2013.02 Activity Report

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This Activity Report captures the activities performed in February 2013.

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

1.Distribute 3rd Advance payment to partners

  • The 2nd payment from EC has been recieved on 24/01/2013
  • Part of it was distributed end of February in a way that all partners have funding until August 2013.
  • PR2 is due at M20(+60days); PR2 timing will have to be discussed (work due in July/August !);
  • Based on effort and cost reported in PR2, the 2nd part of the 2nd EC payment will be released
  • Next payment is therefore expected in August/early September.

2.Collect effort contribution for Jan-Feb 2013

  • 7 effort reports uploaded.
  • 6 missing: E-IIS, TRUST IT, FAO, FIN, CRIA, IRD;
  • Please supply effort report for M15-M16 by Wednesday 13/03 (for SB telco next day).

3.Subcontract (on going)

  • Edward is still discussing with Free University of Brussels to host him as a subcontractor for iMarine;
  • Negotiations are slower than we would like, but Edward is working on the project nevertheless.
  • SB needs to revisit other subcontracts (VLIZ and NEAFC) for timing and relevance;
  • Some of the subcontract budget could be used to serve other activities, such as the iMarine event in May.

4.Monitor and submit of the due deliverables and milestone achievement statements

  • No major issue or delay, as reported in Linh's QATF status report on March 1;
  • Delay on D2.5 discussed today by Anton under WP3.

No major issues

  • 3rd advance payment distribution
  • Submission of Del D2.2, D2.4

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

  • Organization and chairing of monthly Steering Board conference calls (14-19.02);
  • Organization and chairing of the monthly PEB (18.02 );
  • Finalization of D2.2 "Project management report";
  • Drafting of D2.5 "Report on inter-project coordination and collaboration";
  • Initial steps in the scientific organization of an iMarine event in Brussels in May;
  • Dedicated phone calls of SB members with some partners to identify recovery plans from delays;
  • Participation of the Technical Director in 4 conference calls dedicated to Clusters & WPsactivity planning;
  • Collaboration with ERINA+.

No major issues.

  • Two Steering Board conference calls (14-19.02);
  • Finalization of D2.2 "Project management report";
  • More clear planning of Terradue activities (24.02);
  • Collaboration with ERINA+.
  • Monthly PEB (18.02);
  • Coordination and planning of Clusters and WPs activities.

WP3: Governance and Policy Development


  • Presented iMarine at CWP, FIRMS, and discussed with FishFinder group
  • Preparation for Board and advisory council meeting
  • Preparations for other meetings
  • iMarine data access and sharing policies; draft-3 preparation and use case specification started
  • Continued work on geospatial SDI, Cotrix Codelist management, FLOD Content development
  • Analyzed codelists in Europe; DGMARE, French Ministry etc.

ERCIM, reported no activity


  • FishBase and SeaLifeBase databases analysis for taxamatch integration.
  • study opportunity identified by R.Froese for Bayesian model integration


  • Studied the option of integration semantic resources in the e-Infrastructure


  • Continued on the TLO model development
  • Commenced to study the exploitation of FLOD as a TLO source
  • Commenced to populate TLO with WoRMS data


  • Coordinated geospatial cluster activities; meetings and presentations, and managed wiki
  • Coordinated discussion on Legacy applications (Cross cluster)
  • Analysed the World Ocean Atlas (WOA) environmental variables, and their availability for the enrichment of species occurrences with environmental parameters


  • Noting reported. Active in Biodiversity cluster descriptions and meetings 19 and 28 Feb [1].


  • Nothing reported. Active in Biodiversity cluster descriptions and meetings 19 and 28 Feb [2].
  • Initiate specifications for a Trendylyzer VRE.


  • Not reported. Active in Biodiversity cluster descriptions and meetings 19 and 28 Feb [3].


  • Work on guidelines for geospatial cluster and related wiki pages [4] & [5]. This work will be improved in the coming weeks.

