COPO: Guidelines

Welcome to the guidelines for submission, updates and retrieval for the Collaborative OPen Omics project. Please use the links to find instructions specific to your needs.

Getting Started

• Getting Started
  • Accessing COPO Website
• Projects Brokered through COPO
  • Primary Projects
  • Secondary Projects
• New User
  • First time login
• Sample Managers
  • Accessing the Accept or Reject Samples web page
  • Guidelines for Searching Profiles and Samples on the Accept or Reject Web Page
    • Querying using Profiles search box
    • Querying using Samples search box
  • Guidelines for Sample Managers Assigned to Multiple Manifest Groups
  • Accepting or Rejecting Samples
    • Accepting samples
    • Rejecting samples
  • Download Submitted Sample Manifests
  • Download Submitted Permits
  • View Submitted Images
  • Upload Manifest or Update Submitted Manifest on behalf of Manifest Submitters

COPO Profile

• Genomics Profile
  • Steps to Create a Genomics Profile
  • Genomics Profile Components
  • Submitting Virtual Samples
• Tree of Life Profile
  • Steps to Create a Tree of Life Profile
    • 1. Choose Profile Type
    • 2. Provide Profile Details in the Add Profile Form
      • Title & Description
      • Select Associated Profile Type (if applicable)
      • Select Sequencing Centre (if applicable)
      • Input Locus Tag (if applicable)
    • 3. Save Profile Form
    • 4. Profile created
  • Tree of Life Profile Components
• Sharing Profiles
  • Sharer
  • Sharee
• Releasing Profiles (Studies)
• Sorting Profiles
• Profile Types Legend

COPO Data Submission

• General Tree of Life Visual Submission Documentation
• Files Submission
  • How to Submit Files
    • Accessing the Files’ Web Page
      • Use Components’ Button to Navigate to Files’ Web Page
    • Submit Files from your Local (Computer) System
    • Submit Files via the Terminal
  • How to Delete Files
  • Checking ENA File Processing Status
• Assembly Submission
  • How to Submit Assemblies
    • Accessing the Assembly Web Page
      • Use Components’ Button to Navigate to Assembly Web Page
    • Submit Assembly
  • How to Delete Assemblies
• Barcoding Manifest Submission
  • How to Submit Barcoding Manifests
    • Accessing the Barcoding Manifest Web Page
      • Use Components’ Button to Navigate to Barcoding Manifest Web Page
    • Upload Barcoding Manifest
    • Submit Barcoding Manifests
  • How to Delete Barcoding Manifests
• Images Submission
  • How to Submit Images
  • View Submitted Images
    • On Samples web page
    • On Accept or Reject Samples web page
• Permits Submission
  • How to Submit Permits
  • Download Submitted Permits
    • On Samples web page
    • On Accept or Reject Samples web page
• Reads Submission
  • How to Submit Reads
    • Accessing the Reads’ Web Page
      • Use Components’ Button to Navigate to Reads’ Web Page
    • Upload Reads
    • Submit Reads
• Samples Submission
  • How to Download Submitted Sample Manifest
• Sequence Annotations Submission
  • How to Submit Sequence Annotations
    • Accessing the Sequence Annotations’ Web Page
      • Use Components’ Button to Navigate to Sequence Annotations’ Web Page
    • Submit Sequence Annotations
  • How to Delete Sequence Annotations

COPO Data Updates

• Updating Profiles
  • Deleting Profiles
• Updating Samples
• Updating Sequence Annotations
• Updating Reads
• Adding Children Projects to Parent Projects
  • In COPO
  • In Public Repositories

COPO Data Discovery & Retrieval

• Downloading Manifest Templates & Standard Operating Procedures (SOPs)
  • Downloading Manifest Templates
  • Recording Data in Manifests
    • ASG SOP
    • DToL SOP
    • DToL_ENV SOP
    • ERGA SOP
    • POP_GENOMICS SOP
• Using COPO API
  • API End-points
    • Audit Endpoints
      • Fetch Sample Updates Between Dates
      • Fetch Sample Updates by Manifest ID
      • Fetch Sample Updates by COPO ID
      • Fetch Sample Updates by Update Type
      • Fetch Sample Updates by Field and Field Value
      • Fetch Sample Updates by ASG Sample Type
      • Fetch Sample Updates by DTOL Sample Type
      • Fetch Sample Updates by ERGA Sample Type
    • Manifest Endpoints
      • Fetch Manifests
      • Fetch Manifests by Sequencing Centre
      • Fetch Current Manifest Versions
      • Fetch Sample Records in a Manifest by Manifest ID
      • Fetch Manifests between Dates
      • Fetch Manifests between Dates for a Project
      • Fetch Sample Record Status in a Manifest
      • Validate Manifest by Profile ID
      • Validate Manifest by Report ID
      • Validate Manifest
    • Sample Endpoints
      • Fetch Sample Records by Project
      • Fetch Sample Records by Associated Project Type
      • Fetch Sample Project Fields by Manifest Version
      • Fetch Sample Records between Dates
      • Fetch Sample Records between Dates
      • Fetch Updatable Fields by Project
      • Fetch Sample Records by COPO ID
      • Fetch Sample Records by Biosample Accession
      • Fetch Sample Records by Field and Values
      • Fetch Sample Records by Sequencing Centre
      • Fetch Study Records by Sample ID
      • Fetch Sample Records by Study ID
    • Profile Endpoints
      • Create Profile Record
      • Fetch Profile Records
      • Fetch Profile Titles & Associated Tube or Well IDs
    • Statistics’ Endpoints
      • Fetch Number of COPO Users
      • Fetch Number of Sample Records by Sample Type and Date
      • Fetch Tree of Life (ToL) Projects Brokered by COPO
      • Fetch Associated Tree of Life (ToL) Projects Brokered by COPO
    • Mapping’ Endpoints
      • Fetch Mapped fields for the latest manifest version
• Exploring Manifest Wizard
  • Prefill Manifests
• Tree of Life Dashboard
  • Tree of Life Inspection
  • Tree of Life Inspection by Genome Acquisition Lab
• Retrieving Accessions
• COPO Statistics
  • Statistics over Time
  • Statistics by Variable
• Manifest Checklist
  • Barcoding Manifest Checklists
  • Sample Manifest Checklists

