2013.06 Activity Report

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Contents

This Activity Report captures the activities performed in June 2013.

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

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


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

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

  • Organization and chairing of the monthly Steering Board conference call (13.06 and continued on 25.06) and revision of the minutes prepared by ERCIM;
  • Organization and chairing of the Monthly PEB conference call (14.06) and preparation of the minutes;
  • Organization and chairing of the periodic Tcom (7-20.06.2013, Skiathos, Greece);
  • Second project review planning: analysis of recommendations, planning of the rehearsal, preparation of the review Agenda;
  • Liaisons with CSA-Oceans initiative and filling of its questionnaires;
  • Planning of an EMODNET- iMarine meeting;
  • Day-by-day supervision and monitoring of the scientific activities.
  • Liaisons with CSA-Oceans initiative and filling of its questionnaires;
  • Progresses in the liaisons with various initiatives and Communities of Practice (e.g. Biodiversity Informatics Community, Blue Hackathon, EUDAT,RDA);
  • Contribution to the finalization of the ToC of a White Paper on iMarine sustainability;
  • Day-by-day technical and scientific activities supervision and monitoring;
  • iMarine shared workspace operation and maintenance;
  • Participation of the TD in a series of WP specific calls dedicated to the coordination of different activities.


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


  • Monthly SB and PEB conference calls;
  • Periodic TCom meeting;
  • Second project review planning;
  • Liaisons with different initiatives and projects;
  • iMarine shared workspace operation and maintenance;
  • Day-by-day technical and scientific activities supervision and monitoring.

WP3: Governance and Policy Development

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

T3.1

  • Continued mediation tasks with Board members to prepare policy and harmonization activities. Start with organization of Board 4 meeting in October 17-18 in Rome.
  • Discussed new opportunities with several key international projects; TBTI, GOLD, AustralFish

T3.2:

  • Prepared and discussed template for policy and use case to describe and validate practical data access and sharing policies
  • Contribute to VALID use case policy development with French Ministry DGPA, DGMARE (with FLUX documentation)
  • Continued with policy for data access and sharing revision on wiki.

T3.3

  • Cotrix Architecture matured, discussed with ESS for joint development and implementation.
  • Redesign and implementation of the matching component exposing a domain-independent interface to clients (tagline: "general purpose matching component for the identification of relationships between concepts and entities"). CNR will be informed to review the results.
  • Design and implement a standalone library with core functionalities of the matching component and a distributed-computation model that will not necessarily require a supporting distributed infrastructure.
  • Support the sanitization process of species names. The goal is to provide an interface to upload a XLS file with species names as originally reported by external sources and propose alternatives (identified by the matching component) whenever a species name is not found in the reference domain. The proposed VRE would add facilities on top of this)
  • GIS data sharing
  • Intersection engine related to SPREAD
  • Linked Data Publication Workflows proposal writing
  • Implementation of the publication workflow for ASFIS code lists to FLOD


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

  • Succesful meeting with French DGPA, will be followed by a next meeting in July on VALID (validation of fisheries data)
  • A new version of the iMarine data access and sharing policies is prepared.
  • delivered another version of SPREAD application (manage CSV output format instead of JSON) as agreed at Tcom
  • delivered stand-alone library for species matching
  • delivered internal discussion paper on cotrix development / virtual repository
  • Implementation of the publication workflow for ASFIS codelist to FLOD

WP4: Communication, Dissemination and Training

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

Follow-up activities of the May event: Finalisation of the Report with the full recording of the May event and of the Executive Summary. The report will be circulated to the EC and workshop participants.


