Project WP #641

WP5 - Supporting Blue Assessment: VREs Development [Months: 1-30]

Added by Franco Zoppi about 4 years ago. Updated 7 months ago.

Status:ClosedStart date:Oct 09, 2015
Priority:ImmediateDue date:Feb 28, 2018
Assignee:Anton Ellenbroek% Done:

99%

Sprint:WP05
Lead beneficiary:5 - FAO Budget Effort (PM):119.00
Milestones:
Duration: 624

Description

Objectives
This work package aims to support the production of reliable stock and fisheries information. It will provide instruments to share datasets among scientists and to publish them appropriately, e.g. provide dataset with clear metadata, welldefined policies and licenses. The proposed VRE will include a flexible modelling environment, where scientists can add and reuse models from other scientists. This environment will manage the different programming languages (R, Python, JAVA) of the models. The aim is to guarantee the repeatability of model execution and thus the reproducibility of its results. This modeling environment will be open, and facilitate the usage of data, models and techniques coming from other scientific domains, such as Environmental Observations or Spatial planning of the Blue Environment and beyond. The final result will be a robust collaborative environment for stock assessment that can potentially be shared by worldwide users; such an environment can also be flexibly customized in local contexts and for all the phases required by this process. It will help managers and scientists from the beginning of the chain (data collection and aggregation) to the production and publication of indicators for policy makers. In order to achieve this aim technologies enabling the Stock Assessment VRE and the Global Record of Stocks and Fisheries VRE will be developed.

Description of work and role of partners
FAO, ENG, ICES, IRD, FORTH
The work package is divided into three tasks to deliver the technology enabling the two identified VREs. T5.1 has a component for data harmonization, and another to leverage stock assessment models. The task participants, that have an established track in stock assessment and capacity building, provide the models, tools, and datasets. T5.2 builds on components developed in T5.1 to harmonize data yet can proceed without depending on particular offerings of T5.1. It will produce the global record of stocks and fisheries through a knowledge base. The two tasks offer separate capabilities
in the same domain, thus reducing risks and strengthening cross-disciplinary applicability, yet relying on shared data sources. A third task (T5.3) ensures that the WP is aligned with activities in other WP’s, and that new opportunities can be explored to prepare exploitation agreements.


Subtasks

Project Task #642: T5.1 Stock Assessment VRE [Months: 1-30]ClosedJulien Barde

Project Activity #952: Stock assessment output AnnotationClosedAnton Ellenbroek

Project Activity #1674: VRE Stock Assessment WorkplanClosedAnton Ellenbroek

VRE #1677: Ecopath VRERemovedJeroen Steenbeek

Task #1777: Ecopath taxonomy dataformatsRejectedJeroen Steenbeek

VRE #1678: FAO Stock Assessment VREReleasedAnton Ellenbroek

Task #3158: Generate graphs and figures from TabmanClosedEnrico Anello

Task #3781: Connect OpenCPU to WPSClosedEnrico Anello

Task #4844: OpenCPU Library to connect to e-infra WPSClosedEnrico Anello

Project Activity #4613: FAO Stock Assessment VRE First ReleaseClosedAnton Ellenbroek

Project Activity #9670: Add RShiny based module to support SDG14.4.1 Closed_InfraScience Systems Engineer

Project Activity #9671: Add RSchiny CMSY versionsClosedEnrico Anello

Project Activity #9672: Add Rshiny based ELEFAN related modelsClosedEnrico Anello

D4Science Infrastructure - VM Creation #10361: Install a new shinyproxy server Closed_InfraScience Systems Engineer

Project Activity #1679: ICES Stock Assessment VREClosedScott Large

Task #1768: Management Strategy Evaluation (MSE) for western horse ma...ClosedScott Large

Task #1778: Toolbox for Data Limited StocksClosedScott Large

Task #5822: Simple minimal example of Shiny App with ShinyProxyClosedScott Large

Project Activity #5823: Able to deploy docker containersClosed_InfraScience Systems Engineer

Project Activity #7493: Linking work - space with VREs via RClosedScott Large

Task #7491: Length-based indicator applicationClosedScott Large

Task #7492: Use LBI application as shinyproxy use-caseClosedScott Large

Task #9542: DLMtoolkit - FLR data converterRejectedNathan Vaughan

Task #4620: Ensemble modelClosedScott Large

Task #5517: Mixfish OptimizerClosedScott Large

D4Science Infrastructure - Task #5818: Identify log-jams in use-case source codeClosedScott Large

Project Activity #10634: VSURFClosedScott Large

VRE #1779: IRD BFT AssessmentRemovedJulien Barde

Project Activity #5135: WECAFC-FIRMSClosedAnton Ellenbroek

VRE #5136: WECAFC-FIRMS: Add TabMan and Dataminer ReleasedAnton Ellenbroek

Task #11043: Enable advanced DB management features on WECAFC Firms VRERejectedPasquale Pagano

Project Activity #11214: WECAFC-FIRMS data / map dissemination toolsResolvedEmmanuel Blondel

Project Activity #11215: WECAFC-FIRMS - Set-up R Data processing componentsClosedEmmanuel Blondel

Project Activity #11216: WECAFC-FIRMS - Set-up SDI componentsClosedRoberto Cirillo

D4Science Infrastructure - VM Creation #11298: WECAFC-FIRMS dedicated GeoNetworkClosedEmmanuel Blondel

D4Science Infrastructure - VM Creation #11299: WECAFC-FIRMS dedicated GeoServerClosedEmmanuel Blondel

Project Activity #11367: Downgrade WECAFC-FIRMS Geonetwork to 3.0.4Closed_InfraScience Systems Engineer

Project Activity #11406: WECAFC-FIRMS - Geoserver logs are not accessibleClosed_InfraScience Systems Engineer

Support #11217: WECAFC-FIRMS - Need RDB database connection parametersClosedKostas Kakaletris

Project Activity #11286: WECAFC-FIRMS - Enable PostGIS spatial extensionClosedKostas Kakaletris

Project Task #11287: WECAFC-FIRMS - Compute & Provide reference spatial shapef...ClosedEmmanuel Blondel

Project Task #11312: Make country datasets available in pre-production DBClosedYann Laurent

Project Activity #11315: WECAFC-FIRMS - R data/metadata business processClosedEmmanuel Blondel

Project Activity #11317: WECAFC-FIRMS - Enable PostGIS spatial extension in produc...ClosedKostas Kakaletris

Project Task #11399: WECAFC-FIRMS - Refactoring of JS code for easy reuse ClosedEmmanuel Blondel

Project Activity #11424: Enable CORS on WECAFC-FIRMS GeoServerClosed_InfraScience Systems Engineer

