Home Fundamentals Research Data Management FAIR Data Principles Metadata Ontologies Data Sharing Data Publications Data Management Plan Version Control & Git Public Data Repositories Persistent Identifiers Electronic Lab Notebooks (ELN) DataPLANT Implementations Annotated Research Context User Journey ARC specification ARC Commander QuickStart QuickStart (Experts) Swate QuickStart Walk-through Best Practices For Data Annotation DataHUB DataPLAN Ontology Service Landscape ARC Commander Manual Setup Git Installation ARC Commander Installation Windows MacOS Linux ARC Commander DataHUB Access Before we start Central Functions Initialize Clone Connect Synchronize Configure Branch ISA Metadata Functions ISA Metadata Investigation Study Assay Update Export ARCitect Manual Installation - Windows Installation - macOS Installation - Linux QuickStart QuickStart - Videos ARCmanager Manual What is the ARCmanager? How to use the ARCmanager Swate Manual Annotation tables Building blocks Building Block Types Adding a Building Block Filling cells with ontology terms Advanced Term Search File Picker Templates Contribute Templates ISA-JSON DataHUB Manual Overview User Settings Generate a Personal Access Token (PAT) Projects Panel ARC Panel Forks Working with files ARC Settings ARC Wiki Groups Panel Create a new user group Data publications Passing Continuous Quality Control Submitting ARCs with ARChigator Track publication status Use your DOIs Guides ARC User Journey Create your ARC ARC Commander QuickStart ARC Commander QuickStart (Experts) ARCitect QuickStart Annotate Data in your ARC Annotation Principles ISA File Types Best Practices For Data Annotation Swate QuickStart Swate Walk-through Share your ARC Register at the DataHUB DataPLANT account Invite collaborators to your ARC Sharing ARCs via the DataHUB Work with your ARC Using ARCs with Galaxy Computational Workflows CWL Introduction CWL runner installation CWL Examples CWL Metadata Recommended ARC practices Syncing recommendation Keep files from syncing to the DataHUB Working with large data files Adding external data to the ARC ARCs in Enabling Platforms Publication to ARC Troubleshooting Git Troubleshooting Contribute Swate Templates Knowledge Base Teaching Materials Events 2023 Nov: CEPLAS PhD Module Oct: CSCS CEPLAS Start Your ARC Sept: MibiNet CEPLAS Start Your ARC July: RPTU Summer School on RDM July: Data Steward Circle May: CEPLAS Start Your ARC Series Start Your ARC Series - Videos Events 2024 CEPLAS ARC Trainings – Spring 2024 MibiNet CEPLAS DataPLANT Tool-Workshops Frequently Asked Questions

Electronic Lab Notebooks (ELNs)

last updated at 2023-12-01 Protocols – Recipes to knowledge

Protocols form the basis to laboratory procedures. In a kitchen a recipe defines what inputs (flour, milk, eggs, ...) and steps (mix, bake...) are required to achieve what expected outcome (chocolate cake). Just like that a laboratory protocol defines what samples, materials, and components (plant leaves, buffer, centrifuge, ...) can be processed (homogenize, mix, extract, ...) to generate a desired outcome (plant leaf extract). Depending on the type of laboratory procedure, the protocol outcomes may be samples or data. In both cases the protocol is or contains metadata.

Protocols are the key to generate knowledge via predefined experimental processes. Since protocols are key to reproducibility and integrity of scientific results, they are an integral part of publications (e.g. the materials and methods section) to share, evaluate and reuse these methods with peers and communities.

Every lab builds on a collection of protocols. Some protocols may describe routinely performed standard operating procedures, while others may be continuously evolving and adapted to a specific use-case. In pre-digital times, protocols for a scientific project were collected in classical pen-and-paper lab notebooks. By design, the metadata knowledge collected in these single-copy protocols was hard to access (hidden in a shelf) and hard to maintain over generations of researchers or share and communicate with peers during the ongoing scientific process.

ELN – Digital protocol editors

Once a protocol is digitalized, the information that used to be stuck in a single copy of paper can be easily replicated, enabling faster collaboration, sharing, and reuse. This can be done via a combination of text software, local or cloud servers, wiki platforms or by using a specialized software such as – electronic lab notebooks (ELNs).

ELNs are designed to help overcome the limitations of classical pen-and-paper lab notebooks and to align with daily wet-lab routines. ELNs facilitate the editing and sharing of protocols, usually in a closed environment such as a lab or consortium. Designed as lightweight (low-burden, free-text) protocol editors, ELNs are a major step towards digitalization of laboratory processes.

ARCs – Packaging protocols combined with the data

Protocols generated in ELNs integrate well with the Annotated Research Context (ARC). Protocols and the metadata they contain have a dedicated place and schema within the ARC. Each study and assay subfolder in the ARC comes with a folder called protocols. This folder collects all protocols associated with a particular set of data files in the dataset folder. In addition, the isa.study.xlsx and isa.assay.xlsx workbooks associated with each study or assay, help to communicate the protocol metadata in a structured and machine-readable way.

Since ARCs are designed as FAIR digital objects which combine the data files with the metadata into one research data package, they facilitate the storage, shareing, and reuse of the research data as a whole.

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
Contribution Guide 📖
✏️ Edit this page