The University of Luxembourg hosts several interconnected platforms. In Bioimaging, big data is generated regularly, and this data, located on the network-attached storage of the University, needs to be analyzed. The HPC team of the University of Luxembourg manages access to the compute clusters and supercomputers, which are suited to analyze Bioimaging data.
The Bioimaging platform utilizes the HPC infrastructure to provide an image analysis pipeline. The image analysis pipeline is managed by the Bioimaging Platform, while access to the HPC is managed by the HPC team.
It is possible to use the image analysis pipeline service without any knowledge about high-performance computing and programming. The pipeline is designed for the collaboration between image analysis specialists from the Bioimaging Platform and users requesting an image analysis service. The Bioimaging Platform handles the programming, and users can trigger the provided image analysis code on their datasets. The pipeline manages (1) data transfer between the network-attached storage of the University of Luxembourg and the HPC storage, (2) HPC job queuing, and (3) informs the user via email about analysis completion and how to access the analysis results.
The image analysis pipeline uses a custom database, enabling you to run tailored image analysis scripts on your data. This pipeline is designed for University-internal usage, and assumes both raw data and analysis results are located on the storage infrastructure of the University of Luxembourg.
Employees of the University of Luxembourg can connect from their work computer or from anywhere via VPN connection. To access the database and submit image analysis jobs, you need to download DBeaver Community and configure the connection to the database.
DBeaver is open source software, available for all common operating systems, that enables you to interact with databases. To install the free DBeaver Community edition, follow the link:
Add a new connection
Select MariaDB
Click next
Enter the connection parameters:
Server: bip-data-mgmt-srv01.lcsb.uni.lu Port: 3306 Database: HCS Username BIP.User Password bip@Pipeline
Click ‘Test Connection’
Allow the installation of required drivers if prompted