ACDC promotes and enables FAIR research. Our infrastructure supports the creation, management and publication of data and other research assets, such as workflows and models. In addition, we aim to practice FAIR and sustainable software development. Our infrastructure builds on software applications and standards that have been developed and widely adopted by the Life Science Community.
We use the following research software applications in our infrastructure:
The FAIRDOM-SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets, models, processes and research outcomes.
It is the metadata management catalogue for ACDC, allowing Amsterdam UMC researchers to organise and manage their omics and bioimaging (meta)data in the context of the whole experiment, interlinking multi-omics and imaging, across different types of research assets.
The “Just Enough Results Model” ontology describes research assets and the connections between them. It provides a semantic metadata model for the metadata in FAIRDOM-SEEK and encapsulates the core components of the ISA standard (Investigations, Studies and Assays).
OMERO is a database specifically designed to store biological image data and assists users from microscope to publication. It supports more than 150 different image file formats. The Image Data Resource public repository is also an OMERO instance.
Biomero is an extension to OMERO, which has been developed in the NL-Bioimaging initiative. It enables researchers to easily launch image analysis workflows on High Performance Compute infrastructure and facilitates FAIR image analysis.
The Integrated Rule-Oriented Data System (iRODS) is an open source data management platform. It enables secure collaboration and virtualizes data storage resources, to enable researchers to easily migrate data from active to archive storage.
The FAIR Data Station is a metadata ingestion platform that helps to improve the quality of metadata. The station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start.
The public Flow Repository is the international venue for published Flow Cytometry data. We plan to host a local copy for pre-publication sharing and collaboration at the Amsterdam UMC