Task #5238: WECAFC Stock assessment supportClosedAnton Ellenbroek

Task #5810: SS3 Stock Synthesis V3ClosedEnrico Anello

Task #8500: DLM Toolkit for WECAFC casesClosedAnton Ellenbroek

Task #8501: Validate with CMSY for WECAFC ClosedNathan Vaughan

Task #8502: Apply CMSY to US Caribbean stocks- yellowtail, hogfish, ...ClosedNathan Vaughan

Task #8503: CMSY / DLMtool IntegrationClosedEnrico Anello

Task #8504: Apply CMSY to WECAFC specific stock - Test with one country ClosedNathan Vaughan

Task #8505: Apply CMSY to Flying fishClosedAnton Ellenbroek

Task #9430: Modification of CMSYClosedNathan Vaughan

Task #9869: DLMtoolkit - Shiny interfaceClosedNathan Vaughan

VRE #6098: RDB for Fisheries Data Management (WECAFC)ReleasedAnton Ellenbroek

Task #9987: Regional Data Collection and Validation System implementa...ClosedVassilis Floros

Task #9988: Regional Data Collection and Validation Service implement...ClosedVassilis Floros

Task #10038: Implement a web method that lists the available schemas t...ClosedVassilis Floros

Task #10039: Implement a web method that the excel plugin will post th...ClosedVassilis Floros

Task #10041: DSD/SDMX handling and constraint rule management function...ClosedKonstantinos Apostolopoulos

Task #10042: Regional data collection and validation service - gCube i...ClosedVassilis Floros

Task #10644: User management and authorization in RDBClosedVassilis Floros

Task #10647: Regional Data Collection and Validation Service - Tabman ...ClosedVassilis Floros

Task #10648: RDB submission data based on user attributesClosedVassilis Floros

Task #9989: Regional Data Collection and Validation Portlet implement...ClosedVassilis Floros

Task #10034: Data Model (DSD) importing functionalityClosedVassilis Floros

Task #10035: Data model constraint rules managementClosedVassilis Floros

Task #10036: Data collection cycle managementClosedVassilis Floros

Task #10037: Data submission management pageClosedVassilis Floros

Task #9991: Regional Data Collection and Validation Excel Add-In impl...ClosedKonstantinos Apostolopoulos

Task #10043: Authentication and VRE selection on excel pluginClosedKonstantinos Apostolopoulos

Task #10044: Fetch the available data models from the regional data co...ClosedKonstantinos Apostolopoulos

Task #10045: Fetch the data model and constraints from the regional da...ClosedKonstantinos Apostolopoulos

Task #10046: Implement data constraint rules in the excel pluginClosedKonstantinos Apostolopoulos

Task #10048: Post the submission data to the regional data collection ...ClosedKonstantinos Apostolopoulos

Task #10480: Provide a list with RDB Data Submission MetadataClosedYann Laurent

VRE #6870: FLR for JRCRejectedAnton Ellenbroek

Project Activity #2344: Ichtyop modelClosedGianpaolo Coro

Task #3563: Import OSCAR NetCDF in the D4Science Thredds serviceClosedPaolo Fabriani

Project Activity #6760: Support transfer of NetCDF to Threeds Catalog organised i...ClosedFabio Sinibaldi

Project Activity #6761: Run Thredds on a SmartGears enabled containerClosedGianpaolo Coro

gCube - Feature #8361: Thredds migration toolClosedFabio Sinibaldi

D4Science Infrastructure - Task #8926: Unbound content length for threddsClosed_InfraScience Systems Engineer

Task #4621: Python for ensemble model (#4620)ClosedPaolo Fabriani

Task #4643: Improve SDMX capabilitiesClosedCiro Formisano

Task #7121: functional requirements neededClosedAymen Charef

Task #4644: Add ApiaId from WoRMS to species code-listsClosedCiro Formisano

Task #5527: Issue with the FLAssess package installationClosedScott Large

Task #5557: automatize the process of publication of algorithms on da...ClosedPaolo Fabriani

gCube - Task #7928: Normalize ACL for HProxyRejectedAndrea Dell'Amico

Task #8467: Staging dataminer towards DataMiner Pool Manager ServiceClosed_InfraScience Systems Engineer

D4Science Infrastructure - VM Creation #8472: New VM dataminer needed Closed_InfraScience Systems Engineer

D4Science Infrastructure - Support #8498: Adding SSH keys to RPrototypingLab VREClosed_InfraScience Systems Engineer

gCube - Task #9273: Updating dataminer1-devnext.d4science.org at latest versionClosedLucio Lelii

gCube - Task #9607: DataMiner PoolManager - update documentationClosedNunzio Andrea Galante

Project Activity #6348: Integrate FLR library of stock assessment servicesClosedAndrea Dell'Amico

Task #7358: SDMX related activitiesClosedCiro Formisano

Task #7359: SDMX Data Structure Definition exporter/importerClosedCiro Formisano

Task #7535: Define versions of Tabman templatesClosedLucio Lelii

Task #7360: Expose tabular data in SDMX formatClosedCiro Formisano

Task #8717: SDMX and RDBClosedAymen Charef

Project Activity #9944: new Tabman OperationClosedCiro Formisano

Task #9434: Improvements on SDMX export service interfaceClosedLucio Lelii

Project Task #643: T5.2 Global record of Stocks and Fisheries VRE [Months: 1...ClosedAnton Ellenbroek

VRE #1675: GRSF VRE; Global Record of Stocks and FisheriesReleasedAnton Ellenbroek

Project Activity #5085: Create a logo for GRSF Virtual Research Environment ClosedMassimiliano Assante

Project Activity #3398: Sources AnalysisClosedNikos Minadakis

Project Activity #1577: Analysis of the RAM Legacy Database ClosedYannis Marketakis

Project Activity #1060: Requirements Analysis of the FIRMS data sourceClosedYannis Marketakis

Project Activity #3766: Analysis of Fishsource ClosedYannis Marketakis

Project Activity #3400: Mappings definitionClosedYannis Marketakis

Project Activity #2373: Ontological modeling of FIRMSClosedYannis Marketakis

Project Activity #2374: Ontological modeling of RAM ClosedYannis Marketakis

Project Activity #3767: Ontological modeling of FishsourceClosedYannis Marketakis

Project Activity #3402: Inventory of triple storesClosedYannis Marketakis

Project Activity #3403: Construction of the Knowledge baseClosedNikos Minadakis

Task #5525: Merging GSRF data for supporting the construction of GRSF...ClosedNikos Minadakis

