Lab Integrated Data
Attributes
DescriptionLab Integrated Data (LabID) is a web platform for fundamental research data-management, featuring a lab inventory system, an Electronic Lab Notebook (ELN) coupled to a powerful Dataset & Sample management system. It is designed to help individual scientists and research groups better managing their (1) lab inventory including consumables e.g. chemicals, antibodies, plasmids..., equipments e.g. microscopes, sequencers..., specimen e.g. cell lines, mouse strains, fly lines..., (2) samples & biobank , (3) research experiments & protocols, (4) assays (sequencing, light and electron microscopy) and (5) datasets, both primary and derived. Samples, Assays and Datasets are logically connected into studies & projects following the ISA model (https://isa-specs.readthedocs.io/). All objects can also be freely cross-linked in the ELN. LabID overall facilitates documenting and referencing research progress throughout the experimental and analysis chains, effectively preserving data integrity and enhancing traceability. It implements international standards to ease data submission to international data repositories such as EMBL-EBI's ENA or Biostudies. Since 2018, LabID has been used across EMBL sites and units by hundreds of researchers. LabID can be integrated with a local instance of Galaxy (usegalaxy.eu) and attachments can be readily edited online using LibreOffice Online. A REST API and a Command Line Interface are available to automate data ingestion & integrate with your local infrastructure. LabID is free to use and was released open source in 2023.
ProviderGenome Biology Computational Support, European Molecular Biology Laboratory (EMBL)
Information on Providerhttps://gbcs.embl.de
Activity Statusactive
Information on ActiveFrequent release cycle. Last release in February 2024. https://grp-gbcs.embl-community.io/labid-user-docs/releases/
Last checked on20.03.2024
Provider's data safety and data security strategiesUser & Groups, Login, ACL-like permission at object level. Experiments described in the ELN are digitally timestamped. Data archival possible.
Reference usersCharles Girardot, EMBL, girardot@embl.de can answer any question.
Reviews
Exit strategyExport as excel spreadsheet for all collections (inventory, samples, equipement...), MAGE-TAB/tabular export for Studies, Assays and Datasets (using the CLI). Users' ELN can be exported as a static web site (using the CLI)
Communityhttps://gitlab.com/lab-integrated-data
Known usersEuropean Molecular Biology Laboratory (EMBL)
General
LicenseOpen Source, MIT
SubjectBiology, Consumables, Generic, Genetics, Life Sciences
PricingFree
VersionsDemo, https://labid-demo.embl.de/home
Location of providerGermany, Heidelberg
Usability
Customizable user interfaceCustomizable user interface, List pages (column visibility, order) can be customized by users. Admin can define additional properties to any item types (samples, consumables, assays...). Admin can add new annotation types. Admin can load new controlled vocabulary to any CV-controlled field.
LanguagesEnglish
SupportOnline documentation, Support by provider, User training (online, on site), Consulting, Professional consulting available through Lab Rise Consulting (https://labrise-consulting.com/)
Usage statisticsUsage statistics, Available to admin only.
Offline functionalities
Core functions (Daily work)
Data inputBrowser forms, Rich text editor, With internal links, With external links, Table editor
Data import (formats)Image formats, MS Office formats, Table formats, Document formats, Compressed formats, Audio formats, Scientific formats, Structured formats, Video formats, All formats are supported for attachments. Images (png, jpg...) can be embedded in the ELN. MS Word and other LibreOffice compatible documents can be edited online if LibreOffice was configured. Data can be batch loaded from excel documents.
Data import (method)Drag & Drop / File Chooser, Mobile phone photo (via app), Images can be added to experiments using phone or tablets. Datasets (primary & derived) with metadata (assay, samples) can be easily import using the data import wizard (web UI) or the comamd line interface (CLI).
Data exportComplete content in document format, Formats suitable for long term archiving, Formats suitable for publication, Collections (consumables, samples, specimen, equipment) can be exported to excel spreadsheet. ELN experiments can be exported as a static web site. Datasets & Assays (like sequencing) can be exported to MAGE-TAB document or tabular formats.
TemplatesImport of own templates, Define own templates, Most objects can be cloned (ie duplicated). Assay templates can be defined to ease dataset registration.
Search functionsAdvanced search, Conditional search, Full text search
CollaborationRole management, Rights management, Comments, Admin, Manager & User roles
Compliance with legal requirements
Preservation of evidenceTimestamping, Experiment described in the ELN are digitally timestamped upon freezing (including all attached documents). Nightly PDF exports are also generated although these do not represent a proper audit trail.
Compliance
Extended functions (Daily work)
Laboratory management functionsFreezer Management, Inventory (devices), Materials database, Ordering function, Sample Tracking, Orders and ordered items can be saved but ordering is currently not linked to external procurement service. This could be added as a contribution.
Integrations and extensionsIntegration with Galaxy (installed locally) and LibreOffice Online
AutomationAutomation: On request, The REST API and the command line interface (CLI) allow to automate data ingestion, and potentially much more.
Device connection
Project management toolsProject management, experiment can be organized into projects
Workflows
Integration in RDM and IT environment
Application programming interfacesREST API, Command line input, The CLI (written in Python) uses the REST API
Controlled vocabularyControlled Vocabulary, Admin can create (and batch load) vocabulary terms (CV terms) in the AdminUI. CV terms are organized into categories (e.g. "species"). Items properties (e.g. the sample's organism property) can then be controlled by a CV category (here the 'species').
Data accessBrowser based, Responsive Design, Local client, Data can be accessed using the CLI as well
Data storage locationLocal, A central local storage is used for all attachments. Each group has one or more "Data libraries" (a local folder on e.g. NFS) where the datasets are stored. Each group thus directly pays for their storage. Data Libraries must be secured using standard unix permissions to allow group users to READ only, while the unix user running LabID is the only user with full permissions.
Authentication methodsLDAP, Local
User account security measures
Usage optionOn-premises
Server operating systemLinux, MacOS
Version History
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