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LabInform datasafe documentation

A local repository for “warm” research data.

Welcome! This is the documentation for the LabInform datasafe component, the local repository for “warm” research data that is part of the LabInform laboratory information and management system (LIMS). One key aspect of handling data is to safely store them in one place and access them via unique and stable identifiers (here: a Lab Object Identifier, LOI). While data belonging to (textual) publications can often be stored in public repositories, we need a safe place for all our (unpublished) data, starting with their acquisition and independent of their current state. This is meant by “warm” research data – a term coined by scientists from KIT.

Features

A list of features, not all implemented yet but aimed at for the first public release:

  • Repository for “warm” research data: one central place

  • Access to data using unique and persistent IDs (Lab Object Identifier, LOI)

  • Client-server architecture, supporting local and network operation

  • Full control over the data: runs locally on your own hardware

  • Automatic generation of unique IDs for data

  • Pre-register IDs before starting the data acquisition.

  • Checksums for automatically checking data integrity

And to make it even more convenient for users and future-proof:

  • Open source project written in Python (>= 3.9)

  • Developed fully test-driven

  • Extensive user and API documentation

Warning

The LabInform datasafe component is currently under active development and still considered in Beta development state. Therefore, expect frequent changes in features and public APIs that may break your own code. Nevertheless, feedback as well as feature requests are highly welcome.

Requirements

The LabInform datasafe package comes with a rather minimal set of requirements:

  • Python >= 3.9

  • flask and oyaml packages

How to cite

The LabInform datasafe is free software. However, if you use the LabInform datasafe as crucial infrastructure component of your own research, please cite the software:

  • Mirjam Schröder, Till Biskup. LabInform datasafe (2023). doi:10.5281/zenodo.13763299

To make things easier, the LabInform datasafe has a DOI provided by Zenodo, and you may click on the badge below to directly access the record associated with it. Note that this DOI refers to the software as such and always forwards to the most current version.

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Where to start

If you want to know what it is all about or are unsure whether the LabInform datasafe is interesting for you, start right at the beginning. Other good places to start are the Concepts and Use cases sections. If you are interested in contributing to the LabInform datasafe, the developers corner is the right place for you.

Installation

To install the LabInform datasafe package on your computer (sensibly within a Python virtual environment), open a terminal (activate your virtual environment), and type in the following:

pip install labinform-datasafe

Have a look at the more detailed installation instructions as well.

License

This program is free software: you can redistribute it and/or modify it under the terms of the BSD License. However, if you use the LabInform datasafe as crucial infrastructure component of your own research, please cite it appropriately. See How to cite for details.