COPO Presentations

This section entails presentations and other materials that have been used to introduce COPO to various audiences.

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Seminar presentations

  1. New COPO Tools for Brokering Single-cell & Spatial Omics Metadata

    • Presented at the Earlham Institute internal seminar

    • Date: Tuesday 1st July, 2025

    • Abstract:

      The Collaborative OPen Omics (COPO) platform now includes dedicated support for submitting metadata from Single-cell and Spatial Transcriptomics experiments. Whether you’re working with Single-cell Ribonucleic Acid Sequencing (scRNA-Seq), Spatial Transcriptomics Fluorescence In Situ Hybridisation (ST-FISH) or Spatial Transcriptomics Sequencing (ST-Seq), COPO streamlines the process of structuring, validating and submitting your metadata using established standards such as Darwin Core (DwC), Minimum Information about any (x) Sequence (MIxS) and Functional Annotation of Animal Genomes (FAANG).

      This new configuration, tailored for single-cell workflows, also serves as a flexible tool that can be adapted to meet a wide range of metadata requirements across diverse omics domains. COPO does not enforce a fixed metadata model - instead, it supports user-defined metadata structures, making it easy to extend or modify worksheets, add fields and build manifests that suit your specific data submission types.

      With integration to public repositories like the European Nucleotide Archive (ENA) and Zenodo, COPO helps ensure that your data is Findable, Accessible, Interoperable and Reusable (FAIR) with the scientific community.

      Join this seminar to see how COPO can save you time, reduce submission errors and support your single-cell metadata submissions - while remaining fully adaptable for any other metadata needs you may have.

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  2. Leveraging COPO to submit READ/Assembly/Sequencing Annotation data to ENA and get data published

    • Presented at the Earlham Institute internal seminar

    • Date: Tuesday 14th May, 2024

    • Abstract:

      How users can leverage COPO to submit reads, assemblies and sequencing annotation data to European Nucleotide Archive (ENA) and get the data published

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  3. Advancing Biodiversity Research: The Evolution of Collaborative OPen Omics (COPO) Project

    • Presented at the Earlham Institute internal seminar

    • Date: Tuesday 23rd April, 2024

    • Abstract:

      This seminar explores the evolution of the Collaborative OPen Omics (COPO) project as an open-source metadata broker in biodiversity research. With its capability to broker different data seamlessly, COPO has revolutionised the way by which researchers collaborate and share information.

      An integral part of COPO’s development involves standardising as well as enriching metadata and enabling the integration of diverse datasets for publication to the European Nucleotide Archive (ENA) which facilitates public dissemination.

      Additionally, COPO’s user-friendly Application Programming Interface (API) empowers users to query sample data efficiently, further enhancing accessibility and interoperability in biodiversity studies. Through its continuous evolution, COPO continues to drive innovation and collaboration in the field of bioscience research.

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Poster presentations

  1. Collaborative OPen Omics (COPO) - Facilitating Metadata Interoperability with Standards, Formats and APIs

    • Abstract:

      The Collaborative OPen Omics (COPO) platform is a data and metadata broker for researchers seeking to describe and share a wide range of research objects - including genomic reads, assemblies, sequence annotations, samples and images—using standardised metadata. By enabling users to submit metadata through well-defined spreadsheets and web forms, COPO facilitates the publication of this data to public repositories such as the European Nucleotide Archive (ENA) and the National Centre for Biotechnology Information (NCBI). COPO’s integration of community-derived schemas and vocabularies ensures that data is Findable, Accessible, Interoperable and Reusable (FAIR).

      COPO can validate and convert submitted metadata into various standards, making it accessible through its Application Programming Interface (API). This process allows for seamless mapping of metadata from one standard, such as Tree of Life (ToL), to other recognised standards like Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS). Researchers can retrieve this metadata in structured formats such as Research Object Crate (RO-Crate), JavaScript Object Notation (JSON) or Comma-Separated Values (CSV), enhancing data discoverability and reuse.

      Our poster illustrates how COPO supports interoperability across different systems by brokering and sharing metadata, while also ensuring the exclusion of sensitive data such as ORCID identifiers and email addresses. By empowering researchers to securely submit and manage their data in compliance with recognised standards, COPO fosters open science and advances research in the life sciences.

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  2. Collaborative OPen Omics (COPO) - Building, Testing and Deployment

    • Abstract:

      Collaborative OPen Omics (COPO) is a user-friendly platform that allows scientists to easily upload, update and publish metadata while adhering to community standards, promoting transparent data sharing. Built with cutting-edge technology, it utilises Docker Swarm for seamless service management, ensuring continuous availability, scalability and ease of maintenance.

      Security is prioritised in COPO’s architecture, with distinct network layers preventing direct client access to back-end data repositories. Docker secrets are employed to enforce strict measures against unauthorised access, enhancing data protection and platform integrity.

      Overall, COPO provides a sophisticated solution for scientific data management, integrating modern methodologies and security protocols to facilitate collaborative research efforts and promote scientific advancement.

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  3. COPO - Bridging the Gap from Data to Publication in Plant Science

    • Abstract:

      COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories and to facilitate links to data analysis platforms.

      Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces.

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