courses are part of the Master in Océanographie Environnements Marins (OEM).

Overall 66 students will be trained by Gianpaolo Coro, CNR-ISTI on e-Infrastructures for biodiversity data, niche modelling, taxa matching, management of biodiversity data heterogeneity, habitat analysis.

  • iMarine March event: agenda finalisation, invitation message creation & dispatch, participant list identification, online registration creation, event webpage creation
  • Contact with GBIF to add the iMarine e-Training material in the GBIF website.
  • iMarine Christmas Card creation
  • iMarine participation to the Biodiversity Data Integration IG RDA working group. Nicolas Bailly and Yde de Jong are chairs of the group. N. Bailly is more in charge to gather ideas and suggestions to reduce the scattering of efforts on Biodiversity Information Systems, in particular for names.So iMarine developments are of interest, and will be used and cited. https://www.rd-alliance.org/internal-groups/biodiversity-data-integration-ig.html

The major issues faced in the reporting period and the identified corrective actions should be reported here

The WP leader should report here a bullet list highlighting the main achievements of the reporting period

WP5: iMarine Data e-Infrastructure Deployment and Operation

WP Leader: CERN - Participants: CNR, NKUA, FAO, FIN

T5.1 Activities

CERN was coordinating and performing the infrastructure upgrade to gCube 2.17.0 at the beginning of the month(2337)

In addition the QA infra has been then upgrade to gCube 2.17.1 (2469) and the production was also upgraded to 2.17.1 before the holidays.

Some activity related to JAVA 7 integration were performed:

T5.2 Activities


  • keeping up and running the provided nodes hosting development, testing and production GHNs, UMD and project management services.
  • new OBIS db node to load Unesco data
  • Two new server, one for production, one for development, for the upgraded version of StatBase
  • New Xen servers added to the HW infrastructures, completing the resources with more 80 cpu, 384 GB RAM, 8 TB DISK


  • Maintenance of the provided nodes hosting GHNs, UMD and the gcube wiki.
  • Planning upgrade to UMD-3 and installation of Argus.

T5.3 Activities

CERN integrated the portal accounting probe into a WebApp, in order to remove the portal dependency to an external GHN (2215). In the context of this task a new version of the messaging producer gCF free has been developed.

A first version of a Nagios plugin to test Search availability has been developed and deployed on the production Nagios instance. It uses ASL HTTP API to run periodically search queries and check the correctness of results. (2450)

  • CNR recovered data from backup of mongodb server, because a user deleted a full iMarine shared folder, due to a bug (now fixed).

  • Infrastructure upgrade to gCube 2.17.0 and 2.17.1

WP6: Virtual Research Environments Deployment and Operation

WP Leader: CNR - Participants: ERCIM, NKUA, FAO, FIN, UNESCO, CRIA, IRD

For Virtual Research Environments Operation:

  • The BiodiversityLab VRE has been created to support University courses on Species Distribution Modelling;
  • The previously deployed Virtual Research Environments have been maintained in operation;

For resources and tools provision:

  • Cotrix development continued, e.g. completed the permission module, added support for emails;
  • VME-DB development continued, Reports Store Gateway enhancements;
  • Species Name Reconciliation (Bionym) development continued, e.g. YASMEEN enhancements;
  • The RFigisGeo package has been released and its integration in WPS planned;
  • FIGIS species layers revised to support random styles;
  • OAI-PMH support (OAI-TM plugin + Harvester) has been revised, e.g. automatic cardinality update facility removed;

For common interfaces and tools:

  • A lot of Tabular Data Widget have been developed, e.g. Task Widget;
  • Workspace has been enhanced with History filtering facility;
  • Report Management has been reinforced by supporting a "drop down list" component;
  • Home Library has been reinforced by bug fixing, e.g. lack of ‘shared with’ details in subfolders;
  • Users Management Portlet has been reinforced by bug fixing, e.g. resolved an issue with multiple acceptance;
  • Bootstrapper portlet has been enhanced, e.g. added more information on submitted jobs, support indices update tasks;


  • A new VRE - BiodiversityLab - has been created;
  • Existing VREs have been maintained;
  • A number of portlets have been reinforced;

WP7: Enabling-technology Integration and Distribution

WP Leader: E-IIS - Participants: CNR, NKUA

  • Integration of gCube 2.17.1 was completed and closed on 8 Jan.
  • A total of 10 integration builds have been executed.
  • 4 integration issues have been identified and managed through Trac system.
  • Migration to Java 7 started on gcube.HEAD. Identification and fixing of issues related to the migration, in collaboration with CERN and FAO.
  • Enhancement of checks to highlights issues in the release process.
  • Operation of the ETICS service.
  • NKUA updated the distribution site with artefacts and news for gCube 2.17.1

  • None

  • gCube 2.17.1

WP8: iMarine Data e-Infrastructure Enabling Technology Development

WP Leader: CNR - Participants: NKUA, E-IIS, FAO

Completed in October 2013.

