2012.08 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 2012''''' by Beneficiary and Task. 

It is part of '''[[2012.08 Activity Report|August 2012 Monthly Activity Report]]'''.

== T6.1 Virtual Research Environments Operation ==

=== CNR Activities ===
No major activity has been performed in the reporting period apart the maintenance of the Virtual Research Environments developed in the previous period. 

<xh4> Deviations and Corrective Actions </xh4>
No major deviation;

<xh4> Achievements </xh4>
None

=== FAO Activities ===
FAO activities wrt the VRE's and related services were:
* Continued evaluation of the Tuna Atlas use case with ICIS functionality review. 
* Continued discussion on suitablity of geospatial service to support the SPREAD use case.
* Continued validating the suitablity of the environment to e.g. perform analysis with R (and ran into difficulties)
* After WP3 validated the Biodiversity data services, potential new services to build on top of these were identified. 

<xh4> Deviations and Corrective Actions </xh4>
None to report

<xh4> Achievements </xh4>
None to report.

== T6.2 Virtual Research Environments Resources and Tools Provision ==

=== FAO Activities ===
Produced D6.3 in draft

<xh4> Deviations and Corrective Actions </xh4>
''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''

<xh4> Achievements </xh4>
Circulated draft for D6.3

=== ERCIM Activities ===
''The beneficiary should report here a summary of the activities performed in the reporting period ''

<xh4> Deviations and Corrective Actions </xh4>
''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''

<xh4> Achievements </xh4>
''The beneficiary should report here a bullet list highlighting the main achievements of the reporting period''

=== CNR Activities ===
CNR activity focused on fixing bugs in the existing plugins and creating the IRMNG Species Discovery Plugin.

'''IRMNG Species Discovery Plugin'''

IRMNG Species Discovery Plugin downloads the Darwin Core Archive files, containing the Taxonomy database dump, and creates a PostgreSQL database. 

The database is created using the Darwin Core Archive Reader, a jar library by GBIF, that allows to read Darwin Core Archives as defined by the DwC text guidelines. The Darwin Core Archive Reader unzips the files (text data files and a single meta.xml descriptor) and it handles single text files that contain a header row indicating which Darwin Core Archives term the columns represent.

The plugin will be automatically updated every 30 days.

The plugin allows the search by scientific names, supporting Classification and Synonyms Capability.

<xh4> Deviations and Corrective Actions </xh4>
None

<xh4> Achievements </xh4>
*IRMNG plugin
*Bugs fixed in Species Discovery Plugins

=== FIN Activities ===
==== Name reconciliation ====
Carla (and Nicolas) analyzed in depth the algorithm of Taxamatch (Tony Rees, CSIRO), the most advanced algorithm to match names.<BR>

A concise document on the algorithm was created to be used for the Name reconciliation VRE specifications.<BR>

Basic functions were programmed in php to be tested further on FishBase production website. To be translated in java for integration in the VRE.

==== AquaMaps ====
Preparation of the HCAF for the new climate change scenario. Some issues appeared where the extrapolation for some HDC gave negative value for environmental parameters.  Cells had thus to be extra- or interpolated manually.<BR>

A new GBIF dataset was made available and prepared. Data for fishes are ready. Data for non-fish are being processed. Wrong data were eliminated. Not to say that there is no error, but one type of obvious mistake polluting the point maps was removed.<BR>

All datasets to be uploaded in the VRE by the end of September or early October (Nina in 2-weeks vacations from 10 Sept.). 

<xh4> Deviations and Corrective Actions </xh4>
A complete map computation run was delayed since February due to 2 facts, both extra-infrastructure, which has somewhat demobilized the AquaMaps community:
* The occurrence dataset contained wrong records; although they were not taken into account in the AquaMaps algorithm, they polluted the point maps. The dataset was cleaned.
* The computation of the environmental parameter layer (HCAF) was difficult under the new climate change scenario (2100) because of negative extrapolations for environmental parameters.

