LabInform documentation

Welcome! This is the documentation for LabInform, in particular its components written in Python. For general information see its homepage.

LabInform is a framework and toolchain for reproducible research, focussing on free and open-source software components. Integral parts are an electronic lab notebook (ELN) based on DokuWiki, a datasafe as central storage for all your valuable 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.

Features

A list of features, not all implemented yet but aimed at for the first public release (LabInform 0.1):

• Datasafe – a home to your precious data (both, experimental and calculated)

• Lab Object Identifier (LOI) – unique identifiers for samples, data, …

• Electronic Lab Notebook (ELN) – automated access from processing routines

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

• Open source project written in Python (>= 3.5)

• Developed fully test-driven

• Extensive user and API documentation

Warning

LabInform is currently under active development and still considered in Alpha 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.

Installation

Install the package by running:

pip install labinform

This will install the version from the Python Package Index (PyPI). To get the latest development version, clone the repository from GitHub and install it locally. In any case, it is highly recommended to use virtual environments to separate dependencies.

Where to start

Users new to LabInform should probably start at the beginning, those familiar with its underlying concepts an planning to help in further developing may jump straight to the section explaining how to contribute to the development of LabInform.

The API documentation is the definite source of information for developers, besides having a look at the source code.

Contents:

• Target audience
  • Scientists aiming at reproducibility
  • Motivation and general ideas
  • Relation to the ASpecD framework
• Introduction
  • Reproducible research
  • Personal freedom vs. reproducible science
  • Scientists are not software engineers
  • Long-term storage and availability
  • The goal: concepts for reproducibility
• Concepts
  • reproducible
  • modular
  • simple
  • scalable
  • open-source
  • extensible
  • independent
• Components
  • IDs
  • Metadata
  • Labbook (electronic lab notebook, ELN)
  • Datasafe
  • Knowledge base (wiki)
  • Lab Object Identifier (LOI)
  • Version control system (VCS)
• Subpackages
  • Datasafe
  • Lab Object Identifiers (LOI)
  • Electronic Lab Notebook (ELN)
• Developer documentation
  • Virtual environment
  • Autoincrementing version numbers
  • Directory layout
  • Docstring format
  • Unittests and test driven development
• API documentation
  • Subpackages

Indices and tables

• Index

• Module Index

• Search Page

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.