LabNexus – An open-source enzyme kinetics data automation web application based on FAIR principles and STRENDA guidelines.
Authors: C.E. de Beer and J.M. Rohwer
In response to the reproducibility crisis in enzymology and the principles of FAIR (Findable, Accessible, Interoperable, and Reusable) data, we present LabNexus, a novel and user-friendly platform for standardizing procedures related to the collection, processing, and storage of both data and metadata with respect to enzyme kinetics experiments.
LabNexus features a fully integrated web interface that automates the corroboration of raw experimental data with corresponding metadata with minimal user input. This includes integrated search tools for cross-referencing external databases such as PubChem, ChEBI, and UniProt, and efficient data processing capabilities. The platform utilizes the Enzyme Markup Language (EnzymeML), a derivative of SBML, to package data and metadata in adherence to STRENDA guidelines. Users can submit various types of data, including EnzymeML documents and raw spectrophotometric data, both of which can be read into the platform with minimal user intervention.
LabNexus is designed to be accessible to all enzyme kinetics researchers, regardless of their programming literacy, ensuring a broader adherence to FAIR principles in published literature. Users can view their submitted data for validation purposes, ensuring accuracy and consistency in their experimental results. The platform's modular design facilitates the expansion of supported spectrophotometric models and output formats. Users can output their virtual documents (referred to as workspaces) in various formats, including EnzymeML, YAML, or Markdown, enhancing the flexibility and utility of the data management ecosystem.
Optionally, LabNexus offers automated synchronization of spectrophotometric instrument output files to the server via a companion application on the instrument host machine, adding redundancy to experiments.
The platform supports operation in both closed and open networks, incorporating network security protocols to safeguard data. In an open network configuration, automated synchronization allows users to access, view, edit, and annotate their data from anywhere in the world via an internet connection.