Project Activity #3404: Knowledge base browsingClosedNikos Minadakis

Project Activity #3405: MatWare Dashboard RejectedNikos Minadakis

Project Activity #3406: MatWare Serices (New)ClosedNikos Minadakis

Project Activity #6967: GRSF Admin Catalogue - FeedbackClosedCostantino Perciante

Task #7052: Catalogue language configurationClosedCostantino Perciante

Task #7055: Catalogue template improvementsClosedFrancesco Mangiacrapa

Task #7059: Groups and Tags of records in management catalogueClosedCostantino Perciante

Task #7060: GRSF records - metadata checkingClosedCostantino Perciante

Task #7061: Manage facility improvementsClosedCostantino Perciante

Task #6990: GRSF standards - Issues and alternative solution(s)ClosedYannis Marketakis

StocksAndFisheriesKB - Task #6991: Identify problems/missing information in GRSF KB and Cata...NewAureliano Gentile

Task #7142: GRSF-services-core enhancement for checking the intersect...ClosedYannis Marketakis

Task #7166: GRSF - Provide pre-processing to compute overall referenc...ClosedEmmanuel Blondel

Task #7146: Extent GeoGRSF_Intersects algorithm with adjacency criteriaClosedEmmanuel Blondel

Task #7112: GRSF - Develop basic service to know if 2 b-boxes interse...ClosedEmmanuel Blondel

Task #7203: GRSF - Enable SAI/DataMiner/RStudio stack on GRSF_Admin VREClosedEmmanuel Blondel

Task #7392: GRSF Data Miner algoritmsClosedPaolo Scarponi

Task #7393: GRSF VRE and Catalogue Roles ClosedFrancesco Mangiacrapa

Task #7394: Add SAI, Data Miner, RStudio to GRSF adminClosedRoberto Cirillo

Task #7347: Errors when publishing GRSF recordsClosedCostantino Perciante

Task #8277: Re-Export GRSF sources contentsClosedYannis Marketakis

Task #8530: GRSF Mappings updateClosedYannis Marketakis

Task #8531: Update mappings for FIRMSClosedYannis Marketakis

Task #8532: Update Mappings for RAMClosedYannis Marketakis

Task #8533: Update Mappings for FishSourceClosedYannis Marketakis

Task #8607: Update Merging algorithm for GRSF recordsClosedYannis Marketakis

Task #8677: Transform GRSF standard code filesClosedYannis Marketakis

Project Activity #9061: Disable GRSF dataminer algorithms in RPrototypingLabClosedEmmanuel Blondel

Support #9206: GRSF_Admin R version in RStudio needs to be downgraded (o...Closed_InfraScience Systems Engineer

Project Task #9207: GRSF - Provide a batch version of Intersects serviceClosedEmmanuel Blondel

Task #10090: Update GRSF Mappings ClosedNikos Minadakis

Task #10091: Update GRSF-FIRMS mappingsClosedNikos Minadakis

Task #10092: Update GRSF-RAM mappingsClosedNikos Minadakis

Task #10093: Update GRSF-FishSource mappingsClosedNikos Minadakis

Project Task #644: T5.3 Other Use Cases Development [Months: 16-30]ClosedAnton Ellenbroek


Related issues

Related to BlueBRIDGE - Risk #977: 1. Misalignment of user requirements with perceived speci... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #978: 2. Depending technologies / specifications get abandoned Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #979: 3. Community adoption lacks the creation of a critical mass Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #980: 4. Delivered systems miss functional or non-functional (p... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #982: 6. A partner / body underperforms, defaults or faces othe... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #983: 7. Domain or project’s concepts become obsolete or irrele... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #984: 8. Delays in production of deliverables, be it interim on... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #985: 9. Inadequacy of resources to confront specific project’s... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Risk #986: 10. Lack of required competences for the completion of pr... Closed Oct 12, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1462: Blue Assessment - Stock Assessment VRE: Algorithms and mo... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1463: Blue Assessment - Stock Assessment VRE: Scientists exploi... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1465: Blue Assessment - Stock Assessment VRE: Organizations exp... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1466: Blue Assessment - Stock Assessment VRE: Uptake of the app... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1467: Blue Assessment - Global Record of Stocks and Fisheries V... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1468: Blue Assessment - Global Record of Stocks and Fisheries V... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1469: Blue Assessment - Global Record of Stocks and Fisheries V... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1470: Blue Assessment - Global Record of Stocks and Fisheries V... Closed Nov 20, 2015 Feb 28, 2018
Related to BlueBRIDGE - Key Performance Indicator #1471: Blue Assessment - Global Record of Stocks and Fisheries V... Closed Nov 20, 2015 Feb 28, 2018

History

#1 Updated by Franco Zoppi about 4 years ago

  • Start date changed from Sep 11, 2015 to Sep 01, 2015

due to changes in a related task

#2 Updated by Franco Zoppi about 4 years ago

  • Status changed from New to In Progress

#3 Updated by Massimiliano Assante almost 4 years ago

  • Assignee set to Anna Davies

#4 Updated by Massimiliano Assante almost 4 years ago

  • Assignee changed from Anna Davies to Anton Ellenbroek

Sorry The WP5 Leader is Anton Ellenbroekm while Dr. Anna Davies is WP8 Leader

#5 Updated by Anton Ellenbroek almost 4 years ago

September 2015 Activities

No milestone or deliverable was due

In task T5.1 FAO review of TA started with IRD. FAO is planning recruitment. FAO organized a Regional Data Policies workshop for the SWIOarea, with presentations on BlueAssessment; focused on Global registry of stocks and fisheries and tools for data collection.
IRD started with BlueFin Tuna assessment work, and presented BB ; expectation is to have a VRE by March 2016 for some 40 users. Proposes a meeting in Sete. IRD Demoed Ecopath and Ecosim in Brazil
In task T5.2 A first set of competency questions was shared with FORTH, based on the Chimaera system. FAO is planning recruitment
In task T5.3 no activity was expected

Planned 6M activities

T5.1
* IRD to vist 2 RFMO’s; interest in Tuna Atlas related data services. IRD to hire staff for EwE.
* FAO to identify collaboration in the house with other departments; recruit staff (R? JAVA?), discuss support from ENG and CNR.
* FAO to start with ICES (12 Oct) planning activity, align with IRD.
T5.2
* Continue analysis of capability of FORTH tools to support global record of stocks and fisheries; analysis of existing data sources (FiRMS, RAMM, SFP), and data tools.
T5.3
* Nothing scheduled. Propose discussion on Data Collection with Mobile Apps for Stock assessment purposes.