D2.5 is accumulating delay (Due January)

  • iMarine presented at CWP and FIRMS steering commitee
  • Drafting of D2.5 "Report on inter-project coordination and collaboration";
  • Cotrix wiki enriched, first set of UI components reviewed, model drafted
  • Creation of Web services metadata (OGC 19119/19139) for WMS / WFS / WPS related to Tuna Atlas use case. Creation of CSW to delliver these metadata to iMarine through a CSW.
  • Geospatial cluster pages revised

WP4: Communication, Dissemination and Training

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

The article has been reviewed and integrated by FAO & CNR

  • New release of AppliFish 1.2.1 - Bugs fixed, iPad graphics design optimization, new feature (Aquamaps legenda; Aquamaps images hidden when not found).
  • Validation form prepared & distributed by FAO to collect all the comments on futur improvements - virtual meeting between FAO & TRUST on the 11th February to discuss App specs + f2f meeting between CNR & Trust-IT to plan actions related to dissemination activities (22 February).
  • Interaction with FAO Media for publishing a News article on AppliFish (FAO)
  • February events:
    • FIRMS Steering Committee Meeting - 8th Session (Rome, Italy - FAO Headquarters); 4-8 February 2013: The prototype of an integrated search environment developed by FAO (Fisheries department) for the Smartfish project will be presented at the FIRMS Steering Committee Meeting (4-8 February 2013). The prototype tackles requirements of semantic interoperability for three information systems (FIRMS, StatBase and WIOFish) publishing information on fisheries and marine resources. The prototype adopts the Fisheries Linked Open Data (FLOD) semantic knowledge base developed by iMarine as the backbone to facilitated integrated search capabilities. The meeting will showcase to relevant stakeholders how data harmonization with semantic technologies can support the generation of dynamic fact sheets.
      • Outreach to FIRMS FSC8, through presentation of SmartFish, and ICIS use cases.
    • 24th Session of the Coordinating Working Party on Fishery Statistics (Rome, Italy - FAO Headquarters); 5-9 February 2013: Brief Description of Event: The 24th Session of the Coordinating Working Party on Fishery Statistics will see the ICIS - Integrated Capture Information System- VRE capabilities showcased. ICIS integrates regional and global capture and distribution information of aquatic species to improve the quality of global catch statistics. ICIS can equip local institutions with a complete data management suite in support of harmonization and dissemination of their often confidential data.
      • Outreach to CWP24, through presentation of the FLUX initiative and the role of iMarine project.
  • iMarine event preparation: Date selected :14-15 May 2013 @ EC premises. Target: 20 people. Agenda under definition.
  • Internal Training event provided by FAO to gCube developers. The training was focussed on the use of testing tools for gCube services that FAO has developed in iMarine (WP8)
  • WP4 Monthly call - Agenda - iMarine Success Story submission / Training Activities / February iMarine newsletter / iMarin event / AppliFish & other iMarine Apps / February & March Events - Participants FAO - CNR - NKUA - TRUST. minutes available here http://wiki.i-marine.eu/index.php/15.02.2013_WP4
  • Delivery of February eNews: What will be the impact of climate change on the Flathead grey mullet? Find out where the species may be found now and in 2050 through the Aquamaps Distribution Maps in AppliFish (The news article has been reviewed by FAO & CNR), Third iMarine Board meeting, 25-26 March 2013, Rome, Italy .


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

  • Second prize winner in the 'Better society' category of the 10th e-Infrastructure Concertation Meeting Project Success Story Competition
  • AppliFish Total Downloads: 643
  • AppliFish impact: + 15 LinkediIN connections (on 285) - + 10 Twitter followers (on 134) + 44 registered members (on 222)
  • AppliFish article on:
    • iSGTW “AppliFish”, Knowledge on marine living resources at the touch of a button – a novel mobile app from the iMarine initiative


WP5: iMarine Data e-Infrastructure Deployment and Operation

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

regarding T5.1:

CERN was responsible for the pre-production and production deployment of the gCube release 2.12. In particular the following activities were performed:

regarding T5.2:

CNR, NKUA and FAO site managers performed the GHN upgrade for the release 2.12.

CNR and NKUA performed some changes on the VM configurations by adding new disk space and RAM , deployng new GHN for statistical Manager ( CNR) and new node for R and OSGW+ servers. (CNR)

regarding T5.3:

CERN performed some changes on NAgios server :

In addition the Cassandra cluster monitoring has been implemented (https://issue.imarine.research-infrastructures.eu/ticket/1324)

Node upgrade failed, postponed to March. Now completed.