Other news:<BR>
Unfortunately, Carla resigned and left the project mid-August and further programming was suspended. A new programmer is hired and will come in Monday 10 September 2012.

<xh4> Achievements </xh4>
Taxamatch documentation.<BR>
Basic functions for the Taxamatch algorithm  were programmed in php.<BR>
New climate change scenario HCAF ready (year 2100).

=== UNESCO Activities ===
''The beneficiary should report here a summary of the activities performed in the reporting period ''

<xh4> Deviations and Corrective Actions </xh4>
''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''

<xh4> Achievements </xh4>
''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 ''

<xh4> Deviations and Corrective Actions </xh4>
''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''

<xh4> Achievements </xh4>
''The beneficiary should report here a bullet list highlighting the main achievements of the reporting period''

=== IRD Activities ===
''The beneficiary should report here a summary of the activities performed in the reporting period ''

<xh4> Deviations and Corrective Actions </xh4>
''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''

<xh4> Achievements </xh4>
''The beneficiary should report here a bullet list highlighting the main achievements of the reporting period''

== T6.3 Virtual Research Environments Common Interfaces and Tools ==

=== CNR Activities ===
* Enhancement of the '''Species Products Discovery Portlet'''. 
** The code has been updated in order to fit the recent changes in the service stubs.
** The new features supported are the following:
*** filter results by classification at run-time;
*** different grid visualization for occurrence/taxonomy items;
*** search by text query (query examples are available from GUI);
*** enhanced visualization criteria - a new details view is available with cluster of results by scientific name and navigable table of contents (a hyperlinked Table of Contents);
*** revised the occurrence points visualization strategy through the GIS Viewer.

* A '''Species View Portlet''' has been designed and developed. The aim of this portlet is to offer facilities for searching and browsing the species maps produced via the AquaMaps application. It supports the following facilities: 
** simple search by species name;
** advanced search by supporting criteria on species name, code, taxonomy, and/or characteristic;
** support for visualisation of products by image, by detailed record, and by scientific record;

* '''Software Management Widget''' project has been renamed to '''Software Upload Wizard'''. New supported features and modifications:
** Completed development of use case ''GCube Web Service''.
** Modified wizard window dimension and several style attributes in order to let the wizard work with lower laptop screen resolutions.
** Implemented GCubeLoggerClient adapter for slf4j logging system.
** Added wizard step progress indications on wizard window title.
** The application now interacts with the IS in order to get information about available Maven repositories ("MavenRepository" Runtime Resources).
** The application has been tested against all of the developed use cases and prepared for the 1.0.0 release in september.

<xh4> Deviations and Corrective Actions </xh4>
* '''Software Management Widget''' project has been renamed to '''Software Upload Wizard'''. Project has been refactored accordingly.

<xh4> Achievements </xh4>
* Release of an enhanced version of the Species Discovery Portlet;
* Release of the Species View Portlet;
* Software Upload Wizard will be part of the upcoming gCube 2.10 release;

=== NKUA Activities ===
Search portlet minor enhancements. The portlet can be either support semantic search or not depending on whether or not the xSearch portlet will be deployed on a specific VRE.

<xh4> Deviations and Corrective Actions </xh4>
None

<xh4> Achievements </xh4>
None

== T6.4 Virtual Research Environments Development Support ==

=== NKUA Activities ===
* NKUA organized teleconferences with FORTH institute to discuss and support them with the development of the xSearch portlet and the integration with the gCube components.

<xh4> Deviations and Corrective Actions </xh4>
None

<xh4> Achievements </xh4>
None

=== CNR Activities ===
''The beneficiary should report here a summary of the activities performed in the reporting period ''

<xh4> Deviations and Corrective Actions </xh4>
''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''

<xh4> Achievements </xh4>
''The beneficiary should report here a bullet list highlighting the main achievements of the reporting period''