General
Draft agenda available on the SeaDataNet website
For any queries contact SDC Training on sdctraining@naturalsciences.be
Topic outline
Introduction & Welcome
View Section ModulesIODE / OTGA
Instructors
- Serge Scory, RBINS
- Reiner Schlitzer, AWI
- Sebastian Mieruch, AWI
- Paula Oset Garcia, VLIZ
- Daphnis De Pooter, VLIZ
- Sri Harsha Vathsavayi, CSC
- Dick MA Schaap, MARIS
- Peter Thijse, MARIS
- Alexandra Kokkinaki, IFREMER
- James Ayliffe, IFREMER
- Michele Fichaut, IFREMER
- Vanessa Tosello, IFREMER
- Aurélie Briand, IFREMER
- Sophie Bregent, IFREMER
Modules:File: 1Pre 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:
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:
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R Software (RStudio Desktop, R-3.5.0 for Windows (32/64 bit))
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NetCDFViewer or NetCDF Library 4.6.1 for NetCDF 3 to have ncdump function
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Text editor (such as Notepad ++, TextPad) to edit text data files
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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.
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Data Quality: the experience of the regional product managers, recomendations
View Section ModulesSerge Scory, with input from SDC products and EMODnet - Chemistry products
Modules:File: 1Introduction to ODV v5
View Section ModulesReiner 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.
Modules:Files: 2Assignments: 2Using ODV for Quality Control
View Section ModulesReiner 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
Modules:Assignments: 3Folders: 5Biological Data
View Section ModulesPaula Oset & Daphnis De Pooter (VLIZ)
Temporary link to this topic resources: https://drive.google.com/drive/folders/1kYtygYl20KCVL95obD2LMkDRh-5kQcm1
Further reading / Useful Links:
Modules:Files: 2Assignments: 2Import process
View Section ModulesPeter Thijse, MARIS
- Restricted and unrestricted data, dashboard and live demonstration
Modules:File: 1Implementation Plan
View Section ModulesMARIS
Topics to be covered:
- planning, system versions, data preparation, dc groups in time
Modules:File: 1New CDI user interface demo and user trial
View Section ModulesPeter Thijse, MARIS
Presentation of the Beta version and user feedback
Modules:File: 1Vocabulary new developments
View Section ModulesAlexandra Kokkinaki and James Ayliffe (BODC)
Tools:
- BODC Vocab Search
- BODC P01 search
- BODC Vocab Builder
- MARIS Vocab Hierarchical Search
- MARIS faceted search for P01
Modules:File: 1Quiz: 1Improving the workflow from data centre to CDI catalogue
View Section ModulesMichele 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
Modules:File: 1Workshop SeaDataNet tools: NEMO new functions
View Section ModulesMichele 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
Modules:File: 1Assignment: 1Folder: 1Workshop SeaDataNet tools: OCTOPUS
View Section ModulesMichele 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
Modules:Files: 2Assignment: 1Workshop SeaDataNet tools: Mikado
View Section ModulesMichele 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
Modules:File: 1Assignments: 3Folders: 5