  • Infrastructure upgrade to gCube 2.12.0
  • deployment of the iMarineBoardVRE

WP6: Virtual Research Environments Deployment and Operation

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

For Virtual Research Environments Operation:

  • the previously deployed Virtual Research Environments have been maintained in operation;
  • A new VRE for supporting the iMarine Board members (iMarineBoardVRE #1309) has been defined and deployed;
  • A new VRE specifically conceived to offer search (and semantic one) facilities (#1190) has been defined;

For resources and tools provision:

  • CNR and FAO completed the integration of some of their SDI components (namely GeoNetwork);
  • the porting of FishBase and SeaLifeBase databases, from MySQL to Postgres started;
  • the porting of some algorithms (namely TaxaMatch algorithm, an R one for estimating the length-weight relationships) to the Statistical Service started;
  • the development of IRD WPS services continued;
  • A new plug-in of SPD for accessing World Register of Deep-Sea Species (WoRDSS), a taxonomic database of deep-sea species based on the World Register of Marine Species (WoRMS) have been developed;

For common interfaces and tools:

  • social facilities has been reinforced (e.g. folder sharing notification);
  • an enhanced version of the Workspace (including folder sharing) has been released;
  • report and template facilities has been revised;
  • a number of portlets have been mavenized (Workspace, Templates, Reports);
  • the Android mobile application for Search has been revised, Google-like facility added;
  • the development of GWT widget supporting data visualisation continued;
  • Index Management facilities has been revised (namely IRBootstrapper portlet and FullTextIndex portlet);
  • The registration email sent to new users from the UsersManagement portlet has been revised;
  • the revision of the Results portlet to make it compatible with the TreeManager and to remove any direct dependencies to gCubeServices started;


  • Existing VREs has been maintained;
  • The iMarineBoardVRE has been deployed;
  • The FAO GeoNetwork has been indexed by the iMarine GeoNetwork;
  • social facilities has been reinforced, e.g. folders sharing notification is enabled;
  • Report and Template portlets have been revised;
  • a revised version of the Workspace has been released;
  • a number of portlets have been mavenised;
  • index management facilities has been revised;

WP7: Enabling-technology Integration and Distribution

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

In the context of gCube release 2.12.0 following activities have been done:

  • E-IIS finished the integration of gCube 2.12.0. In total 35 complete builds plus several partial builds have been executed
  • In total (between integration, deployment and distribution issues) 71 tickets have been reported on the Trac
  • Joint effort between WP7 and WP8 to adequate Software Gateway to new versioning system
  • NKUA updated the gCube distribution site with artifact list and release news for gCube 2.12.0

E-IIS continued the activity of installing a new instance of ETICS tool on its own infrastructure and preparing the environment for hosting gCube builds. The new ETICS service has been installed with some worker nodes (12 at the moment). An import script to transfer the gCube data model from ETICS@CERN to ETICS@ENG has been developed.

Nothing to report

  • gCube 2.12.0

WP8: iMarine Data e-Infrastructure Enabling Technology Development

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

In T8.1:

FAO and CNR collaborated on the redesign and implementation of several components:

  • registry-publisher: Registry publisher now allows the registration of gCube resources using the FWS related library common-gcore-resources and ic-client. The component is going to be released with milestone 2.14.
  • common-encryption (replaces former common-utils-encryption): the library supports the encryption (AES algorithm) of strings. The component has been released with 2.13 milestone.

During february CNR, ENG, and NKUA had an online online training session on MyContainer hosted by Fabio Simeoni. MyContainer is a testing tools which can be used for gcube services unit testing. FAO furthered development on components related to the Featherweight Stack:

  • common-gcore-stubs 1.1.0 (part FWS): delegates handling of outgoing calls do an arbitrary number of dinamically discovered handlers. This is going to be used be Engineering in order to secure outgoing calls. Going to be released in 2.14.
  • common-scope 1.2.0 and common-configuration-scanner 1.0. Do not use third party dependencies that proved to not be integrated within some platforms (gHN, portal).

FAO also collaborated with Engineering on the integration of security components and testing with MyContainer.

In T8.2:

Engineering furthered development on gCube Security stack in order to reach compliancy with Featherweight Stack. According to the plan clients based on security stack (common-security) must be able to interact with gcube services by leveraging the globus security stack. As FWS leverages Java Security Socket Extension a thin integration layer was needed. Moreover the gcube distribution was also updated with a more recent cryptography library that solved a problem with HTTPS handling. Integration tests related to TLS auth have been completed succesfully.

In T8.3:

NKUA focused on:

  • Development of the Workflow Orchestration Layer. The new layer will be placed between WorkflowEngine and Execution Engine and will be responsible for:
    • Distributing workflows among all available Execution Engines
    • Store workflows for later use
    • Reporting on execution status and provenance tracking (mapping between nodes and outputs).
    • Failure recovery and error handling
  • Development on PE2ng operators has continued.
  • Improvement on perfomances related file transfer between nodes.
  • Fixed several bugs.

