SeaDataCloud

Topic outline

• General
  

  General

  Draft agenda available on the SeaDataNet website

  For any queries contact SDC Training on sdctraining@naturalsciences.be
• Introduction & Welcome

  IODE / OTGA

  Instructors

  • Serge Scory, RBINS
  • Reiner Schlitzer, AWI
  • Sebastian Mieruch, AWI
  • Paula Oset Garcia, VLIZ
  • Daphnis De Pooter, VLIZ
  • Sri Harsha Vathsavayi, CSC
  • ** MA Schaap, MARIS
  • Peter Thijse, MARIS
  • Alexandra Kokkinaki, IFREMER
  • James Ayliffe, IFREMER
  • Michele Fichaut, IFREMER
  • Vanessa Tosello, IFREMER
  • Aurélie Briand, IFREMER
  • Sophie Bregent, IFREMER
• Pre Assignments

  In case you are not familiar with the SDC infrastructures and services, please review the Technical Documentation Catalog prior to the course.

• Mandatory Software

  All participants need to install the following software to follow the course:

  • ODV 5.0.0

  • NEMO 1.6.6

  • MIKADO 3.5.1

  • OCTOPUS 1.4.1

  All the above are available on https://www.seadatanet.org/Software

  Note: to ensure Octopus runs properly, the laptop should have a minimum resolution of 1920 x 1080.

  Additionally, make sure to install the following:

  • R Software (RStudio Desktop, R-3.5.0 for Windows (32/64 bit))

  • NetCDFViewer or NetCDF Library 4.6.1 for NetCDF 3 to have ncdump function

  • Text editor (such as Notepad ++, TextPad) to edit text data files

  • Open Office for tests in MIKADO

  • make sure that the java version (Java Runtime Environment (JRE)) on your computer is ≥ 1.8. If not, please install it:  Java

  NOTE: If you run NEMO and OCTOPUS with Java 9 or 10, you need to install the following patch:

  • NEMO-OCTOPUS - Patch for Java 9/10 (Linux) : Unpack the zipfile and follow the instructions of the Readme.txt file.
  • NEMO-OCTOPUS - Patch for Java 9/10 (Windows): Unpack the zipfile and follow the instructions of the Readme.txt file.

• Data Quality: the experience of the regional product managers, recomendations

  Serge Scory, with input from SDC products and EMODnet - Chemistry products

• Introduction to ODV v5

  Reiner Schlitzer & Sebastian Mieruch, AWI

  1. What is new in ODV 5.0.0
  
  ODV 5.0.0 for the first time allows working with multiple open views at the same time. The new Views Bar located just below the main menu bar lets you easily open and save views, undo or redo recent view changes, switch to or from layout mode, or select one of the open views by clicking on its tab.

  
  Figure 1: Example views bar with plus, undo, redo, layout and save buttons as well as tabs for three open views

  
  2. ODV Importers
  The ODV import system was completely revamped and the class structure was simplified. Importing data from other ODV collections is now possible for the first time. All importers, including ODV Spreadsheet, now support multi-file import, and zipped files are automatically un-zipped before import. Importers such as Argo, SeaDataNet and WOD now extract more metadata and data from the files. The speed of the SeaDataNet importer has improved by almost ten-fold.

  
  3. New Features
  • Collection > Create Overview Plots: Automatically generates SCATTER overview plots showing all data for all data variables of the collection.
  • Tools > Other Collection > Compare Data Availability: Compares data availability of open collection with data availability of another collection.
  • Tools > Other Collection > Inherit View File(s): Inherits view files from another collection for use with the open collection.

  Installation: ODV 5 is installed side-by-side to any previous ODV version on your system, and you can continue using your older ODV version. Please note that the .odv and .var file extensions are associated with ODV 5 during installation, and double-clicking on these files will run the new ODV 5. Also please note that view files created with the new ODV 5 cannot be opened by previous ODV versions.

  Note: to follow this session you will need to install ODV 5.0.0, available at ODV Download.

