Laboratory Notebook and Database Extensions - a RDM Marketplace pilot project

Description

Abstract (English)

Concept

The main idea of LabNDB from the first RDM call remains in place: to collect, manage, store, analyse and reuse results from material testing processes in laboratories. Creating a scientific body that supports transparency and reusability in the research and publication process is mandatory. Beyond the already implemented basic functionalities, the need for further improvement points was identified in the first LabNDB development phase and will be handled in the extension phase.

Rationale

The aim is to provide the researchers with an electronic lab notebook in the form of a database where experimental protocols and related data are managed in connection with laboratory management. Products such as SENAITE , eLabNext, ResearchSpace, elabFTW, or bookkit only cover one or two of these aspects, and none of them offer a solution for FAIR RDM that is flexible enough: open for enhancements such as building a database that connects to other RDM services; accessible for data re-use; and field-specific data classification. Even if a limited re-design is allowed in the above-mentioned tools, their integration into the existing IT-environment (CyVerse, Repository, TUG-Online, etc.) would be complicated and/or costly. Out of these tools, SENAITE is FOSS and can be adopted for the institutes' needs through an intense labour process. However, sustainability issues are foreseen as its framework has a limited developer community. Therefore, it can be obsolete in the future.

Objectives

The main objective of the proposal is to improve the functionalities of LabNDB to prepare for product roll-out, which can be adopted by different institutes of TUG at the very least. LabNDB is designed to aid users in ensuring FAIR data practices and laboratory management of, e.g., devices and materials. The main objective is divided into eight sub-objectives, each of which are additional LabNDB functionalities, namely: (O1) preview of raw data for commonly used device file formats, (O2) booking calendar for test devices and workbenches, (O3) user authentication and authorization, (O4) SQL look-ups to TUG-Online inventory tables, (O5) end-user testing and documentation, (O6) code documentation, (O7) export to TUG repository and CyVerse, (O8) message board & notification.

Table of contents (English)

Content of archives

• pitch-video.zip ... short pitch-video with a brief introduction to the project
• presentation.zip ... presentation slides (meetings, events)
• project_management ... presentation slides (project kick-off workshop)
• proposal_reports.zip ... project proposal, interim report, final report

Technical info (English)

Laboratory Notebook and Database Extensions is a database-driven web application based on the Django web framework.

Software stack

• PostgreSQL (database)
• Apache Webserver (reverse proxy)
• gunicorn (WSGI enabled web-server)
• Django (web development framework)
• redis (key-value store)
• Debian 11 (operating system)