In T8.4:

Complete (This task was active from M1 to M8).

In T8.2:

Since the issues encountered on the integration of security components with the GHN caused a delay of two weeks in february for other tasks, those tasks that were bound for the end of february are going to be addressed in the first half of march.

None to report.

WP9: Data Management Facilities Development

  • In T9.1:

FAO provided support and coordinated activities around the integration of the tree-based access subsystem with other gCube subsystems. CNR enhanced the Darwin Core Archive generation by SPD, fixing bugs in the taxonomy ranks.

  • In T9.2:

CERN worked on Data Transfer facilities, in particular the following features were added: (i) the portlet is able to browse transfer destinations folders on the remote services, (ii) multi-roles management, (iii) outcomes contain info on the number of transferred bytes, (iv) an extension to monitorTransferProgress is available, (v) the agent checks for the available space on the destination before transferring, (vi) common messaging has been implemented.

Terradue begun to define and investigate the usage of Cloudera’s Distribution including Apache Hadoop. Furthermore, they defined operations environments for WPS-hadoop and associated resources to be used in the iMarine infrastructure. Finally, Terradue discussed with IRD about the four legacy applications to be integrated in WPS.

  • In T9.3:

CNR studied several software solutions related to the field of Data Warehouse, Data Integration and Data Analysis with the idea of integrating them within a new version of the TimeSeries service. CNR investigated the following software: Mondrian, Kettle, Drools, Data Cleaner and AnalyzerBeans.

No deviations to report.

  • Data Transfer was endowed with new functionalities

WP10: Data Consumption Facilities Development

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

In T10.1, the integration of ElasticSearch with Fulltext Index has been completed. More specifically, the new Fulltext Index has been integrated with IRBootstrapper and tested exhaustively, required changes have been made on WorkflowSeachAdaptor and RRGCubeBridge. In the context of the data fusion functionality, a corresponding component is under implementation. Also, various issues related with SearchSystem, IndexManagement and ResourceRegistry have been investigated.

As for the XSearch, the integration with gCube Search continued and during this procedure, identified problems/issues were reported. Also, a document containing queries for useful test cases is under preparation.

Lastly, the implementation of the WOA2009 data cleansing web service has started.

In T10.2, only bug fixing in gCube Data Transformation Service took place, like DataSource retrieval timeout and ScopeProvider issue since previous release changes.

In T10.3, work has been done on the parallelization of the AquaMaps Native, Suitable 2050, Native 2050. The parallel execution of those algorithms was held by GenericWorker. Also, Time Series Spectral Analysis is being integrated with the Statistical Manager.

Furthermore, an implementation of the visualisation use case "Quantitative properties visualisation" has been created in order to be used for integration purposes.

Finally, the development of an "OWS context" example has started in order to complement the visualisation capabilities.

In T10.4, xsearch-portlet has changed the way that locates the available running instances of xsearch-service, by exploiting IS. Also, The serialisation of objects that are transferred between xsearch-portlet and xsearch-service has changed from XML to JSON. Moreover, the exploitation of RDF-properties in XSearch has been investigated. The main focus has been the identification of the most important entities based on well-known techniques (i.e. link-analysis).


  • The AquamMps Native, Native 2050, Suitable 2050 can run in parallel.

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

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

During February, in T11.2, effort was spent on the integration of Data Trasfer Client Libraries with the Featherweight Stack. Also, the integrations test of the common-security with the Featherweight Stack and the GHNs was continued with some issues on TLS authentication. Moreover, a Guidelines page for the exploitation of OWS Context 1.0 documents across iMarine services was started.

In T11.3, effort was spent on enhancing the application support layer to provide a generic search functionality as well as solving compatibility issues and bug fixing on the the same component. The generic search functionality is available through a new servlet that has been deployed. Also, the development of a gCube Data Transformation Service client library with the Featherweight Stack has been completed. Finally, the investigation on the new design of the XSearch components continued and ended up in two alternative approaches that will be evaluated.

In the context of integration of the common-security with the Featherweight Stack some integration issues occurred between Featherweight Stack and GSS and bug on criptix library used. These problems introduced a delay of common-security with of about two weeks. The activities planned for February will be completed by the first half of March.

New Guidelines for OGC Standards draft http://wiki.i-marine.eu/index.php/OGC_OWS_Context_1.0_Guidelines

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

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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