#6 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #977: 1. Misalignment of user requirements with perceived specifications added

#7 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #978: 2. Depending technologies / specifications get abandoned added

#8 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #979: 3. Community adoption lacks the creation of a critical mass added

#9 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #980: 4. Delivered systems miss functional or non-functional (performance, scalability, etc.) requirements added

#10 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #982: 6. A partner / body underperforms, defaults or faces other severe operation issues added

#11 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #983: 7. Domain or project’s concepts become obsolete or irrelevant during project’s lifetime added

#12 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #984: 8. Delays in production of deliverables, be it interim ones (with dependencies) or final ones added

#13 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #985: 9. Inadequacy of resources to confront specific project’s challenges raised by Functional Areas users added

#14 Updated by Pasquale Pagano almost 4 years ago

  • Related to Risk #986: 10. Lack of required competences for the completion of project’s tasks added

#15 Updated by Yannis Marketakis almost 4 years ago

  • Start date changed from Sep 01, 2015 to Oct 09, 2015

due to changes in a related task

#16 Updated by Anton Ellenbroek almost 4 years ago

October 2015 Activity Report

In task T5.1 FAO review of TA with IRD continued.

IRD continued with BlueFin Tuna assessment work; expectation is to have a VRE by March 2016 for some 40 users. IRD completed recruitement of EwE staff, located in Cape Town
In task T5.2 Analysis with FORTH of FAO FIRMS X-Path output. FAO is planning recruitment
In task T5.3 no activity was expected

Project milestone or deliverable

No milestone or deliverable was due

#17 Updated by Pasquale Pagano almost 4 years ago

#18 Updated by Pasquale Pagano almost 4 years ago

#19 Updated by Pasquale Pagano almost 4 years ago

#20 Updated by Pasquale Pagano almost 4 years ago

  • Related to Key Performance Indicator #1466: Blue Assessment - Stock Assessment VRE: Uptake of the approach by 3 other organizations with co-funding; ICES, FAO Projects, etc. added

#21 Updated by Pasquale Pagano almost 4 years ago

#22 Updated by Pasquale Pagano almost 4 years ago

  • Related to Key Performance Indicator #1468: Blue Assessment - Global Record of Stocks and Fisheries VRE: Stocks and fisheries described with a unique id added

#23 Updated by Pasquale Pagano almost 4 years ago

  • Related to Key Performance Indicator #1469: Blue Assessment - Global Record of Stocks and Fisheries VRE: External repositories integrated in a semantic repository added

#24 Updated by Pasquale Pagano almost 4 years ago

  • Related to Key Performance Indicator #1470: Blue Assessment - Global Record of Stocks and Fisheries VRE: Access to the global register of stocks through FAO FIRMS added

#25 Updated by Pasquale Pagano almost 4 years ago

  • Related to Key Performance Indicator #1471: Blue Assessment - Global Record of Stocks and Fisheries VRE: Uptake of data-mining facilities by data owners added

#26 Updated by Yannis Marketakis almost 4 years ago

#27 Updated by Anton Ellenbroek over 3 years ago

November 2015 Activity Report

In task T5.1

In task T5.2

In task T5.3 no activity was expected

Project milestone or deliverable

No milestone or deliverable was due

#28 Updated by Anton Ellenbroek over 3 years ago

December 2015 Activity Report

In task T5.1

In task T5.2

In task T5.3 no activity was expected

Project milestone or deliverable

#29 Updated by Anton Ellenbroek over 3 years ago

January 2016 Activity Report

In task T5.1
IRD

ICES presented the plan for models and analytical features at the TCom: http://goo.gl/t0dKT6

FAO

  • Presented the VRE overall opportunities, and especially the options supporting regional databases to Regional projects in the caribbean (Barbados) and South America (Colombia) in lieu of stock assessment requirements engineering ENG provided support to IRD with EwE integration
  • Collected staff participated to the TCom to understand Stock assessment opportunities, and follow-up discussion ensued

In task T5.2

In task T5.3 no activity was expected

Project milestone or deliverable

  • D5.1 VRE - Type other - Preparation commenced

#30 Updated by Anton Ellenbroek over 3 years ago

February 2016 Activity Report

In task T5.1
IRD

ICES internally discussed the plan for models and analytical features at the TCom: http://goo.gl/t0dKT6, identified need for a consultant on stock assessment services

FAO

  • Prepared the TWG-1

ENG provided support to IRD with EwE integration

  • Collected staff participated to the TCom to understand Stock assessment opportunities, and follow-up discussion ensued

In task T5.2

  • FORTH: #2374: Ontological modeling of RAM
  • FORTH: #2373: Ontological modeling of FIRMS
  • FAO discussed data and services needs with RAM and SFP with FORTH

In task T5.3 no activity was expected

Project milestone or deliverable

  • D5.1 VRE - Type other - Preparation commenced

#31 Updated by Anton Ellenbroek over 3 years ago

March 2016 Activity Report

In task T5.1

IRD continued with the support plan for ICCAT DFT WG:

  • Executed ICCAT VPA "statistical-manager.d.d4science.org",
  • Learnt to use the Statistical Algorithms Importer to deploy code
  • Used the SAI and tested the result on the statistical manager.
  • Completed the ICCAT workflow deployment and testing
  • Improved the automated report generation (for ICCAT Eastern Bluefin tuna working group report)
  • Test publishing of both html and netCDF outputs of the ICCAT use case
  • Prepare ichthyop model, codes have been tested successfully on the infra.

  • Management of ESRI GRID ASCII files to feed EwE models

  • Ecopath and Ecosim: Linkage EwE and FishBase, Updating EwE and the global ocean model, Debugging EwE.

  • Ecopath and Ecosim: discussions about how to link Ecopath with FishBase and Sealifebase

ICES

  • Continued identification of overall workplan

FAO

  • Host TWG-1 and EAB; relevant materials on WP5 for slides, meeting content and programme.

  • Following the TWG, liaised with external parties (WECAFC in particular) to negotiate VRE content and algorithms/models and their use cases internally; negotiated contracts and ToR for Stock assessment consultant. First consultant started 01-04-16

ENG

  • Support integration activities, no new activity intitiated.

In task T5.2

  • FORTH: Continued modelling and development of GRSF knowledge base and Matware tool. Presented the progress and interim results to FIRMS-TWG-5, BlueBRIEDGE TWG-1, and EAB; all in Rome.
  • FAO defined data and services needs with RAM and SFP, and prepared requirements for FORTH. Especially a discussion with FORTH initiated on exploitation after the project of GRSF tools and services.

In task T5.3 no activity was expected

Project milestone or deliverable

  • D5.1 VRE - Type other - Preparation contunued, in absence of clear VRE development and exploitation plans by some partners, the Deliverable was not produced, and accumulates delay. Progress can continue of aspects of teh VRE, but an overall plan could not yet be produced.