• Using ODV for Quality Control

  Reiner Schlitzer & Sebastian Mieruch, AWI

  Hands on Exercises

  Topics to be covered on this session:

  • Hands-on-practice: Customization and general procedures 
  • Data QC using automatic and visual procedures

  Note: to follow this session you will need to install ODV 5.0.0, available at ODV Download.

  For more questions please check the ODV Forum

• Biological Data

  Paula Oset & Daphnis De Pooter (VLIZ)

  Temporary link to this topic resources: https://drive.google.com/drive/folders/1kYtygYl20KCVL95obD2LMkDRh-5kQcm1

  Further reading / Useful Links:

  • http://iobis.org/manual/emof-bodc/
  • http://iobis.org/vocab/
  • https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/
  • http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P01 (abundance%entity)

  Example dataset fully processed

• Upgrade of the CDI Services: introduction with background and system components

  ** Schaap, MARIS

• EUDAT Services SeaDataCloud

  Sri Harsha Vathsavayi, CSC

• The Replication Manager

  Aurélie Briand (IFREMER) & Sophie Bregent (Altran)

• Import process

  Peter Thijse, MARIS

  • Restricted and unrestricted data, dashboard and live demonstration
• Implementation Plan

  MARIS

  Topics to be covered:

  • planning, system versions, data preparation, dc groups in time
• New CDI user interface demo and user trial

  Peter Thijse, MARIS

  Presentation of the Beta version and user feedback

• Vocabulary new developments

  Alexandra Kokkinaki and James Ayliffe (BODC)

  Tools:

  • BODC Vocab Search
    • https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/
  • BODC P01 search
    • https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/P01/
  • BODC Vocab Builder
    • https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/
  • MARIS Vocab Hierarchical Search
    • http://seadatanet.maris2.nl/v_bodc_vocab_v2/vocab_relations.asp?lib=P08
  • MARIS faceted search for P01
    • http://seadatanet.maris2.nl/bandit/browse_step.php
• Improving the workflow from data centre to CDI catalogue

  Michele Fichaut & Vanessa Tosello, IFREMER

  Summary

  • Improving the work flow from data centres to CDI catalogue using the SeaDataNet tools
  • Presentation and Hands-on session on tools
    • NEMO: last developments and corresponding exercises
    • OCTOPUS: New software developed in SeaDataCloud
    • MIKADO: last developments and corresponding exercises
• Workshop SeaDataNet tools: NEMO new functions

  Michele Fichaut & Vanessa Tosello, IFREMER

  Summary:

  • Reminder of NEMO main features and principles
  • NEMO last developments
  • NEMO future developments
  • Hands-on session

  Hands on Session Objectives:

  • Be trained on the last functions implemented in NEMO software
  • Management of the sdn_reference (links to CSR and CDI catalogue and to the C17 vocabularies in the datafile)
  • Management of the instruments
  • Management of the fall rate for XBTs
  • New method for managing CSV files
• Workshop SeaDataNet tools: OCTOPUS

  Michele Fichaut & Vanessa Tosello, IFREMER

  Summary:

  • Reminder on OCTOPUS, and all its functions
  • Releases of Octopus
  • New developments
  • Next release
  • Detailed presentations of the functions

  Hands on Session Objectives:

  • Be trained on the OCTOPUS software:
    • Test all the functions
    • Work on the file previously created using NEMO
    • Find errors in data files
• Workshop SeaDataNet tools: Mikado

  Michele Fichaut & Vanessa Tosello, IFREMER

  Summary:

  • Reminder of MIKADO main features and principles
  • MIKADO last developments and main changes
  • Best practice for EDMED, EDIOS, CDI content
    • Recurrent errors 
    • Recommendations
  • Hands-on session

  Hands on session objectives:

  • Be trained on specific functions of the MIKADO softwar, specifically:
    • Generation of CDI XML files using the NEMO summary file
    • Adding CSR and EDMED references in CDI files using MIKADO manual and MIKADO automatic
    • Alternative solutions for CDI generation for Excel users
• Online feedback survey

  Not available