LabInform documentation
The open-source modular Laboratory Information System
Welcome! This is the documentation for LabInform, a modular Laboratory Information system for scientists interested in truly reproducible research, focussing on indivuduals and small groups with limited resources. It is a collection of best practices from more than fifteen years of personal experience in everyday laboratory work. All components are (based on) free and open-source software, the core idea is simplicity and scalability. The system should fit as easily as possible into existing processes, offer the user maximum freedom, but at the same time help to maintain an overview (or get a new one) when the data volumes grow and the group grows.
Integral parts are an electronic lab notebook (ELN) based on DokuWiki, a repository for warm research data (datasafe) as central storage for all your valuable (and largely unpublished) data, and unique identifiers (Lab Object Identifier, LOI, much like the well-known DOIs) for datasets, samples, and alike.
Together with ASpecD (Analysis of Spectral Data), a framework for handling spectroscopic data focussing on reproducibility, it forms the basis of fully reproducible research without additional costs. Eventually, SOLVed-IT, your friendy IT stack for small scientific work groups fostering digital methods and processes, will provide the “glue” and automation to deploy all components.
Overview
LabInform is a modular Laboratory Information system consisting of a series of individual components. Fig. 1 provides a first overview. For further details, see the Components section.
Fig. 1 Overview of the components and aspects of the LabInform framework. Not all of these components are implemented in Python, and the electronic lab notebook (ELN), lab setup management, and knowledge base in particular are based on DokuWiki. For further details, see the Components section.
A (slightly dated) description of LabInform is available as preprint via ChemRxiv:
Till Biskup. LabInform: A Modular Laboratory Information System Built From Open Source Components. ChemRxiv, 2022 doi:10.26434/chemrxiv-2022-vz360
Individual projects
The LabInform framework consists of a series of individual projects that all address individual aspects of reproducibility and comprehensibility and hence good scientific practice. The most important and most mature projects are summarised below. For a full(er) list of the components written in Python see the Subpackages section.
Warning
LabInform is currently under active development and the individual components are in quite different state – from production-stable and used since >10 years (LabInform ELN) to beta (mostly usable) to alpha (planned, very early stage). Therefore, please check carefully the description of the individual components and come back frequently. Nevertheless, feedback as well as feature requests are highly welcome.
Data provenance: Infofile
A simple text file format developed to document research data. It allows researchers in the lab to record all relevant metadata during data acquisition in a user-friendly and obvious way while minimising any external dependencies. The resulting machine-actionable metadata in turn allow processing and analysis software to access relevant information, besides making the research data more reproducible.
- Further information and templates:
- Publication with further details:
Bernd Paulus, Till Biskup. Towards more reproducible and FAIRer research data: documenting provenance during data acquisition using the Infofile format. Digital Discovery 2:234–244, 2023. doi:10.1039/D2DD00131D
- State:
Production stable
Used in production since 2012
Documentation: LabInform ELN
A lightweight and flexible electronic laboratory notebook for academic research based on the open-source software DokuWiki. Contains as well an inventory for samples and alike. Pages are created using forms and user-adjustable templates. Key is a well-conceived digital mapping of processes and workflows for as intuitive operation as possible.
- Further information and documentation:
- Demo instance:
- Preprint with further details:
Mirjam Schröder, Till Biskup. LabInform ELN: A lightweight and flexible electronic laboratory notebook for academic research based on the open-source software DokuWiki. ChemRxiv, 2023. doi:10.26434/chemrxiv-2023-2tvct
- State:
Production stable
Used in production since 2012, approx. 10 installations
Local repository: LabInform Datasafe
A local repository for “warm” (i.e. unpublished and largely not yet processed and analysed) research data. One key aspect of handling data is to store them in one place and access them via unique identifiers (here: a Lab Object Identifier, LOI). The Datasafe is the data storage component of the LabInform framework.
- Further information and documentation:
- State:
Beta: mostly working
License
All components of the LabInform framework are free software. Those who originate by the authors of LabInform can be redistributed and/or modified under the terms of the BSD License. For third-party components, please see the individual licenses. However, if you use LabInform or any of its components for your own research, please cite it appropriately. See the preprint referenced above and the documentation pages of the individual components for details.
A note on the logo
The “L” originates from the Computer Modern Roman font originally designed by Donald E. Knuth for his TeX typesetting system. As such, it represents science and the scientific method. Harbouring the “i” representing the information bit puts things right: Proper and reproducible science is the solid support for all the information we can retrieve. The copyright of the logo belongs to J. Popp.