#32 Updated by Pasquale Pagano over 3 years ago

#33 Updated by Anton Ellenbroek over 3 years ago

April 2016 Effort report

Task 5.1

IRD

  • publication of netCDF files on the infra (#3138) from WPS (through R code)
  • deployment of Ichthyop model (#2344) by packaging R & Java codes with SAI and validation with statman.
  • deployment of ICCAT BFT-E codes (#1983) with SAI and validation with statman.
  • publication of html files on the infra (#2520) from statman
  • Discussion about annotation of charts, discussion about identified tools and possible options (#3153) to make use of such services on the infra (#3153, #3787).
  • requirement for providing RStudio in the e-Infrastructure VREs (#2516 & VRE #1779: IRD BFT Assessment)
  • Ecopath taxonomy dataformats (#1777)

ICES

  • Participated to training in Pisa,
  • Discussed data poor models to propose for integration with FAO and WECAFC
  • Initiated the integration work on the first model (CEFAS Horse Mackerel)

FAO

  • Commenced on using OpenCPU; first case are Statlant data for CCAMLR statistical reports (#1678, #3158, #3787)
  • Discussed data poor models to propose for integration with FAO and WECAFC

ENG

  • Import script for OSCAR NetCDF developed and tested in development infrastructure.

Task 5.2

Deliverables and Milestones

M5.1 was produced with delay

#34 Updated by Anton Ellenbroek about 3 years ago

May 2016 Effort report

Task 5.1

IRD

  • publication of netCDF files on the infra (#3138) from WPS (through R code)
  • deployment of Ichthyop model (#2344) by packaging R & Java codes with SAI and validation with statman.
  • deployment of ICCAT BFT-E codes (#1983) with SAI and validation with statman.
  • publication of html files on the infra (#2520) from statman
  • Discussion about annotation of charts, discussion about identified tools and possible options (#3153) to make use of such services on the infra (#3153, #3787).
  • requirement for providing RStudio in the e-Infrastructure VREs (#2516 & VRE #1779: IRD BFT Assessment)
  • Ecopath taxonomy dataformats (#1777)

ICES

  • Participated to training in Pisa,
  • Discussed data poor models to propose for integration with FAO and WECAFC
  • Initiated the integration work on the first model (CEFAS Horse Mackerel)

FAO

  • Commenced on using OpenCPU; first case are Statlant data for CCAMLR statistical reports (#1678, #3158, #3787)
  • Discussed data poor models to propose for integration with FAO and WECAFC

ENG

  • Import script for OSCAR NetCDF developed and tested in development infrastructure.

Task 5.2

Deliverables and Milestones

None required

#35 Updated by Anton Ellenbroek about 3 years ago

June2016 Effort report

Task 5.1

  • Preparation and particpation to Tcom
  • On-line seminar of Villy Christensen on Ecopath
  • Investigation to prepare ToR's and identify stock assessment support consultants ongoing
  • Initial dynamic reports developed and being extended
  • Stock assessment modules loaded through SAI with difficulty because users have to familiarize with an infrastructure environment
  • Identification and integration of additional models ongoing
  • issues identified with complex user work-flows and new software (python) requirements

Task 5.2

  • Preparation and particpation to Tcom
  • Construction of KB continued
  • Discussion on content classification, exposure, and retrieval intensified

Deliverables and Milestones

None required. Prepareation of D5.2 initiated

#36 Updated by Anton Ellenbroek about 3 years ago

July 2016 M11 Effort report

Task 5.1

  • Selection of SS3 model to start with WECAFC stock assesment activity
  • Initial dynamic reports based on OpenCPU and Sardara data developed and being extended
  • IRD Stock assessment modules loaded through SAI with difficulty because of coding styles etc.
  • Identification and integration of additional models ongoing

Task 5.2

  • Construction of KB continued
  • Discussion on content classification, exposure, and retrieval continued

Deliverables and Milestones

D5.2 was produced

#37 Updated by Anton Ellenbroek about 3 years ago

August 2016 M12 Effort report

Task 5.1

  • Analysis with consultant of SS3 and other models model for WECAFC stock assesment activity
  • Initial geospatial time based reports based on OpenCPU and Sardara data developed
  • IRD Ichtypop and stock assessment models loaded through SAI
  • IRD Ecopath activity to be re-adjusted to reduced developer availabiity
  • ICES request to use R-Shiny server
  • Identification and integration of additional models ongoing

Task 5.2

  • Construction of KB continued
  • Discussion on content classification, exposure, and retrieval completed

#38 Updated by Anton Ellenbroek almost 3 years ago

September 2016 M13 Effort report

Task 5.1

  • Shared WECAFC models and data with consultant (SS3 and other models model) and testing on R
  • Reporting time series based based on OpenCPU and Sardara data coninued
  • IRD Ichtypop and stock assessment models development continued
  • IRD Ecopath activity scaled down
  • ICES presented work at the ICES ASC workshop and worked on model preparation

Task 5.2

  • Construction of KB continued
  • Discussion on content alignment and maintenance

#39 Updated by Anton Ellenbroek almost 3 years ago

October 2016 M14 Effort report

All partners contributed to TCom

Task 5.1

  • WECAFC tested CMSY with consultant, and is testing SS3
  • Reporting time series based based on OpenCPU and Sardara data continued
  • IRD received and incorporated feedback from ICCAT WG stock assessment
  • IRD and FAO continue on Tuna atlas (Sardara and FAO Tuna Atlas) R and OpenCPU based services
  • ICES selected models, and performed test with infrastructure R-Studio for DLM tools (including Rshiny)
  • ENG Automating the process of publication of algorithms on dataminers
  • eng Completed the first prototype of SDMX data source

Task 5.2

  • Construction of KB continued
  • Discussion on content alignment and maintenance continued

#40 Updated by Anton Ellenbroek almost 3 years ago

November 2016 M15 Effort report

Task 5.1

Task 5.2

  • Construction of KB continued; Discussion on content alignment and maintenance continued; merging the (transformed) contents of the GRSF-related sources for ingesting them to the GRSF KB
  • Continued investigating storage solutions for content of the GRSF KB.
  • Continued development of data publishing in the CKAN catalog
  • FAO Validated the competency queries of the knowledge base

#41 Updated by Anton Ellenbroek over 2 years ago

December 2016 M16 Effort report

Task 5.1

Task 5.2

  • Created and updated a report version of the deliverable D5.2 #6014
  • Finalized the definition of mappings and created first version of KB
  • FAO Validated the competency queries of the knowledge base

Deliverable D.1 produced as a report

Deliverable D5.3, an update of D5.1 due this month was delayed to 2017.

