An introduction to NIRD and SIOS

Luke Marsden, UNIS

(data.nleg@unis.no)

Introduction

Have you ever asked yourself any of these questions?

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• What is the difference between SIOS and NIRD?
• What are they used for in AeN?
• Where should I put my data?
• What is expected of me in relation to data management as a researcher in AeN?

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Then you have come to the right place!

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Contents

• What is SIOS used for in AeN?

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• What is NIRD used for in AeN?

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• NIRD project areas

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• Steps to get you up and running with NIRD

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• Navigating to different areas in NIRD

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• Using the work area in NIRD

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What is SIOS used for in AeN?

• SIOS is used for
• Uploading event meta-data for data collected during cruises. This is done by a data manager, using the excel template filled in by the researchers during the cruise. This should be done as soon as possible after the cruise.
• Searching for event metadata relating to samples using the event catalog

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• Published AeN datasets are included as a separate collection (AeN) in the SIOS Data Management System search interface which is available at SIOS data search catalogue.

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• The data itself is not stored on SIOS. SIOS simply provides a search interface that can direct you to the data.

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• Published datasets are served by contributing data centres, including NMDC, NPI, NorDataNet, MET and NIRD Research Data Archive (i.e. not the project area mentioned on slide 6).

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What is NIRD used for in AeN?

• NIRD (formerly known as Norstore) provides large amounts of storage to researchers who need to store their data.

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• In AeN, NIRD is used for
• Viewing and sharing unpublished AeN data
• Viewing read-only raw data from the cruises
• Creating a work area involving multiple collaborators
• Staging data for publication
• Data can be published through the NIRD Research data Archive, but must be searchable in the SIOS Data Management System (i.e. not the project area mentioned on slide 6).

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NIRD project areas for AeN

NIRD contains a number of project areas. The following project areas are used in AeN:

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• NS9610K:
• Data from cruises are uploaded to this project. Only used by data managers.

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• NS9677K:
• Read-only access to raw data. Data from NS9610K that are made available for AeN users are shared via NS9677K. It is then accessible through the area of NS9530K. This approach means that the raw data is read only for all users that are accessing these through NS9677K.

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• NS9530K:
• To be used for staging of data before publication or further analysis. All data from NS9610K that are shared via NS9677K are available through this project. This can be used to prepare your own data or make modifications to data.

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AeN users should request access to projects NS9530K and NS9677K

(instructions slides 8-15).

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NIRD project areas for AeN

The following directories are particularly important for AeN users:

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• Raw data:

/projects/NS9530K/nansen_legacy/raw_data

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• Processed data:

/projects/NS9530K/nansen_legacy/processed_data

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• Work area:

/projects/NS9530K/nansen_legacy/work

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Each directory contains a README file that instructs the user on how to use it. This should be read before you start working in the directory.

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Steps to get you up and running with NIRD

1. Applying for a NIRD account
2. Accessing NIRD:
1. Using WinSCP
2. Using the command line

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Steps to get you up and running with NIRD�1. Applying for an account

• To access NIRD, you must first register for an account. You can do this by following the link below.
• NIRD/Norstore

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• If you need any help filling in the form, instructions are linked below.
• https://www.sigma2.no/how-apply-user-account

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• If you need access to multiple projects, you can fill in the form as many times as you need, in the same way. The first application will create your account and any following applications will update it.

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• AeN users should request access to projects NS9530K and NS9677K (described slide 6).

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• Once you have received your password, you have to change it
• https://www.sigma2.no/how-change-passwords

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Steps to get you up and running with NIRD�1. Applying for an account

You will receive email confirmation that your account has been created

Steps to get you up and running with NIRD�1. Applying for an account

If you applied to more than one project, you will receive additional emails stating that your account has been updated.

Steps to get you up and running with NIRD�2. Accessing NIRD

• NIRD can be accessed using WinSCP or via the command line.

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• For most people, using WinSCP is easiest, as it contains a user-friendly graphical interface. This software is available for Windows users only, but alternative software is available such as FileZilla or Cyberduck.

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• If you are comfortable using the command line, you can also access NIRD using secure shell (ssh) in your terminal.

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• Introductory instructions for both methods are next!

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Steps to get you up and running with NIRD�2a. Accessing NIRD using WinSCP

• To download WinSCP, please follow the instructions linked below, or download it from your software centre.
• https://documentation.sigma2.no/files_storage/file_transfer/WinSCP.html

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• Instructions on how to access and use WinSCP are also provided in the link above.

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• Use these details when logging in
• Host name: login.nird.sigma2.no
• User name: Your NIRD username
• Password: Your NIRD password

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Steps to get you up and running with NIRD�2b: Accessing NIRD using the command line

• Access to NIRD is only permitted using secure shell (ssh). See some instructions linked below:
• https://documentation.sigma2.no/files_storage/file_transfer.html
• To connect to NIRD in your terminal, you can use ‘ssh’, which provides a secure encrypted connection between NIRD and your local machine.

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• You can then navigate then use terminal commands as usual, for example:

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• Exit by typing exit or pressing CTRL+D.

username@host:filepath

Enter your NIRD password when prompted

Steps to get you up and running with NIRD�2b: Accessing NIRD using the command line

• To copy a file from your host computer to your home directory on NIRD:

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• Note that you should not be ‘connected’ to NIRD in your terminal before doing this.
• Tip: Open a second terminal window, so you are connected in one but not in the other.

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Secure copy

File name

username@host:filepath

Enter your NIRD password when prompted

Navigating to different areas in NIRD

When you log in via WinSCP, you will be located in your home directory. First, navigate to the ‘root’ directory. Then you can navigate to projects, and into NS9530K.

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Files can be copied to or from your host machine by dragging and dropping between panels. Alternatively, right click the file/folder and select upload/download.

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Raw data:

/projects/NS9530K/nansen_legacy/raw_data

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Processed data:

/projects/NS9530K/nansen_legacy/processed_data

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Work area:

/projects/NS9530K/nansen_legacy/work

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Using the work area

• The work area can be used to create shared working directories in which a group of researchers can share their data and work.

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• A folder may be created in this directory:
• /projects/NS9530K/nansen_legacy/work

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• Your working area must contain a README.txt file that should include:
• Who is responsible for the project
• Contact information
• An approximate date that you expect the data to be published by.

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• You can copy and edit the ‘Template_README.txt’ file in the ‘work’ directory.

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• Please make sure the directory is deleted once the data has been published.

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