🤔 Problem

The Renku Team in collaboration with NEXUS has funding for an ORD Grant (See ‣). Here’s a selected excerpt from the grant’s problem statement:

We see a plethora of different ELNs (Electronic Lab Notebooks) and LDMs (Lab Data Management) used for oftentimes similar purposes across the ETH Domain, e.g., to register and track measurements performed in the wet lab, or to store data and code that is involved in data analysis. While openBIS, LabKey, and B-Fabric allow a highly- controlled management of the underlying data, they – by design – limit flexibility on data formats, addition of novel data types, or sophisticated calculations on the data, to protect data integrity. However, computational groups often perform large-scale and versatile data analyses generating new types of files and formats. Therefore, these groups require more flexible solutions. For instance, using git to control the version of the code they are developing in combination with the underlying data being stored on the file system and/or in databases. However, software versioning repositories are not meant to store large data. Thus, the code that is used to analyze the data and the data itself are usually managed separately, provoking the risk that their association is lost. This is also true for joint collaborations, where data needs to be transferred between groups, sometimes across different file systems and compute clusters. In addition, this can impair both the findability and integrity of the data.

There are already efforts to connect data managed in an ELN with a user interface to simplify data access and calculations on the data. However, most of these efforts aim at solving this issue just for one type of ELN, e.g., openBIS, and fail to see the diverse needs of research groups across the ETH Domain, which might extend beyond the capabilities of a data management tool.

In summary, there are many different ELNs (Electronic Lab Notebooks) used across the ETH Domain. Oftentimes these address redundant tasks and work in silos next to each other, thereby increasing the risk that for a given project data sharing, findability, long-term preservation, and even adequate analysis is impaired.

We propose to build connections between existing ELN systems through a RenkuLab as a centralized service. An appropriate system will reduce the burden for researchers to comply with regulations and requirements, make cross-group/institution collaboration simpler, and increase efficiency in the long run.

As a first step towards this larger goal, we want to make it possible to open and use OpenBIS datasets RenkuLab sessions.

🍴 Appetite

How much time is this idea worth?

We’re willing to invest 6 weeks into developing a solution.

🎯 Solution

To add a cloud storage to a project in RenkuLab, from a project, navigate to:

→ ‘Settings

→ ‘Cloud Storage’

→ click on ‘Add Cloud Storage’.

This opens the start of the Cloud Storage modal.

The RenkuLab ‘Add Cloud Storage’ modal.

The end goal is to add OpenBIS datasets as an option in this modal, and have the OpenBIS dataset available for use in a Session.

Once the user completes the guided setup in this modal, the cloud storage is configured for their project. When they start a session, the cloud storage is mounted (via RClone) into the session, where is accessible as a folder in the working directory.