  • Events:
  • MAES (Mapping and Assessment of Ecosystems and their Services) Marine Workshop
Venue: Brussels, Belgium - EC DG Environment
Dates: 19 June 2013
URL: http://www.bsrac.org/archive/Dokumenter/External%20events/2013/COM/MaeS%20Marine%20WKShop_draft%20outline_FINAL.pdf
Brief Description of Event: The objective of the workshop is to allow experts and stakeholders to be updated on what the Working Group on Mapping and Assessment of Ecosystems and their Services (MAES), working under the EU Biodiversity Strategy's Common Implementation Framework, has achieved so far, and discuss how the MAES process in the marine domain could be supported and strengthened at EU and national level. Synergies with related EU processes, in particular under the Habitats Directive and N2000 at sea, MSFD, and with similar international (regional) initiatives within and outside the EU, will also be discussed.
Reason of iMarine Participation: iMarine has been invited to attend the workshop by Anne Teller at the May meeting. iMarine will present its offer to the participants.
  • iMarine Blue Hackathon event
Venue: The first part will take place between the 28th and the 30th of June 2013, at the Natural History Museum of Crete, whereas the second one will be hosted by the Hellenic Centre for Marine Research from July 1st to July 2nd 2013.(Crete, Greece)
Dates: 28 June 2013 - 2 July 2013
URL: http://wiki.agroknow.gr/agroknow/index.php?title=BlueHackathon2013&oldid=9076
Brief Description of Event: Blue Hackathon is the first in a series of events that aims to use the information technology to solve environmental problems related to water and the atmosphere. Developers, designers, environmental scientists and scientists of other disciplines, will meet to form groups that will use open data available on the web, in order to produce innovative software solutions for the environment protection.The first two days focus on brainstorming sessions and cooperation, helping the participants identify novel applications of large data sets on environmental issues. Users of large data sets will be there and will have the chance to explain their requirements to tackle major environmental challenges. Participants will identify areas and ideas on which they would like to work forming teams of developers, graphic designers and scientists to embark on a 24hour hacking spree! This hacking experience will end with the presentation of the results and awards for the best hacks of the event!
Reason of iMarine Participation: iMarine is one of the organiser of the event together with agINFRA (http://aginfra.eu/) and ViBRANT (http://vbrant.eu/).
  • Dissemination Material:
    • June Flier: Data e-Infrastructure services supporting the marine ecosystem management. the flier has been distributed at the MAES event.
  • Dissemination Activities:
    • iMarine Blue Hackathon invitation sent to all iMarine contacts and to the iMarine database (as a special issue of the iMarine newsletter)
    • iMarine Blue Hackathon event news published on the channel http://www.i-marine.eu/Content/Multimedia.aspx?id=82950c05-1b4d-4940-bfd6-1af92bf08384
    • iMarine Blue Hackathon event news published on iSGTW & CORDIS
    • Submission of 2 applications for the ICT2013:
      • Exhibition booth
      • Networking session
    • preparation of the text for the iMarine workshop within the EUDAT conferewnce in October 2013
    • drafting of the workshop text for the participation to the EUDAT conference

Media Channel: Request from iSGTW for a special issue on iMarine to be published on the 11th of September 2013

Media Channel: Collaboration request from the Mobile Maritime Hub in the Western Mediterranean Sea via the website.


Training: Review of 11 training videos.


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

In the context of T5.1:

CERN in collaboration with CNR completed the deliverable D5.3 which has been sent to SB for approval. ( sent to EC beginning of July)

In the context of the scheduling and implementation of the infrastructure upgrade to gCube 2.15 the following activities have been performed:


In the context of T5.2:

CNR installed several new VMs both in production and development infra and performed upgrade to gCube 2.15

NKUA installed the virtuoso software needed for the activity of the semantic cluster.

FAO upgraded the 2 production nodes to gCube 2.15.


In the context of T5.3:

nothing to report.


NKUA repaired DNS server and made services available again in a 6 hours period.



  • Deliverable D5.3 completed
  • Infrastructure upgrade to gCube 2.15

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;

For resources and tools provision:

  • ingestion of www.marineregions.org layers in iMarine SDI;
  • development of a names matching component;
  • COTRIX development continuation;
  • Reinforced the OAI-PMH TM plugin (e.g. bug fix);
  • Reinforced the FIGIS TM plugin (for accessing FishFinder material);
  • Started working on data.fao.org TM plugin (metadata only, no support for data access yet);
  • Tuna Atlas use case development: design and development of a dedicated website interfacing with TLO and iMarine WPS;

For common interfaces and tools:

  • Reinforcement of the geo-related portlets (e.g. support for ISO10139);
  • Reinforcement of workspace portlets (e.g. share link, bug fixing);
  • Reinforcement of resource management portlet (e.g. attributes encryption management);
  • Reinforcement of report template portlets (e.g. bug fixing);
  • Reinforcement of IRBootstrapper (e.g. content management dismissal);
  • Development of record visualisation for FIGIS;
  • Reinforcement of Search portlet (e.g. browsing, bug fixing);


No activity has been reported by ERCIM, FIN, UNESCO, and CRIA

D6.4 Virtual Research Environments Activity Report (June 2013) has not been completed.


  • Existing VREs have been maintained;
  • www.marineregions.org indexed by the iMarine SDI;
  • Release of a new version of the OAI-PMH TM Plugin and FIGIS TM Plugin;
  • Reinforcement of a number of portlets including geo-related portlets, workspace, resource management, report template, IRBootstrapper, Search portlet;

WP7: Enabling-technology Integration and Distribution

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

  • gCube 2.15.0 released on 18th June. In total for this release 16 integration builds and 17 integration issues have been identified and managed through Trac system.
  • Distribution site and News have been upgraded by NKUA for this release.
  • Operation of the ETICS service.
  • Backup mechanism for ETICS datamodel activated; backup performed every night.
  • deliverable D7.3 "Software Release Activity Report" mostly complete (reviewed internally and sent to the Steering Committee early in July)


  • dns problems made ETICS service intermittently unavailable
  • harmonization of package names for distribution site not yet started


  • release of gCube 2.15.0

WP8: iMarine Data e-Infrastructure Enabling Technology Development

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

T8.1:

  • Started working on update capability of Deployer component. A modification to the deployer which allows to update only gCube services has been produced and tested. Integration of the modified deployer with the Resource Manager has yet to be tested. Activity on this area as been freezed as effort was needed in another area (storage).
  • Resumed development activities on common-ghn-service, the new facilities that allows to integrate non-gCore JAX-WS servlet in the infrastructure. The library enforces gCube service specific behavior thanks to jax-ws filters and handlers managing operations related to service lifecycle transitions and wrapping service calls.
  • Work on common-ghn-service was presented at the 6th TCom in Skiathos
  • Bugfixing activity on common-gcore-stubs. Going to be released in gCube 2.16.