WP9: Data Management Facilities Development

WP Leader: CNR - Participants: NKUA, CERN, TERRADUE, FAO

  • In T9.1:

CNR dealt with a restore operation on the Workspace and on the Storage system, which resulted in an overall enhancement of the robustness of such system.

  • In T9.2:

CERN implemented a new functionality in the Storage Manager portlet to allow for bulk folder copy, which required enhancements also on the Home Library side. They also started working on further portlet enhancements to manage and display file attributes.

  • In T9.3:

CNR developed a pluggable operation to validate codelists. Furthermore they worked on the definition of a template-model for tabular data and on sharing and unsharing operations on tabular objects. Finally, they worked on improvements in the operations\expressions model by defining a new set of operators.

No deviations to report

  • A new functionality to perform bulk folder copy was developed on the Storage Manager portlet side.

WP10: Data Consumption Facilities Development

WP Leader: NKUA - Participants: CNR, FORTH, TERRADUE, FAO

During the month of December, in T10.1, the new Resource Accounting framework has been integrated with PE2ng. In the context of Enterprise/Federated Search, the design of supporting external datasources has been completed. Furthermore, Opensearch collection have been harmonized with the rest of the exploited resource, as it has been transformed to GenericResource with DataSource type. ForwardIndexNode and SearchSystemService has been updated to change their status to FAILED upon Resource Registry initialization failure. Various bugs have been fixed and two more wiki pages have been reviewed and validated. At last, MyOcean data having depth suitable for 4D extractions have been identified.

In T10.2, the gCube Data Transformation Service is being expanded to include one more data source supporting data in xml format transferred over HTTP protocol.

In T10.3, BiOnym procedure has been adjusted to enhance the performance. Furthermore, the problem of finding an automatic definition of Common Species was addressed, where the focus moved to threatened/unthreatened species. On the Service side, Statistical Manager is being updated in order to be able to import of generic files, where a text file or a Darwin Core Archive file can be uploaded into the system. Activities also concentrated on enhancements of the service, in registering external databases, adjusting tooltips and managing the presence of a single SM in two VOs. Finally, the SM portlet was transformed into a widget.

In T10.4, the construction of a new warehouse which stores the contents coming from different sources is ongoing to separate graphspaces. Moreover it computes various quality metrics for evaluating the warehouse and allows to incrementally refresh it. An issue in the communication between xsearch-service and the SPARQL endpoint of the warehouse has been resolved. At last, bug fixing in xsearch-portlet took place.


  • Integration with new Resource Accounting Framework.
  • The SM can correctly manage its presence in several VOs.
  • Release of the following components in 2.17.1:
    • org.gcube.execution.RRModel.1-5-1
    • org.gcube.execution.MadgikCommons.1-5-0--1
    • org.gcube.index-management.elasticsearch-gcube.1-2-1
    • org.gcube.portlets-user.xsearch-portlet.1-1-2
    • xsearch-service.1-1-2

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

WP Leader: NKUA - Participants: CNR, CERN, E-IIS, FORTH, TERRADUE, FAO

During December, in T11.2, effort was spent on implementing a library that enables persistant logging for the executed jobs in the gCube system as part of the ASL. Also, the integration of SAML Identity Federation with Registration and Login portlets has been continued and the Portal-side Identity Federation has been deployed in the testing infrastructure. Furthermore, the implementation of WFS Utils for the OWC4J has been continued.

In T11.3 effort was spent on completing the integration of the ASL with the Personalization Client Libraries. Also, the design of the XSearch APIs has continued.



Progress and Achievements by WP and Beneficiary

WP1: Administrative and Financial Management Monthly Activity By Task and Beneficiary

WP2: Project Management Monthly Activity By Task and Beneficiary

WP3: Governance and Policy Development Monthly Activity By Task and Beneficiary

WP4: Communication, Dissemination and Training Monthly Activity By Task and Beneficiary

WP5: iMarine Data e-Infrastructure Deployment and Operation Monthly Activity By Task and Beneficiary

WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

WP7: Enabling-technology Integration and Distribution Monthly Activity By Task and Beneficiary

WP8: iMarine Data e-Infrastructure Enabling Technology Development Monthly Activity By Task and Beneficiary - Completed in October 2013

WP9: Data Management Facilities Development Monthly Activity By Task and Beneficiary

WP10: Data Consumption Facilities Development Monthly Activity By Task and Beneficiary

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development Monthly Activity By Task and Beneficiary

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