This tutorial introduces infrastructures, standards, and computational approaches that support modern plant sciences. It covers data management practices and repositories, comparative genomics for orthology and functional annotation, knowledge graph frameworks that integrate datasets from multiple sources from omics to phenomics, and pan‑genome research. The pan‑genome component includes construction and representation, evaluation of assemblies, annotations, and variant detection, strategies for linking genotypic and phenotypic diversity, and methods for sharing and visualizing pan‑genome information for reuse and comparison. The goal is to provide participants with practical knowledge of current methods and resources, demonstrate workflows, and highlight practices that improve reproducibility and interoperability. The motivation comes from the rapid growth of publicly available plant data, which requires harmonized standards and interoperable tools to realize its full potential. The scope is introductory to intermediate, combining conceptual overviews with illustrative examples, and is relevant for plant scientists, bioinformaticians, and data managers working with complex biological data.
Plant sciences are rapidly evolving, producing large and heterogeneous datasets from phenotyping, multi-omics, and pan-genome studies. Managing and analysing these data requires clear standards, interoperable infrastructures, and computational approaches that support integration across different data types. This tutorial provides an overview of key resources, beginning with community-driven metadata standards, federated portals for data discovery, and repositories for long-term archiving.
Participants will then examine comparative genomics methods for identifying orthologs and functional relationships across species, followed by knowledge graph frameworks that integrate datasets from multiple sources to enable new biological insights. The program continues with recent advances in pan-genome research, emphasizing assessment of genome assemblies, annotations, and variant detection, with attention to sequencing data quality. Strategies for connecting genotypic and phenotypic diversity through presence/absence variation and structural rearrangements will also be presented, alongside effective practices for sharing and visualizing pan-genome information.
By the end of the tutorial, attendees will gain familiarity with plant data standards, comparative genomics methodologies, and knowledge graph approaches, and will gain practical insights into pan-genome evaluation and visualization. The session is aimed at an introductory to intermediate level and will give practical insights for plant scientists, bioinformaticians, and data managers working with diverse plant data.
Systems biology, multi-omics integration and modeling
| Time | Session | Description | Contributor |
|---|---|---|---|
| 13:45–13:55 | Welcome & Objectives | Introduction by organizers, overview of tutorial goals and structure | |
| 13:55–14:35 | Session 1 | Overview of metadata standards in plant sciences and federated discovery | Dr. Pommier |
| 14:35–15:15 | Session 2 | Approaches for orthology, annotation, and cross-species comparisons | Dr. Zagorščak |
| 15:15–15:30 | Coffee Break & Networking | ||
| 15:30–16:10 | Session 3 | Knowledge graph approaches for linking datasets to uncover new biological insights | Dr. Bleker |
| 16:10–16:50 | Session 4 | Building and Evaluating Plant Pangenomes | Dr. Beier |
| 16:50–17:10 | Session 5 | Approaches for presenting and disseminating pan-genome information | Dr. Beier |
| 17:10–17:30 | Discussion & Wrap-up | Open Q&A, summary of key takeaways, and outlook for future development |
The tutorial is open to all ECCB2026 participants and is accessible to anyone working with complex biological data. Participants with backgrounds in plant sciences, computational biology, or data management may benefit most, but the content is designed to be broadly relevant across different areas of biology and integrative research.
There are no prerequisites to attending.
- Heuermann MC, Barros P, Beier S et al. White paper: standards for handling and analyzing plant pan-genomes. F1000Research 2026, 14:739 (https://doi.org/10.12688/f1000research.166538.3)