Tools and solutions

In the phase of active research, various tools available at University of Basel may help organize your data. This page lists key (sometimes domain specific) data management services available to support your research.

If you need customized consulting on IT-related topics, you can contact ITS Professional Services (PRS). The team consists of professionals with research experience and works closely with the relevant subject specialists. They provide support with requirements analysis, role clarification and responsibilities, and help develop sustainable, fit-for-purpose solution architectures.

secuTrial is a browser-based and GCP-compliant Clinical Data Management System for collecting patient data. It offers high flexibility with regard to study design and user roles and rights, and a variety of additional features typically used in clinical trials, such as complex visit plans, dedicated workflows for the management of (Serious) Adverse Events and for Clinical Monitoring, Randomisation, electronic signatures, and data consistency checks. Please contact the Department of Clinical Research to use secuTrial in your research project.

REDcap (Research Electronic Data Capture) is a web application offering a free, easy-to-use, and secure method for flexible yet robust data collection. Developed by the Vanderbilt University, it has a web interface that allows users to quickly build and manage online surveys and databases. It is designed to provide a secure environment so that research teams can collect and store sensitive information. University of Basel members who wish to setup a project in REDCap can contact sciCORE to get started.

When transferring research data, the method chosen should align with the data's sensitivity and size.

For non-sensitive data, the transfer method varies based on the size of the data:

  • For small datasets, options include Switch FileSender, e-mail, or physical transfer using devices such as USB drives.
  • For large datasets, network-based transfer methods are recommended, such as Switch FileSender (up to 300GB per dataset), SCP/SFTP (if supported by the storage provider or repository), or Globus File Transfer (if supported by the storage provider or repository; note that this is not currently part of the University of Basel’s infrastructure). Network file systems, such as CIFS or NFS, may also be suitable but are only relevant for internal data transfers.

For sensitive data of any size, it is recommended to use secure transfer methods such as SETT or 2FA-protected SFTP to ensure data protection.
With Switch FileSender, files can be sent end-to-end encrypted (based on AES-256 encryption) with a secret password. This form of authentication ensures that only the receivers identified by the sender have access to the files. After the set transfer period, files are automatically deleted without a trace. Share passwords securely and do not send them to the same email address as the file link — this prevents attackers from accessing both via one channel. Password managers like Proton Pass or Bitwarden offer secure sharing features that let you send encrypted passwords without giving full access to your password manager. When using such sharing features, sending to the same recipient address is acceptable. Another option is to use end-to-end encrypted messengers such as Signal or Threema. Avoid standard, unencrypted channels like regular email, SMS, or shared spreadsheets, as these methods increase the risk of data breaches.

In cases where network bandwidth or reliability is limited, physical transfer using devices such as hard drives, solid-state drives, or portable NAS appliances can still be an efficient and practical option for transferring large datasets.

DaSCH (Swiss National Data and Service Center for the Humanities) develops and operates a FAIR-compliant, trusted digital repository for open research data in the Swiss humanities. Its DaSCH Service Platform (DSP) is designed for the long-term preservation, reuse, and precise citation of complex research data—supporting relational, graph, and NoSQL databases.

Beyond traditional archival functions, DSP provides researchers with a Virtual Research Environment where they can actively create FAIR data and work with their data while ensuring its long-term preservation.

Key Features of DSP:

  • Direct, long-term access to data through an integrated Virtual Research Environment
  • Continuous editing capabilities - data remains alive and workable, not just archived
  • Support for researchers throughout the data lifecycle (from creation to preservation)
  • Interoperability with tools and standards used in the humanities, arts and cultural sciences.

Collaboration & Goals: DaSCH partners with national and international organizations (e.g., FORS) to align its services with the Swiss open research data landscape. Its primary objectives are:

  • Preserving and curating humanities research data for the long term.
  • Ensuring permanent access to enable reuse in future research.
  • Fostering digital interoperability across Swiss and international databases.
  • Training and advisory services in research data management, promoting open data and standards.

LabKey is a general purpose web-based data management platform for quantitative data (labkey.com). It is an open-source software developed by a commercial company specialized in clinical data management. Despite being rooted in clinical data, the platform is generic enough to suit most natural (and other quantitative) sciences. LabKey provides an audit trail, a flexible role-based user management, a file manager, a configurable user interface, including a programmable wiki and is ideal if/when managing your research data with Excel becomes “too complicated”. Please contact sciCORE to get an access to the system.

OMERO is a client-server software for managing, visualizing and analyzing microscopy images and associated metadata. The data repository does not only support the management of microscopy image data but also allows for their visualisation, annotation, archiving, and export of images. OMERO moreover lets the user collaborate with colleagues in the lab or anywhere in the world by creating user groups. OMERO is supported by Bio-Formats, which allows for over 120 different microscopy file formats to be imported into the OMERO software.At the Biozentrum, an OMERO server is jointly operated by the department’s Imaging Core Facility (IMCF) and Biozentrum Research IT.

For details about the OMERO project, please see the OME project web site: openmicroscopy.org/site/products/omero

A significant number of research groups, predominantly at the Biozentrum, are using a wiki solution as a light-weight tool to keep electronic laboratory notebooks. This ELNwiki platform is based on the enterprise-level Confluence software and is operated by the Biozentrum Research IT group. Wiki systems provide substantial flexibility in the way data can be recorded. This allows researchers to easily make the transition from paper lab books to an electronic format. However, this flexibility also requires some up-front planning and decisions when a group’s ELN is first established. Biozentrum Research IT therefore also provides consulting and training, in particular during the early phase of ELNwiki adoption in a group.

The University Library of Basel lists and presents further methods and tools for Digital Humanities on its website: UB Basel - Digital Humanities | digital services.

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. For users with a sciCORE account, RStudio can be accessed here.

EvaSys is suitable for the secure execution of large surveys and evaluations. At the University of Basel, the campus license can be used to conduct surveys as part of research projects, as well as for other purposes. In this case, it must be clarified whether the license conditions are complied with. In particular, the research project must be affiliated with the University of Basel and may not be commissioned and financed by third parties (mandate research). Check the intranet pages of the EvaSys Survey Services at the University of Basel and its Q&A section for more information. The university also regularly offers courses on EvaSys in its training program and presents EvaSys at the yearly Welcome Day for new employees.

Contact: evasys-surveys@unibas.ch

The Faculty of Psychology offers various data management services that can help organize research data. For example research data management with REDCap or the Research Data Management Organiser (RDMO).

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