#42 Updated by Anton Ellenbroek over 2 years ago

January 2017 M17 Effort report

All partners contributed to Review and Event in Brussels

Task 5.1

  • FLR was suggested by JRC, CNR added the R packages, FAO liasing with communty
  • WECAFC Regional Databse workplan and VRE plan development started
  • IRD incorporated feedback from ICCAT WG stock assessment for BFT
  • ENG continued with the first prototype of SDMX data source, waiting for integration
  • ICES has continued to develop the Data Limited Stock assessment apps and to identify functions within stock assessments that can be sent to BlueBridge for increased efficiency
  • Preparing P2 workplan:
    • VRE - RDB #6098 ; improved / simplified Tuna Atlas VRE for data collation (focus on WECAFC, see #5238)
    • VRE - FLR #6870 ; VRE serving te needs of the JRC community involved in stock assessment capacity building
    • VRE - WECAFC #5238 ; VRE serving the (simple) stock assessment needs in the WECAFC region, focus on training

Task 5.2

  • FORTH Started implementing patch services for updating parts of the GRSF Catalogue #6660
  • FAO Validated the competency queries of the knowledge base
  • Preparation for EAB TWG meeting in Rome started with community and developers; 29 Feb - 1 Mar

D5.3 in delay; all partners contributed to workplan, compilation of report on-going

#43 Updated by Julien Barde over 2 years ago

February 2017 M18 Effort report

D5.3 is in Delay; FAO wants to integrate the results of the EAB TWG and RDB meetings in the plan

Task 5.1: Support to stock assessment

  • RDA: writing a document defining data structures for some examples of Fisheries datasets

  • FAO_Tuna_ATLAS VRE :

    • update the public Web page of the VRE (as decided after the review in Brussels)
    • update the 'TunaAtlasToNetCDF.R' to generate NetCDF files in an automated way from Sardara database that comply with CF-Conventions and have additional global attributes. The creation of a generic algorithm to transform any table of data into NetCDF file is still ongoing. Validation will be done by testing this algorithm with new queries (other variables and dimensions of Sardara database).
  • Ichthyop_Model VRE; the identification of new algorithms to be deployed in the new VRE: comparison and simulation of trajectories (3 algorithms until now)

  • Several automated reports are in progress: using the VRE for the collaborative edition of an article by IRD using sharelatex that supports users to validate methods and compile the code in the infra. FAO continues on the use of OpenCPU and RNotebooks. A reconciliation of effort is needed to prevent parallel reporting tools.

  • Stock assessment support continued; FLR in FAO, and DLM Tool in ICES are progressing. The progress in the SDMX approach to manage data through DSD's is rather slow.

  • RDB: A succesful meeting was prepared an held in Rome on the requirements engineering of a template driven data collection tool; CNR to evaluate th euse of TabMan service; FAO to recruit a consultant

Task 5.1: GRSF

  • A EAB TWG was convened in FAO to discuss with major stakeholders the progress and pans for GRSF.

Task 5.3: Other

  • On re-usability; WP5 and WP7 are discussing the sharing of webviewer components

#44 Updated by Anton Ellenbroek over 2 years ago

March 2017 M19 Effort report

D5.3 is in Delay; FAO wants to integrate the results of the EAB TWG and RDB March meetings in the plan

Task 5.1: Support to stock assessment

  • RDA: Prepared for Plenary Barcelone on Fisheries data interoperability (for WP2)

  • FAO Stock assessment VRE :

    • RDB meeting in Rome, and prepared workplan => consultant need identified; TabMan backend (API Rest/Soap) developer for Regional database development and a front-end developer (May-Sep activity)
    • FAO continues on the use of OpenCPU and RNotebooks; recruited consultant to add stock assessment algorithms to RShiny
  • ENG

    • released a new version of SDMX exporter from Tabman. It supports Fusion Registry 8 and Data Structure export from tables and templates (for the latter feature the Portlet should be updated)
  • IRD

  • Ichthyop_Model VRE;

  • IRD using sharelatex that supports users to validate methods and compile the code in the infra.

  • Stock assessment support continued; FLR in FAO, and DLM Tool in ICES are progressing. The progress in the SDMX approach to manage data through DSD's is rather slow.

Task 5.2: GRSF

  • A EAB TWG was convened in FAO to discuss with major stakeholders the progress and plans for GRSF.
  • Republished GRSF records in the catalogue for administrators based on the feedback received.

Task 5.3: Other

  • On re-usability; WP5 and WP7 are discussing the sharing of webviewer components

#45 Updated by Anton Ellenbroek over 2 years ago

April 2017 M20 Effort report

D5.3 is in Delay; FAO wants to integrate the results of the EAB TWG and RDB March meetings in the plan

Task 5.1: Support to stock assessment

  • RDA: Participated to Plenary Barcelone on Fisheries data interoperability (with WP2)

  • FAO Stock assessment VRE :

    • RDB consultant needs identified; TabMan backend developer for Regional database development and a front-end developer (May-Sep activity)
    • RDB Consultant recruitement on hold => action needed
    • FAO recruited consultant (starts 08 May) to add stock assessment algorithms to RShiny => Discussed CMSY with WECAFC
    • Progress on several models; IRD recruited SS3 developer (in-kind contribution in a collaboration with IFREMER and IOTC) ; Added algorithms for Ichthyop_Model VRE (for now on StockAssessment VRE) and ICCAT_BFT-E VRE,
  • ENG delivered new SDMX expport facilities for DSD and data

Task 5.2: GRSF

Task 5.3: Other

  • On re-usability; WP5 and WP7 are discussing the sharing of webviewer components
  • A meeting with MSC is planned in Pisa; preparations on-going
  • A presentation on data collection is being planned in the Bahamas (Yann and Anton to attend in June)
  • Interest in the BoBLME VRE was repeated

#46 Updated by Anton Ellenbroek over 2 years ago

May 2017 M21 Effort report

D5.3 is in Delay; FAO wants to integrate the results of the EAB TWG and RDB March meetings in the plan

Task 5.1: Support to stock assessment

  • RDA: Participated to Plenary Barcelone on Fisheries data interoperability (with WP2)

  • FAO Stock assessment VRE :

    • RDB consultant needs identified; TabMan backend developer for Regional database development and a front-end developer (May-Sep activity)
    • RDB Consultant recruitement on hold => action needed
    • FAO recruited consultant (starts 08 May) to add stock assessment algorithms to RShiny => Discussed CMSY with WECAFC
    • Progress on several models; IRD recruited SS3 developer (in-kind contribution in a collaboration with IFREMER and IOTC) ; Added algorithms for Ichthyop_Model VRE (for now on StockAssessment VRE) and ICCAT_BFT-E VRE,
  • ENG delivered new SDMX expport facilities for DSD and data

Task 5.2: GRSF

Task 5.3: Other

  • On re-usability; WP5 and WP7 are discussing the sharing of webviewer components
  • A meeting with MSC is planned in Pisa; preparations on-going
  • A presentation on data collection is being planned in the Bahamas (Yann and Anton to attend in June)
  • Interest in the BoBLME VRE was repeated

#47 Updated by Anton Ellenbroek about 2 years ago

June 2017 M22 Effort report

D5.3 is in Delay; FAO wants to integrate the results of the EAB TWG and RDB March meetings in the plan

Task 5.1: Support to stock assessment

  • RDA: Participated to monthly RDA Call, and RDA BB Datathon.