Advanced

• COPO Project Local Setup
  • Project Setup With Docker
    • Install Docker
    • Initialise Docker Swarm
    • Add Docker Node Labels
      • Adding One Docker Node Label
      • Adding More than Docker One Node Labels
    • Create Docker Volumes
    • Create Networks on Docker Swarm Manager
    • Create Secrets on Docker Swarm Manager
    • Build COPO Project Docker Image
    • Deploy Docker Image on Docker Swarm Manager
    • Set up PostgreSQL database
    • Updating COPO Website Service
    • Launch COPO Website
    • Tips
  • Project Setup Without Docker
    • Set Up COPO Project on Linux
      • Install Python
      • Install Python Development Tools
      • Install Required Packages
      • Install Integrated Development Environment (IDE)
      • Configure IDE
        • PyCharm
        • VSCode
      • Declare Environment Variables
      • Set up Python Virtual Environment
      • Set Up Mongo Database in COPO Project
        • Set up MongoDB in Studio3T
      • Set Up PostgreSQL Database in COPO Project
      • Launch COPO Website
    • Set Up COPO Project on Windows
      • Option 1: Using Ubuntu Terminal
      • Option 2: Using Windows Terminal
• COPO Project Application Structure
  • Project Root Directory (myproject/)
  • Project Directory (myproject/myproject/)
  • Application Directory (myproject/myapp/)
• Navigating to, Accessing and Using the Django Admin Interface
  • 1. Setting Up the Admin Interface
  • 2. Navigating to the Admin Interface
  • 3. Logging into the Admin Interface
  • 4. Using the Admin Interface
• Profile Configuration and Setup using Python and Django
  • 1. Defining the Profile Structure
    • ProfileType
      • ProfileType Database Table Structure
      • Usage of ProfileType
      • Visualisation of ProfileType in Project
    • Component
      • Component Database Table Structure
      • Creation of Component
      • Visualisation of Created Component
    • RecordActionButton
      • RecordActionButton Database Table Structure
      • Referencing Created RecordActionButton in Project
      • Visualisation of RecordActionButton in Project
    • TitleButton
      • TitleButton Database Table Structure
      • Referencing Created TitleButton in Project
      • Visualisation of TitleButton in Project
  • 2. Defining Django Model
  • 3. Registering Django Model with Django Admin site
  • 4. Make Migrations and Migrate the Django Model
  • 5. Automating Profile Creation with manage.py
    • Management Command
  • Visual Representation of Profile Subparts within COPO Project
• Managing Profiles on Django Admin Interface
  • Viewing data
  • Adding data
  • Editing data
  • Deleting data
  • Using the Search and Filters

Policies

• Brokering Data in COPO with FAIR Data Principles
  • Findable
    • Using DataTables’ search engine
    • Using COPO API
  • Accessible
  • Interoperable
  • Reusable
  • FAIR Webinars
• Licence
  • How to apply the Apache Licence to your work
• Contributor Covenant Code of Conduct
  • Our Pledge
  • Our Standards
  • Enforcement Responsibilities
  • Scope
  • Enforcement
  • Enforcement Guidelines
    • 1. Correction
    • 2. Warning
    • 3. Temporary Ban
    • 4. Permanent Ban
  • Attribution
• Privacy Notice
  • Lawful basis for processing your data
    • Data Collected
      • Information collected:
      • Usage of information collected:
  • Storing and Sharing of your information
  • Data Retention
  • Cookies
  • Your Rights
  • Questions
• Terms of Use

Help

• Contact COPO
• Frequently Asked Questions
  • Assemblies
  • Dashboard
  • Files
  • Images
  • Other
  • Permits
  • Profiles
  • Reads
  • Samples
  • Sample Managers
  • Sequence Annotations
• Glossary

Research Outputs & Presentations

• COPO Presentations
  • Seminar presentations
  • Poster presentations
• COPO Publications