Data access and transfer#

The UNLOCK FAIR Data Platform provides long-term, structured storage for all project data and metadata, and supports flexible access and data transfer across different analysis tools and systems. This storage and management is handled through iRODS, according to the UNLOCK ontology.

Data management backend#

The underlying storage system of the UNLOCK FDP is powered by iRODS (integrated Rule-Oriented Data System), an open source data management software solution. It enables the UNLOCK FDP to capture all data that is generated during an experiment and to access and transfer this data. For example, this could be data obtained from bioreactor measurements, proteomics or standard sequencing procedures. Through standardisation procedures the data becomes better organised, containing essential metadata elements and loss or corruption of data should not happen anymore. Currently, standards for genomics, transcriptomics and amplicon sequencing are in place. Other formats will become available when an agreement on standardisation has been made.

Accessing and transferring data#

There are various ways to access and transfer the data on the UNLOCK FDP. Broadly, these methods can be split into WebDAV-based and directly iRODS-based.

  • WebDAV-based methods offer a user-friendly way to browse, upload, and download data using standard tools such as web browsers, file explorers and graphical file transfer clients.

  • iRODS-based methods provide more powerful and flexible options for managing, scripting, and automating data transfers.

WebDAV-based access#

The connection details for the UNLOCK FDP are:

Field

Value

Host

https://data.m-unlock.nl/

Port

443

User

SRAM USERNAME

Token

SRAM TOKEN

Web interface#

As stated in the previous page, the most straightforward way to access the UNLOCK FDP is to use your credentials at the web interface: https://data.m-unlock.nl. This method uses Davrods, which integrates the WebDAV protocol with iRODS and is compatible with all major browsers. This method is limited to file browsing.

Graphical transfer clients#

Graphical file transfer clients are intuitive and easy to use. They are also suited for uploading large amounts of data to the system. To find out how to install such a client with WebDAV support, follow the instructions in the dropdown menu below. Usage is as simple as dragging and dropping files, with added features for each client.

Graphical transfer client installation

Click the tab that corresponds to your operating system.

For Windows users there are two options: WinSCP, which is native to Windows, or Cyberduck which also has Mac support. WinSCP is more lightweight, but note that some older versions had a limitation when uploading individual files over WebDAV, with a maximum size of 4 GB per file.

  • WinSCP

  1. Download WinSCP from https://winscp.net/eng/download.php

  2. Install and open up WinSCP

  3. You will be prompted to fill in a New Site (if not open one yourself), then select the WebDAV protocol and turn on encryption

  4. Fill in your credentials, refer to the image below:

../../_images/winscp_login.png

  • Cyberduck

  1. Download Cyberduck from https://cyberduck.io

  2. Install and open up Cyberduck

  3. Add a new connection by clicking on the “Open Connection” button

  4. Select the WebDAV protocol and fill in your credentials, refer to the image below:

../../_images/cyberduck_login.png

Cyberduck is available for both Mac and Windows.

  1. Download Cyberduck from https://cyberduck.io

  2. Install and open up Cyberduck

  3. Add a new connection by clicking on the “Open Connection” button

  4. Select the WebDAV protocol and fill in your credentials, refer to the image below:

../../_images/cyberduck_login.png

Network drive#

It is possible to mount the UNLOCK FDP storage locally as a network drive. To accomplish this, follow the instructions in the dropdown menu below.

Network drive usage

Click the tab that corresponds to your operating system.

In Windows, you can mount the WebDAV system as a network drive:

  1. Open File Explorer

  2. Right-click on This PC or the computer icon

  3. Select Map network drive

  4. Paste the full WebDAV URL in the Folder field and fill in your SRAM credentials

../../_images/webdav_windows.png

Click Finish. When prompted for username/password, provide your SRAM credentials.

On a Mac you can mount a network drive using Finder:

  1. Open Finder

  2. Press CMD + K and paste the WebDAV URL in the popup

  3. After clicking Connect, enter your SRAM credentials and the UNLOCK FDP storage will be mounted as a network drive in the Finder

../../_images/webdav_mac.png

When prompted for username/password, provide your SRAM credentials.

In Linux you can mount other locations such as WebDAV using your file browser:

  1. Open your file browser

  2. Click on ‘Other Locations’ and provide the address of your WebDAV server. Note, if the WebDAV server uses SSL encryption you might have to use the protocol davs:// instead of dav://:

  3. Fill in your SRAM credentials

../../_images/DavRodsMount-linux2.png

When prompted for username/password, provide your SRAM credentials.

iRODS-based access#

There are multiple methods that leverage iRODS directly to access the UNLOCK FDP. The most accessible option is iBridges, which offers both command-line usage and a graphical interface. It is also available as a Python package, making it ideal for integrating into analysis workflows. This Python package is used in various analysis tutorials within the Tutorials section.
iCommands is the most powerful and flexible command-line option, supporting advanced operations not supported by other methods. However, it is also the most difficult to install and run when not on a Linux operating system.
GoCommands offers a simple, portable alternative to iCommands for all platforms. It does not include all its features but does support other convenient features for ease of use.
The table below depicts a comparison between the tools. For more details and installion instructions, visit their corresponding pages.

Method

Graphical user interface (GUI)

OS Compatibility

Advantages

Recommendation

iBridges

Yes

Windows, macOS, Linux

Easy to understand and use, Python-compatible

Use Python module for analysis workflows

iCommands

No

Limited to Linux

Scriptable, more advanced control

Advanced users only

GoCommands

No

Windows, macOS, Linux

No install required, simpler than iCommands

Use for most general purposes (data transfer)