  • FAO Stock assessment VRE :

    • RDB development; TabMan backend developer for Regional database development
    • RDB front-end developer identified (Aug-Oct activity)
    • FAO consultant (started 08 May) continued CMSY DLM method in RShiny => With WECAFC
    • Progress on several models; Added algorithms for Ichthyop_Model VRE (for now on StockAssessment VRE) and ICCAT_BFT-E VRE,
  • ENG delivered new SDMX expport facilities for DSD and data

Task 5.2: GRSF

Task 5.3: Other

  • On re-usability; WP5 and WP7 are discussing the sharing of webviewer components
  • A meeting with SFP planned on new training VRE; July 6th
  • A presentation on data collection was given to meeting in the Bahamas (Yann and Anton attended)
  • IRD continued SS3 development (in-kind contribution in a collaboration with IFREMER and IOTC) ;

#48 Updated by Anton Ellenbroek about 2 years ago

July M23 and August M24 2017 Effort report

D5.3 is in Delay; FAO wants to integrate the results of the EAB TWG and RDB March meetings and april / May progress on stock assessment in the plan

Task 5.1: Support to stock assessment

  • FAO Stock assessment VRE :

    • RDB development; TabMan backend needs identified; requires PSC and GA approval
    • RDB front-end developer identified (Aug-Oct activity) ; started in AUG
    • Produced modified CMSY code using vectorization that significantly reduced runtime of CMSY (#8501 #8503).
    • Identified issue of species specific extreme runtime for CMSY (#8501 #8503).
    • Working with CNR to benchmark new code against expanded example species set and implement new code in dataminer (#8501 #8503).
  • FAO consultant (started 08 May) completed CMSY DLM method in RShiny => See T5.3

  • IRD continued on several models; algorithms for Ichthyop_Model VRE (for now on StockAssessment VRE) and ICCAT_BFT-E VRE,

  • ICES received new VSURF capability,

  • ICES will share stock assessment developer with FAO

Task 5.2: GRSF

Task 5.3: Other

  • FAO continues developing a VRE oriented business model for GRSF and stock assessment services (Started Aug)
  • IRD continued SS3 development (in-kind contribution in a collaboration with IFREMER and IOTC) ;
  • FAO identified (WP8 related) opportunity to develop SDG 14.4.1 stock assessment self-training module

#49 Updated by Anton Ellenbroek almost 2 years ago

M25 September 2017 Effort report

Task 5.1: Support to stock assessment

  • Thredds confguration: working on configuration of Thredds to set up catalogs for VREs
  • IOTC SS3 VRE:
    • keep on developing a shiny application and dynamic report for IOTC / SS3 outputs
    • creating a workflow to extract metadata from NetCDF files using Thedds / OPeNDAP and R Codes
  • ICCAT BFT-E VRE: update metadata of NetCDF (2014 stock assesment outputs), same (ongoing work) for 2017 and dynamic report (with Sharelatex)
  • Ichthyop model:
    • "Enrichment_From_Netcdf" algorithm: can now use more than one product (natively OSCAR)
    • "Enrichment_From_Netcdf" algorithm: parallelization (ongoing)
    • "SCATTERPLOT_DIAGRAM" algorithm: possibility to create scatterplots diagram from 2 variables (to be specified as input parameters)
  • Tickets: #9826

FAO

  • Developing mean-length based mortality estimator attachment for Stock assessment shiny app
  • Developing a how-to guide for the development of Shinyproxy docker images. #8902
  • Implementing new fast CMSY package within data-miner
  • SDMX related activities (#7358)

FAO / WECAFC

  • Testing existing DLMtoolkit shiny application to identify further development requirements. #9869
  • Developing preliminary training plans for introduction workshop to VRE and data limited methods

FAO / ICES

  • Started to look into the Transparent Assessment Framework (TAF) as an option / inspiration for sharing fisheries data across stock assessment methods

ENG

  • SDMX related activities progressing; excel exporter module of Tabman, SDMX Data Source

Task 5.2: GRSF

  • FAO FORTH Presentation of currently ongoing GRSF technical activities in 6th TCOM (Sophia Antipolis)
  • FORTH pdated mappings from GRSF underlying sources; FIRMS (#10091), RAM (#10092), FishSource (#10093)

Task 5.3: Other

  • FAO continues developing a VRE oriented business model for GRSF and stock assessment services (Started Aug)
  • IRD continued SS3 development (in-kind contribution in a collaboration with IFREMER and IOTC) ;
  • FAO identified (WP8 related) opportunity to develop SDG 14.4.1 stock assessment self-training module

#50 Updated by Anton Ellenbroek almost 2 years ago

M26 October 2017 Effort report

Task 5.1: Support to stock assessment

  • Thredds confguration: working on configuration of Thredds to set up catalogs for VREs
  • IOTC SS3 VRE:
    • keep on developing a shiny application and dynamic report for IOTC / SS3 outputs
    • creating a workflow to extract metadata from NetCDF files using Thedds / OPeNDAP and R Codes
  • ICCAT BFT-E VRE: update metadata of NetCDF (2014 stock assesment outputs), same (ongoing work) for 2017 and dynamic report (with Sharelatex)
  • Ichthyop model:
    • "Enrichment_From_Netcdf" algorithm: can now use more than one product (natively OSCAR)
    • "Enrichment_From_Netcdf" algorithm: parallelization (ongoing)
    • "SCATTERPLOT_DIAGRAM" algorithm: possibility to create scatterplots diagram from 2 variables (to be specified as input parameters)
  • Tickets: #9826

FAO

  • Developing mean-length based mortality estimator attachment for Stock assessment shiny app
  • Developing a how-to guide for the development of Shinyproxy docker images. #8902
  • Implementing new fast CMSY package within data-miner
  • SDMX related activities (#7358)

FAO / WECAFC

  • Testing existing DLMtoolkit shiny application to identify further development requirements. #9869
  • Developing preliminary training plans for introduction workshop to VRE and data limited methods

FAO / ICES

  • Started to look into the Transparent Assessment Framework (TAF) as an option / inspiration for sharing fisheries data across stock assessment methods

