Advance Features

• JupyterHub for openBIS
  • Overview
    • Nomenclature
    • Prerequisites for testing in a local environment
  • How to run the official JupyterHub for openBIS image in your local machine
  • How to extend the official JupyterHub for openBIS image
  • Modify a currently running container - From UI (for users)
    • Check Available Python 2 Libraries
    • Add Python 2 Library
    • Check Available Octave Libraries
    • Add Octave Library
    • Check Available Python 3 Libraries
    • Add Python 3 Library
    • Check Available R Libraries
    • Add R Library
  • Modify a currently running container - From Console (for admins)
    • Add Python Library
    • Add R Library
    • Save the state of a running container as a new image
  • Extend a docker image using a docker recipe (for maintenance)
  • How to start a jupyterhub-openbis docker image on a productive JupyterHub server
  • Other useful Docker commands
    • Save an image as a tar file to share it
    • Load an image from a tar file
    • Remove an image
    • Remove all stopped containers
  • openBIS ELN Integration Configuration
  • Troubleshooting Connectivity to openBIS
    • Session is no longer valid. Please log in again error
      • Session is no longer valid. The openBIS server has a self-signed certificate
      • Session is no longer valid. The session has timeout
• openBIS Command Line Tool (oBIS)
  • 1. Prerequisites
  • 2. Installation
  • 3. Quick start guide
  • 4. Usage
    • 4.1 Help is your friend!
  • 5. Work modes
  • 5.1 Standard Data Store
  • 5.1.1 Commands
    • 5.1.2 Examples
  • 5.2 External Data Store
    • 5.2.1 Settings
  • 5.2.2 Commands
    • 5.2.3 Examples
  • 6. Authentication
    • 6.1. Login
    • 6.2. Personal Access Token
  • 7. Big Data Link Services
  • 8. Rationale for obis
  • 9. Literature
• openBIS Data Modelling
  • Data model in openBIS ELN-LIMS
  • Inventory
  • Lab Notebook
  • openBIS parents and children
  • Examples of parent-child relationships
  • Protocols
• Excel Import Service
  • Introduction
  • Modes
  • Organising Definition Files
  • Organising Definitions
    • Text cell formatting (colours, fonts, font style, text decorations)
    • Definition, rows and sheet formatting
  • Entity Types Definitions
    • Vocabulary and Vocabulary Term
  • Experiment Type
    • Sample Type
    • Dataset Type
    • Property Type
    • Entity Type Validation Script and Property Type Dynamic Script
    • Entity Types Update Algorithm
      • General Usage
  • Entity Definitions
    • Space
    • Project
    • Experiment
    • Sample
      • Defining Parent and Children in Samples
    • Properties and Sample Variables
  • Master Data as a Core Plugin
  • Known Limitations