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For more information visit the symposium website: https://slas.org/events/slas-2020-european-sample-management-symposium
Tuesday, March 17 • 11:00am - 11:20am
Data - Advanced Integrated Approach for Data and Sample Management in Academia

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"CZ-OPENSCREEN: National infrastructure for Chemical Biology” operates the state-of-art infrastructure for basic and applied research in the field of chemical biology and genetics. The Compound management (CM) department handles chemical libraries which contain more than 100,000 unique chemical compounds from various commercial and private sources. Laboratory automation is used on regular basis to effectively store and process the extensive number of samples.

At the CZ-OPENSCREEN we use our in-house developed web-based LIMS SW solution ScreenX which provides a comprehensive set of functionalities necessary for the execution of CM pipelines. ScreenX is used to store and handle all sample, experiment and instrument data, and allows their processing by multiple users with various roles and access rights levels (admin, project leader, screener, chemist, etc). Typical CM workflow starts with the input/import of the sample data in the database, realized by either manual entry or by the import of data files in CSV format. Large data files obtained from the suppliers are transformed into the importable format by employing external KNIME workflows. KNIME analytical platform SW is equipped with open cheminformatics plugins such as OpenBabel, RDKit, ChemAxon / Infocom, etc. which can be used for interconversion between different chemical structures’ notations. Integrity of the inventory data within the ScreenX is assured by using unique identifiers for each DB entry together with physical barcoding of all the labware and samples. ScreenX enables to design and execute routine CM procedures such as reformatting, cherrypicking, diluting, quality control (QC), etc. and to generate lists of instructions for the automation platforms to perform the procedures. Post-run feedback from the automation is realized by the import of the labware reports and log files into the ScreenX. CM works in close cooperation with the SW development team and serves as both the end user and beta tester entity of the ScreenX. The user feedback and new function requests are realized via JIRA-based tracking environment.

 To achieve even more effective CM and data processing pipelines, we’ve developed some dedicated standalone SW tools, such as PROBES & DRUGS portal, RackScanner, PrintServer, or InCHlib. These are used for working with the current bioactive compound space, scanning 2D-barcoded tubes/racks, remote barcode printing directly from the ScreenX, and interactive heatmap clustering and visualization (in respective order). We offer such tools as open-source projects for the scientific community.


Martin Popr, RNDr., PhD.

Head of Compound Management at CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences
Martin Popr studied Charles University in Prague and received his master’s degree in analytical chemistry and toxicology. He finished a PhD programme in organic chemistry in 2016 by defending his thesis on Synthesis of cyclodextrin derivatives for practical applications. Since 2014... Read More →


Tuesday March 17, 2020 11:00am - 11:20am
Room Saphir