ENG

  • SDMX related activities progressing; excel exporter module of Tabman, SDMX Data Source

Task 5.2: GRSF

  • FAO FORTH Presentation of currently ongoing GRSF technical activities in 6th TCOM (Sophia Antipolis)
  • FORTH pdated mappings from GRSF underlying sources; FIRMS (#10091), RAM (#10092), FishSource (#10093)

Task 5.3: Other

  • FAO continues developing a VRE oriented business model for GRSF and stock assessment services (Started Aug)
  • IRD continued SS3 development (in-kind contribution in a collaboration with IFREMER and IOTC) ;
  • FAO identified (WP8 related) opportunity to develop SDG 14.4.1 stock assessment self-training module

#51 Updated by Anton Ellenbroek almost 2 years ago

M27 November 2017 Effort report

Task 5.1: Support to stock assessment

IRD

  • first version of a shiny application for IOTC / SS3 outputs has been dockerized and deployed
  • improvements to the workflow to extract metadata from NetCDF files using Thedds / OPeNDAP and R Codes have been successfully tested
  • interoperability through harmonization of headers of NetCDF files (names of variables and related attributes) will enable to reuse ICCAT shiny apps to visualize SS3 outputs

FAO

  • Developed the RShiny based tool, and this was used in teh SDG14.4.1 workshop

FAO / WECAFC

  • Testing existing DLMtoolkit shiny application to identify further development requirements.
  • Developing preliminary training plans for introduction workshop to VRE and data limited methods

FAO / ICES

  • Started to look into the Transparent Assessment Framework (TAF) as an option / inspiration for sharing fisheries data across stock assessment methods

ENG

  • SDMX related activities progressing; excel exporter module of Tabman, SDMX Data Source

Task 5.2: GRSF

  • FAO FORTH Preparing release of new GRSF Admin mid-December
  • FAO Forth preparing Feb 6-8 Technical Working group meeting in Rome

Task 5.3: Other

  • FAO continues developing a VRE oriented business model for GRSF and stock assessment services (Started Aug)
  • IRD continued SS3 development (in-kind contribution in a collaboration with IFREMER and IOTC) ;
  • FAO identified (WP8 related) opportunity to develop SDG 14.4.1 stock assessment self-training module

#52 Updated by Anton Ellenbroek over 1 year ago

M28 December 2017 Effort report

Task 5.1: Support to stock assessment

IRD

  • first version of a shiny application for IOTC / SS3 outputs has been dockerized and deployed
  • improvements to the workflow to extract metadata from NetCDF files using Thedds / OPeNDAP and R Codes have been successfully tested
  • interoperability through harmonization of headers of NetCDF files (names of variables and related attributes) will enable to reuse ICCAT shiny apps to visualize SS3 outputs

FAO

  • Developed the RShiny based tool, and this was used in teh SDG14.4.1 workshop

FAO / WECAFC

  • Testing existing DLMtoolkit shiny application to identify further development requirements.
  • Developing preliminary training plans for introduction workshop to VRE and data limited methods

ICES

  • Worked with N.Vaughan on

ENG

  • SDMX related activities progressing; excel exporter module of Tabman, SDMX Data Source

Task 5.2: GRSF

  • FAO FORTH Preparing release of new GRSF Admin mid-December
  • FAO FORTH Preparing Feb 6-8 Technical Working group meeting in Rome

Task 5.3: Other

  • FAO continues developing a VRE oriented business model for GRSF and stock assessment services (Started Aug)
  • IRD continued SS3 development (in-kind contribution in a collaboration with IFREMER and IOTC) ;
  • FAO continued (WP8 related) opportunity to develop SDG 14.4.1 stock assessment self-training module

#53 Updated by Anton Ellenbroek over 1 year ago

M29 January 2018 Effort report

Task 5.1: Support to stock assessment

IRD
* Stock Assessment / Ichthyop VRE:
- Update of algorithm "Enrichment_From_Netcdf" (https://i-marine.d4science.org/group/rprototypinglab/data-miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ENRICHMENT_FROM_NETCDF) on DataMiner to manage a new satellite product (SST/OSTIA) and better manage time data type
- Validation of the code by comparing SST collected by OSTIA (remote sensing) with in situ data collected by onboard observers working with french fishing vessels. Outputs (plots) have been processed by reusing algorithms of the ‘FADs Vs Drifter’ knitr article (in prep).

  • IOTC SS3 VRE:

    • update of scripts to manage a new SS3 version (from ss3.24ab to ss3.24z)
    • adapting NOAA greater amberjack and Atlantic bluefin tuna code to VRE ss3write* scripts and editing shiny to account for a new spp
  • Tuna Atlas VRE finalization of the workflow (R & SQL) for the setup and update of the Tuna atlas DB and successful test of this workflow (i.e. filling of the new tuna atlas DB). Samples of outputs can be seen here: https://goo.gl/QtS6LZ

  • Metadata workshop Montpellier:

FAO

  • Continued development of the RShiny based tool, this was discussed for use @ FAO corporate level for SDG14.4.1 eLearning

FAO / WECAFC

  • Developing preliminary training plans for introduction workshop to VRE and data limited methods
  • Test of RDB features

ENG

  • SDMX related activities progressing; excel exporter module of Tabman, SDMX Data Source pre production Tests and bug fixing

Task 5.2: GRSF

  • FAO FORTH Preparing release of new GRSF Admin and competence queries
  • FAO FORTH Preparing Feb 6-8 Technical Working group meeting in Rome

Task 5.3: Other

  • FAO initiated the CWP catalogue for statistical reference data related to fisheries.

#54 Updated by Anton Ellenbroek over 1 year ago

M30 February 2018 Effort report and closing statements

Task 5.1: Support to stock assessment

IRD
* Stock Assessment / Ichthyop VRE:

  • IOTC SS3 VRE:

  • Tuna Atlas VRE

  • Other activities:

FAO

  • Continued development of the RShiny based tool, this was discussed for use @ FAO corporate level for SDG14.4.1 eLearning

FAO / WECAFC

  • Developing preliminary training plans for introduction workshop to VRE and data limited methods

ENG

  • SDMX related activities progressing; excel exporter module of Tabman, SDMX Data Source pre production Tests and bug fixing

Task 5.2: GRSF

  • FAO FORTH Preparing release of new GRSF Admin and competence queries
  • FAO FORTH Preparing Feb 6-8 Technical Working group meeting in Rome

Task 5.3: Other

  • FAO initiated the CWP catalogue for statistical reference data related to fisheries.
  • Test of RDB features by consultant

#55 Updated by Pasquale Pagano over 1 year ago

  • Status changed from In Progress to Closed

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