T8.2:

  • Presented work at the 6th TCom in Skiathos: Authorization, Accounting and portlets.
  • Continued implementation of the accounting system.
  • Continued development of Resource Accounting portlet.

T8.3:

  • Developed a gCube service and client libs that expose the functionality of the workflow adaptor. The service allows clients to send JDL representation of jobs and execute them over a variety of processing infrastructures. The service and client libs will be released in gCube 2.17.


T8.2:

  • Due to requirements devised in May a redesign of the Accounting Portlet started, following the MVP pattern in order to reduce the complexity and future maintenance required effort. This should not impact the deadlines.


None

WP9: Data Management Facilities Development

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

  • In T9.1:

FAO focused on upgrading the Tree Manager, adding longer timeouts for slow plugins. FAO also upgraded the Trees library to version 1.4.1, to fix a problem with the XML parsers.

CNR worked on the Storage Manager. They implemented a backup strategy for the storage cluster. The backup strategy consists in adding a dedicated hidden member to the cluster. The hidden member is a peculiar node that is not advertised as part of the cluster set, which prevents it from receiving read-only queries.

  • In T9.2:

CERN completed the implementation of the Tree Transfers and released the Scheduler portlet.

Terradue added IRD algorithms for Tuna Atlas indicators on WPS-Hadoop. these include: (i) filtering of process inputs on the species names (ii) filtering of process inputs on the species names and gear type (iii) filtering of process inputs on a species name and a year of reference (iv) filtering of process inputs on a species name and a time interval

Terradue also added the SPREAD algorithm to the WPS-Hadoop service.

  • In T9.3:

CNR analyzed the EXL language specifications. They compared functionalities that should be offered by an implementation of an interpreter of the EXL language.

CNR presented the work done on TabularData/Timeseries at the 6th TCom in Skiathos. CNR continued the development on the Tabular Data System working on "adding filtering" capabilities on the TabularQuery module. In order to address this new feature CNR developed a library that allows to describe conditions on tables by the means of java beans.


no deviations to report.


  • Enhancements in the Tree Manager
  • Backup strategy on MongoDB
  • Activity Tree Transfer is complete
  • The Scheduler Portlet has been released
  • IRD Tuna Atlas algorithms are available on WPS-Hadoop
  • SPREAD is available on WPS-Hadoop

WP10: Data Consumption Facilities Development

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

In task T10.1, mostly bug/issue fixing was the focus. In more details, ForwardIndex faced a bug on creation of a new index and a timeout in the feeding process, a Search node had memory requirements issues, a problem with Bing OpenSearch configuration was fixed and capabilities and limitations of OpenSearch gCQL were discussed.

In task T10.2, gCube Data Transformation Service was refactored in order to remove Content Management dependencies, as the latter is being dismissed. Also, prefetching mechanism of Tree Manager DataSource was improved.

In task T10.3, the Length-Weight estimation algorithm by Raner Froese was integrated in Statistical Manager. A comparison procedure was released which involves accuracy and Cohen's Kappa calculations that will be used in map comparison. Furthermore, Trendylyzer portlet now uses static charts to display the results.

Moreover, QuantitativeProperties visualisation library’s functionality has been covered by InteractiveLayers component. Development of the former is discontinued.

In task T10.4, xSearh-portlet now is offering the ability to retrieve at real time semantic information about a detected entity. Also, xSearch-portlet has been improved in terms of scalability and functionality, by changing the fetching and analyzing mechanism. In advance all the available running instances of xSearch-service are retrieved from IS, in order to exploit them using a round robin algorithm. Look and feel of xSeach-portlet has been modified for giving a homogenized view within the iMarine portal. Lastly, X-Link library has been released, that based on the information found in a knowledge base, analyzes the contents of a document and enrich the identified entities with URIs.


  • The implementation of XLink was not planned from the beginning, but since some partners are interested in, FORTH decided to work also on this.


  • First runs of the Length-Weight estimation were executed
  • A first version of the Trendylyzer portlet was implemented
  • A first version of the maps comparison procedure was implemented
  • InteractiveLayers support the following advanced visualisations for marked regions:
    • Bubbleplots (WMS layers)
    • CummulativePlots (WFS layers)
    • Timelines (WFS layers)

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

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

During June, in T11.2, effort was spent on extending the Data Transfer Agent Service and Scheduler Service CLs in order to support Tree transfers. Also, some information about integration of clients with common-security library was provided during the TCOM. Furthermore, the first version of a new library, called OWC4J, for binding OWC XML Documents and Java Object model has started.

In T11.3, effort was spent on bug solving and enhancements on the Application Support Layer for supporting browsing capabilities. Also, Resource Registry integration with the FeatherWeight Stack has been continued.


None


Validation of OWC4J Java classes

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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