Related papers: menoci: Lightweight Extensible Web Portal enabling…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
Workflow management systems allow the users to develop complex applications at a higher level, by orchestrating functional components without handling the implementation details. Although a wide range of workflow engines are developed in…
Medical data sharing needs to be done with the utmost respect for privacy and security. It contains intimate data of the patient and any access to it must be highly regulated. With the emergence of vertical solutions in healthcare…
Many science advances have been possible thanks to the use of research software, which has become essential to advancing virtually every Science, Technology, Engineering and Mathematics (STEM) discipline and many non-STEM disciplines…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
A full-fledged data exploration system must combine different access modalities with a powerful concept of guiding the user in the exploration process, by being reactive and anticipative both for data discovery and for data linking. Such…
This article describes a data center hosting a web portal for accessing and sharing the output of large, cosmological, hydro-dynamical simulations with a broad scientific community. It also allows users to receive related scientific data…
Reproducibility should be a cornerstone of science as it enables validation and reuse. In recent years, the scientific community and the general public became increasingly aware of the reproducibility crisis, i.e. the wide-spread inability…
Objective: The Learning Health System (LHS) requires integration of research into routine practice. eSource or embedding clinical trial functionalities into routine electronic health record (EHR) systems has long been put forward as a…
Centralized electronic health record repositories are critical for advancing disease surveillance, public health research, and evidence-based policymaking. However, developing countries face persistent challenges in achieving this due to…
As data-driven methods are becoming pervasive in a wide variety of disciplines, there is an urgent need to develop scalable and sustainable tools to simplify the process of data science, to make it easier to keep track of the analyses being…
Biobanks are indispensable resources for medical research collecting biological material and associated data and making them available for research projects and medical studies. For that, the biobank data has to meet certain criteria which…
This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…
Clinical decision-making relies on the integration of information across various data modalities, such as clinical time-series, medical images and textual reports. Compared to other domains, real-world medical data is heterogeneous in…
This paper proposes an interactive repository type for research software metadata which measures and documents software sustainability by accumulating metadata, and computing sustainability metrics over them. Such a repository would help to…
Scientific data across physics, materials science, and materials engineering often lacks adherence to FAIR principles (Barker et al., 2022; Jacobsen et al., 2020; M. D. Wilkinson et al., 2016; S. R. Wilkinson et al., 2025) due to…
Modern HPC file systems can contain billions of files and hundreds of petabytes of data, making even simple questions increasingly intractable to answer. Traditional file system utilities such as find and du fail to scale to these sizes.…
This paper takes up the problem of medical resource sharing through MicroService architecture without compromising patient privacy. To achieve this goal, we suggest refactoring the legacy EHR systems into autonomous MicroServices…
Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data…
BCI algorithm development has long been hampered by two major issues: small sample sets and a lack of reproducibility. We offer a solution to both of these problems via a software suite that streamlines both the issues of finding and…