🟀Data Storage & Collaboration

Data Storage, Collaboration, and HPC Resources at reNEW, UCPH

Data Storage, Collaboration, and HPC Resources at UCPH

Introduction

Biomedical research at reNEW – The Novo Nordisk Foundation Center for Stem Cell Medicine, UCPH, is data-intensive, often involving large imaging datasets, sensitive patient information, and complex analyses. Effective Research Data Management (RDM) ensures data security, meets legal and ethical obligations (including GDPR compliance), and supports high-quality, reproducible science.

A critical component of RDM is data storage management throughout the Research Data Lifecycle. Each stageβ€”from planning to archivingβ€”requires careful consideration of storage infrastructure, data privacy, security protocols, and collaboration needs, especially in projects that involve personal data or multi-institutional teams.

This guide provides an overview of best practices and the University of Copenhagen (UCPH) facilities supporting data storage, sharing, and high-performance computing (HPC) tailored to the needs of biomedical researchers at reNEW.

The Research Data Lifecycle and Storage Management

At reNEW, researchers must ensure that storage planning and security measures are integrated at every stage of the data lifecycle:

1. Plan & Design Stage

Develop a Data Storage Plan outlining:

  • Storage options

  • Backup strategies

  • Access controls

  • Data classification and risk assessment (mandatory before data collection) This ensures that legal, ethical, and security requirements are addressed immediately.

2. Collect & Create Stage

As you acquire or generate data (e.g., imaging, genomic, patient-derived data), consider:

  • Secure data transfer and ingestion

  • Protection of sensitive information

  • Version control and documentation

  • Compliance with UCPH Information Security Policy and GDPR

3. Analyze & Process Stage

Data analysis can require:

  • Updated storage and backup strategies

  • High-performance or specialized storage for large-scale analyses

  • Security controls to prevent unauthorized access

  • Traceable workflows for reproducibility

4. Evaluate & Archive Stage

At project completion:

  • Choose suitable repositories (e.g., Zenodo, Dataverse) for sharing

  • Plan long-term preservation to ensure access and transparency.

  • Consider confidentiality and ethical sharing of sensitive data.a

Information Security and GDPR Compliance

Handling personal or sensitive data is common in biomedical research. Researchers at reNEW must:

UCPH Data Storage and Collaboration Solutions

Below is a summary of UCPH facilities suited to various data types and collaboration needs:

Personal Drive

  • For individual use (Windows/Linux)

  • Suitable for small amounts of non-sensitive research data

  • Not designed for sharing with collaborators

Shared Network Drive - Windows / Linux

  • For collaboration among UCPH employees

  • Ideal for research groups needing shared access

  • Not suitable for storing sensitive or personal data

  • Designed for sharing sensitive data among designated UCPH users

  • Complies with GDPR

  • Suitable for storing and sharing confidential or personal data internally

Microsoft OneDrive for Business

  • Cloud storage meeting UCPH security standards for non-sensitive data

  • Up to 5TB for sharing with colleagues and external partners

  • Covered by a data processing agreement with Microsoft

  • Recommended cloud solution (note: Dropbox and other providers do not have such agreements with UCPH)

ERDA (Electronic Research Data Archive)

  • Managed by the HPC Center, Faculty of Science

  • Centralized storage, archiving, and synchronization service

  • Ideal for non-sensitive research data

Sensitive Information Facility (SIF)

  • For storing and sharing sensitive information, including personal data

  • Enables secure sharing with UCPH and external partners

  • Requires GDPR compliance and pre-approval

  • Currently provided by the SCIENCE HPC Center; expansion to all UCPH researchers under consideration.

DATA DOI Service

  • Built on ERDA

  • Data sharing is open to all UCPH employees.

  • Facilitates assigning DOIs to datasets for findable, citable research outputs

UCPH Policy for Research Data Management

UCPH Policy for Research Data Management emphasizes:

  • Choosing an appropriate, secure infrastructure

  • Supporting collaboration while ensuring compliance with information security policies and legal requirements

  • Protecting personal data in line with GDPR

Researchers at reNEW must carefully select solutions that meet their data sensitivity and collaboration needs while upholding UCPH policies.

High-Performance Computing (HPC) for Biomedical Research

Biomedical research at reNEW often involves large-scale imaging analyses, computational modeling, and multi-omics integration that require HPC resources. UCPH offers access to both local and national HPC systems tailored to diverse research needs:

Key National HPC Systems Available to UCPH Researchers

Type 1 – Interactive HPC

  • Focus on interactivity and easy user access

  • Includes YouGene Cluster hosted at UCPH (via UCloud)

  • Supports iterative data exploration and analysis

Type 2 – Throughput HPC

  • Optimized for high-volume data processing

  • Systems include Computerome 2.0, GenomeDK, and Sophia.

  • Suitable for large-scale, batch analyses

Type 3 – Large Memory HPC

  • Designed for workloads needing large, globally addressable memory

  • Hosted at UCPH

  • Ideal for complex, memory-intensive biomedical simulations

Type 5 – LUMI Capability HPC

  • Pan-European pre-exascale system

  • Located in Finland (EuroHPC initiative)

  • Suitable for cutting-edge, large-scale computational needs

Special Note: DanGPU HPC at reNEW

  • Owned by DanStem/reNEW, SUND, and KU

  • Specialized GPU server for image data analysis

  • Connects large datasets stored on KU-IT storage for advanced computation

Access and Support

  • UCloud provides a user-friendly interface for accessing many of these HPC resources, with guidance and application processes streamlined for researchers.

  • Support is available via UCPH IT and the Faculty of Science HPC Center.

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