FAIRDOM-SEEK user documentation

Your profile

• Registering in SEEK
• Logging into SEEK
  • Logging into SEEK via ELIXIR AAI
• Managing your account
  • Managing your identities/alternative login methods
• Editing your profile
• Favourites

Yellow pages

• Browsing content
• Creating and managing your own Programmes
• Creating a Project
• Joining a Project
• Project Dashboard
• Viewing Project in Single Page

• Specialist user roles and their capabilities

  Specialist user roles

  • Programme administrator
  • Project administrator
  • Asset housekeeper
  • Asset gatekeeper

  Capabilities

  • Assign people to Project roles
  • Flag when a person becomes inactive in a Project
  • Create Organisms
  • Create Profiles
  • Create Institutions
  • Add and remove people from a Project

Experiments

• Generating the ISA structure
  • Creating an Investigation
  • Creating a Study
  • Creating an Experimental assay
  • Creating a Modelling analysis

• ISA Overview Graph

• Designing experiments in Single Page
  • Creating an Investigation in Single Page
  • Creating a Study in Single Page
  • Creating an Assay in Single Page
• ISA in Single Page advanced

• Export experiments from Single Page as ISA-JSON

• Making an Investigation, Study or Assay citable
  • Making public
  • Snapshotting
  • Creating a Research Object
  • Assigning a DOI

Assets

• Adding assets (data, models, SOPs, publications) to SEEK
• Data Files
  • Data file wizard
• Model
  • Simulate a model on JWS Online
• SOPs
• Publications
• Collections
• Document
• Workflow
• File template
• Creating new asset versions
  • Comparing two versions of a Model

Samples

• Samples
  • Create a Sample Type
  • Create a Sample
  • Legacy Biosamples
• Samples in Single Page
  • Viewing samples in Single Page
  • Create Study Sources in Single Page
  • Create Study Samples in Single Page
  • Create samples in a first Assay Single Page
• Templates
  • Apply templates to design experiments in Single Page
  • Creating templates for system administrators
• Browsing samples
  • Browse samples by Sample Type
  • Browse samples by templates

General attributes and links

General attributes and links

• Title
• Description
• Projects
• Investigation details
• Study
• Biological Problem Addressed
• Assay Type
• Experimental assays and Modelling analysis
• Technology Type
• Organisms
• Experimentalists
• Attributions
• Creators
• Tags
• Discussion channel
• Licenses
• Sharing
  • Bulk changing of sharing permissions

Activities

• Presentation
• Events

Integrations

• Using SEEK with openBIS
• Using Copasi in SEEK
• Single Page view
• Single Page advanced

User guide for API

• API Introduction

Contribute

• Reporting a bug or feature request
• Contributing to these SEEK Documents