Medical-Blocks: A Platform for Exploration, Management, Analysis, and Sharing of Data in Biomedical Research.

Valenzuela, Waldo; Balsiger, Fabian; Wiest, Roland; Scheidegger, Olivier (2022). Medical-Blocks: A Platform for Exploration, Management, Analysis, and Sharing of Data in Biomedical Research. JMIR formative research, 6(4), e32287. JMIR Publications 10.2196/32287

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Biomedical research requires healthcare institutions to provide sensitive clinical data to leverage data science and artificial intelligence technologies. However, providing healthcare data to researchers simple and secure, proves to be challenging for healthcare institutions.


We describe and introduce Medical-Blocks, a platform for data exploration, data management, data analysis, and data sharing in biomedical research.


The specification requirements for Medical-Blocks included: i) Connection to data sources of healthcare institutions with an interface for data exploration, ii) management of data in an internal file storage system, iii) data analysis through visualization and classification of data, and iv) data sharing via a file hosting service for collaboration. Medical-Blocks should be simple to use via a web-based user interface and extensible with new functionalities by a modular design via microservices ("blocks"). The scalability of the platform should be ensured by containerization. Security and legal regulations were considered during the development.


Medical-Blocks is a web application that runs in the cloud or as a local instance at a healthcare institution. Local instances of Medical-Blocks access data sources such as electronic health records and picture archiving and communications system (PACS) at healthcare institutions. Researchers and clinicians can explore, manage, and analyze the available data through Medical-Blocks. The data analysis involves classification of data for metadata extraction and the formation of cohorts. In collaborations, metadata (e.g., number of patients per cohort) and/or the data itself can be shared through Medical-Blocks locally or via a cloud instance to other researchers and clinicians.


Medical-Blocks facilitates biomedical research by providing a centralized platform to interact with medical data in collaborative research projects. The access to and management of medical data is simplified. Data can be swiftly analyzed to form cohorts for research and be shared among researchers. The modularity of Medical-Blocks makes the platform feasible for biomedical research where heterogenous medical data is needed.


Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Department of Radiology, Neuroradiology and Nuclear Medicine (DRNN) > Institute of Diagnostic and Interventional Neuroradiology
04 Faculty of Medicine > Department of Head Organs and Neurology (DKNS) > Clinic of Neurology

UniBE Contributor:

Valenzuela, Waldo Enrique, Balsiger, Fabian, Wiest, Roland Gerhard Rudi, Scheidegger, Olivier


600 Technology > 610 Medicine & health




JMIR Publications




Pubmed Import

Date Deposited:

03 Mar 2022 12:05

Last Modified:

02 Mar 2023 23:36

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