Contemporaneous sample data tracking for the generation of genome edited cell lines.

It is difficult to capture the large numbers of steps and details that often characterize research in the biomedical sciences. We present an approach that is based on commercial spreadsheet software so it is easily adaptable by the experimentalist. The approach is designed to be compatible with an experimentalist's workflow and allows the capture in real time of detailed information associated, in this use case, with laboratory actions involved in the process of editing, enriching and isolating clonal gene-edited pluripotent stem cell (PSC) lines. Intuitive features and flexibility allow an experimentalist without extensive programming knowledge to modify spreadsheets in response to changes in protocols and to perform simple queries. The experimental details are collated in a table format from which they can be exported in open standard formats (e.g., Extensible Markup Language (XML) or Comma Separated Values (CSV) for ingestion into a data repository supporting interoperability with other applications. We demonstrate a sample- and file-naming convention that enables the automated creation of file directory folders with human readable semantic titles within a local file system. These operations facilitate the local organization of documentation and data for each cell line derived from each transfection in designated folder/file locations. This approach is generalizable to experimental applications beyond this use case.

NexusLIMS: A Laboratory Information Management System for Shared-Use Electron Microscopy Facilities.

This work introduces NexusLIMS, an electron microscopy laboratory information management system designed and implemented by the Office of Data and Informatics and the Materials Science and Engineering Division at NIST for a multi-user electron microscopy co-op facility. NexusLIMS comprises network infrastructure, shared information technology resources, a custom software package to harvest and extract experimental information and construct experimental metadata records, and an intuitive web-based user-facing interface for searching, browsing, and examining research data. These metadata records conform to the Nexus Experiment schema, which is introduced in this work. The NexusLIMS suite of tools requires minimal input and adjustments to user behavior, instead relying on existing organizational procedures and the collection of information from a multitude of sources to construct a complete picture and record of a research experiment. The underlying infrastructure and design considerations for a multi-user data management system are discussed. The core codebase for NexusLIMS is made publicly available alongside this work, and its modular design encourages the adaptation of the presented methods at other research organizations.