2014.08 WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

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This WP6 Activity Report described the activities performed in August 2014 by Beneficiary and Task.

It is part of August '14 Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

In the month of August, CNR merged two VREs, named Biodiversity Research Environment (BRE) and Biodiversity Lab (BL), the latter containing more facilities than the former. Users were moved from BRE to BL, which is now supplied with public access.


none to report


  • the Biodiversity Research Environment VRE was merged with the Biodiversity Lab VRE

FAO Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

In Cotrix, progress was reported on the implementation of many user requests:

  • code markers
  • validation services
  • changelog services
  • UI/UX rehaul
  • code filters
  • code list logbook
  • table layout controls

Cotrix Validation continued in August, and several bugs were reported as a consequence; this resulted in

  • general bug fixing

Several feature specific tickets were addressed: #3021, #3024, #3025, #3026, #3027, #3028

NEAFC2ICES was delivered, and is now pending actions from:

  • NEAFC to validate the delivered component in a production environment (validation was done on a test environment)
  • CNR to develop and deploy a portlet to call the service in NEAFC and transfer the VMS and related data records

BiOnym

  • Continued support for BiOnym development #3001
  • As a results, BiOnym passed validation (although with comments on performance before it can be used beyond the target audience of Taxonomists)


Nope to report


  • Cotrix was validated by the User Community.
  • BiOnym was validated by the User Community.

ERCIM Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

CNR Activities

During August, CNR worked on enhancements and bug fixing for the Database Management portlet #2960. On the community side, CNR was contacted by Kristin Karshner (Univ. if Kiel) to bring forward the activity on Maps Comparison #1432. The contact came after a paper accepted on the GIScience & Remote Sensing (Fancis & Taylor Ed.). The activity about Maps Cmparison was brough forward during the work for the paper.


No deviations to report


No relevant achievements to report

FIN Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

UNESCO Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

CRIA Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


CRIA developed a program (written in Perl) to check scientific names using its phonetic algorithm and the Catalogue of Life (2013 Annual Checklist) as the Authority file. The program was tested using files sent by Edward Vanden Berghe that had been used to test BiOnym. The program first does a parsing of the name, and searches for names that are phonetically equal - just genus, just species, just subspecies - and then combines all names and, if found, presents the scientific name + author in the name_found column, exactly how it is spelled in the Catalogue of Life. The system then checks the status of the name - accepted or synonym - and if the result is a synonym, the system presents the accepted name of that synonym. For names not found the name_found column is blank and the status is NOTFOUND. There is also a 4th possible status that we called AMBIGUOUS. An example is Synbranchus doringii. The Catalogue of Life has Symbranchus doeringii and Symbranchus döringii. So in this case, both of these names will be presented in the name_found column and the status is AMBIGUOS and the system does not search for an accepted name. We produced results both for a phonetic comparison and an exact comparison. The impact of the phonetic comparison in this example influences 290 names, about 0,5% of the total number of names. A report with the result was sent to Nicolas Bailly, Edward Vanden Berghe and Anton Ellenbroek for their analysis. If approved we will send the code of the program (Scientific Name Checker) and of the phonetic algorithm used.

IRD Activities

Activities to improve observations enrichment with environmental parameters (from netCDF files), enrichment of RDF metadata describing bibliographic references, databases, agents with ontologies URIs. Imrpvment of fact sheet generator based on Tuna Atlas use case.


  • creation of a depth profile (sst, chlo a...) for a given biological observation
  • creation of a Hövmoller diagram for a given feature (polygon)


Process now includes on the fly (browsing databases through SQL queries) generation of following triples:

  • creation of triples to describe the temporal and spatial extent of databases and related datasets,
  • list of species observed.


  • update connection and queries for TLO warehouse version 4,
  • new design for the Webiste,
  • improvement of WPS outputs integration by delivering HTML ouputs
  • dipslay agents and bibliographic references linked to species by using the work on Zotero and foaf:agents

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

A large part of the activities of this month was dedicated to improve the usability and user experience of the iMarine portal. We revised several components that we found causing "troubles" to the users, during the registration phase for instance, but also during the normal use of the portal. First the user registration to the portal was made more easy, precise and secure. Secondly the possibility of accessing VREs is now easier for users, from some VRE you no longer need to ask for access. We also added the possibility for users to leave VREs. Finally the user profiles were largely enhanced. Details follow:

  • Gateway create new account:
    • The create account portlet was enhanced with two new features:
    • It now allows users to choose their password when registering, and the sending of the password in clear via email has been stopped due to security reasons.
    • Is also allows the user to enter his email twice. This is because we noticed that with one single field only the probability users committed typos in writing their email was quite high.
  • Social Profile:
    • The portlet has been largely enhanced, it now allows to enter users professional background information or to Import it automatically from their LinkedIn Profile via OAuth2 Protocol.
  • VRE Members:
    • The component is completely new, it allows users to see who are the members of the current VRE they have joined. For each user a photo and work position information is displayed. Moreover by clicking on a user the whole profile is displayed.
  • Join New Environment:
    • The portlet has been largely enhanced, it has been restyled and it now allows user to freely enter a VRE without asking for confirmation, if and only if, the VRE was set so by an administrator.
  • Environment Home:
    • The portlet has been enhanced by allowing user to freely leave a VRE, if and only if, the VRE was set not-mandatory by an administrator. See 5


On Tabular Data component:

  • On "Tabular Data Column"
    • updated change label column. see #3008
  • Create "Monitor" component
    • a single operation monitor for all operations
  • Enhancements on "Tabular Data Common Events"
    • updated the types of events
  • Enhancements on "Tabular Data Portlet"
    • updated menu and behavior
  • Enhancements on "Tabular Data GWTService"
    • updated operations

On Home Library component:

  • Fixed bug in Copy and Paste facility: the operation was not properly notified on the target node.
  • Moved URI resolver from workspace to HL library. Now 'getPublicLink' method can be applied to every WorkspaceItem and if such facility is not available, an InternalErrorException is thrown. #2744
  • Fixed character escape problem in getCollectionName() method.


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

NKUA Activities

NKUA activities for this period include:

  • Results portlet minor enhancement to avoid throwing exception when the store of external documents to the workspace fails.
  • IRBootstrapper portlet offers a new task for indexing the workspace's documents in order to make it available for search
  • Enhancing the Advanced search portlet in order to offer the functionality to search per collection, when multiple collections are selected and thus the user can retrieve the results per collection


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

T6.4 Virtual Research Environments Development Support

NKUA Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

CNR Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

T6.5 Serving New Scenarios

CNR Activities

CNR created a new VRE named EGIP, containing applications for geothermal data inspection and processing. The new VRE is available under the scope "gCubeApps/EGIP" and contains algorithms to report geothermal energy trends. Furthermore, the GeoExplorer interacts with an external repository of geothermal GIS layers.


none to report.


  • the EGIP VRE was build and contains geothermal energy layers and processing facilities for these layers

FAO Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

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