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 sensitive data of any size, it is recommended to use secure transfer methods such as SETT or 2FA-protected SFTP to ensure data protection.

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.

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.

SWITCH is a private foundation with the mission to enable, maintain and promote a secure and networked research and education infrastructure in Switzerland. It provides IT solutions such as SWICHdrive and SWITCHfilesender that facilitate collaboration:

• SWITCHdrive: Cloud-based storage service. Files can be saved, synchronised for offline use, and shared and edited with other members of Swiss universities and third parties. SWITCHdrive can be operated via browser, desktop client or mobile app. Users are responsible for backing up their data themselves, as SWITCHdrive does not offer automatic backups.
  The servers are located in Switzerland, making SWITCHdrive a good alternative to many commercial cloud providers. However, it should be noted that SWITCHdrive is not a suitable storage location for unencrypted sensitive research data.
  Consult the service catalogue of the University of Basel (in German only) for more information on SWITCHdrive.
• SWITCHfilesender: web-based service for sending large files (up to 300 GB). Consult the service catalogue of the University of Basel (in German only) for more information on SWITCHfilesender.

The Swiss National Data and Service Center for the Humanities (DaSCH) was initate by the Digital Humanities Lab (DHLab, University of Basel) and the Swiss Academy of Humanities and Social Sciences (SAGW). Since 2021, DaSCH has operated as a national research data infrastructure primarily funded by the Swiss National Science Foundation (SNSF), which includes a repository for research data in the Humanities, especially in the field of qualitative data and visual media.
The primary goals of the DaSCH are:

• Preservation of research data in the humanities and their long-term data curation.
• Ensuring permanent access to research data in order to make it available for further research and thus facilitating the reuse of existing research data in future research.
• Providing services for researchers to assist them with research data lifecycle management.
• Encouraging the digital interconnection and interoperability of databases created in Switzerland or in other countries.
• Collaboration and networking with other institutions on digital literacy.

The repository is based on the „Knowledge Organization and Annotation“ (Knora) infrastructure, an open source repository framework developed by DaSCH, DHLab and PlaTec (University of Lausanne). The DaSCH repository follows the FAIR principles of open data and is a registered re3data.org site. It offers a comprehensive RESTful API, media filesaccess  according to the IIIF 2.0 API (see iiif.io) and access control if necessary. The staff of the DaSCH may provide several service to researchers of all faculties of the University of Basel. Please see dasch.swiss and dhlab.unibas.ch.

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

Depending on the user needs, the University of Basel offers the appropriate infrastructure for document and file storage:

• For daily research files and documents (e.g. office documents, small to mid-scale research data), ITS offers group shares
• For special projects with large storage requirements (tens of TBs or more) sciCORE can provide high-performance storage.

Both ITS and sciCORE central storage units are backed up.

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).