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StackWave SDMS at the Broad Institute for Analyical Chemistry Data Aggregation

from StackWave

Most modern labs continue to employ time consuming and error prone manual processes for collecting, validating, and publishing raw device data. Although there are a number of self-hosted Scientific Data Management Systems (SDMS) that claim to alleviate at least one aspect of these processes, most of these solutions are built on outdated technology, have no support for cloud deployments, and do not facilitate the use of validation and export pipelines. At the Broad Institute, we set out to build a cloud-hosted informatics solution for the automation of our analytical data that does more than just file aggregation, enabling scientists to work smarter by automatically collecting, validating, and exporting all of their data through a flexible, cloud-hosted pipeline. This solution minimizes errors, saves valuable scientist time, and provides a comprehensive, fully auditable, record of data as it moves from the device to the LIMS. The analytical lab in the CDoT (Center for Development of Therapeutics) group at the Broad Institute has a set of UPLC devices that are able to be used interchangeably. Attached to each device is a computer that, by default, is used as the primary storage of both raw and processed data files. To begin a run, an input file is generated by the LIMS and placed into a directory accessible by the device computer. The operator uses this input file to initiate a run on the device. The result of the run is a set of raw result files, some of which store transient data and are ignored. Once the run is complete, the operator performs an integration, effectively producing a Chromatogram for each sample in the run. The data collection solution sends all of these files, along with the summarized run output, to the cloud in real-time. Collected data is then automatically checked for completeness, and valid results are subsequently transformed and exported to the LIMS in a LIMS-ready format. Over the course of 5 months, our automated solution has processed chromatograms for more than 7,400 samples from two devices, saving countless hours for operators and analysts. The system has captured at least 624 invalid documents, segregating them and informing the lab manager to prevent erroneous data from being imported into the LIMS.

about 4 months ago

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