Software tools in the academic HTS workflow
CZ-OPENSCREEN: National Infrastructure for Chemical Biology at the in Institute of Molecular Genetics in Prague provides services for basic and applied research in chemical biology and genetics. State-of-the-art equipment and a trained staff enable studies with high-throughput and high-content screening (HTS). The HTS is supported by fully automated compound management unit for compound storage, quality control and reformatting and by cheminformatics unit performing complex data mining and cheminformatics analysis.
As academic institution, the centre typically works on joint projects with external collaborators to develop selective probes for various biological processes using a wide range of biochemical assays including binding and enzymatic activity assays, cell based functional and phenotypic assays, and cell based label-free assays. The robotic integration allows a throughput for up to 100 000 samples per day, which needs to be handled by corresponding computational resources.
They developed LIMS system ChemgenDB/ScreenX, tailored for our specific needs and instrument setup. The system is based on PostgreSQL and is used for the complex management of compounds, chemical structures, recorded data and is capable of advanced analysis of HTS activity data such as data normalization, dose response curve analysis, generation of graphs and reports. Basic cheminformatics functionality is provided by integrated RDKit.
They have also incorporated cheminformatics tools provided by ChemAxon in the HTS workflow such as Instant JChem, JChem for Office, Marvin, Chemical Name and Structure Conversion or JKlustor to perform structure-based cluster analysis of compounds, reporting and bridging activity data with cheminformatics analysis.