Meetings
BioHackSWAT4HCLS 2025
BioHackathon Europe 2024
3rd BioHackathon Germany
DBCLS BioHackathon 2024
ELIXIR INTOXICOM
Recent preprints
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BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports
The first BioHackrXiv preprint was published in 2020, using a platform based on the idea of using Markdown, and just weeks ago, BioHackrXiv published their 100th preprint. Machine-readable etadata added to the Markdown that is added includes the title, keywords, the author names, their affiliations, and details about the Biohackathon event the preprint is related to. The metadata in 2000 already supported listing the ORCID identifier of the authors, but this was not added to the author list in the generated PDF. This report describes two improvements of the platform: visualization of the ORCID identifiers in the preprint PDF and support for Research Organization Registry (ROR) identifiers of the affiliations. -
BioHackGermany24 report: User-friendly ISA-based metadata annotation of life science experiments with ISA Wizard
As a contribution to BioHackathon Germany 2024, the following report details the work conducted during that event for project 8: User-friendly ISA-based metadata annotation of life science experiments with ISA Wizard. -
BioHackJP24 report: Running a WikiBlitz
During BioHackathon 24 in Fukushima, we organized a WikiBlitz, a collaborative effort to integrate biodiversity observations from iNaturalist into the Wikimedia ecosystem. A WikiBlitz is inspired by the concept of a BioBlitz, where participants document as many species as possible within a limited time frame, while also contributing structured data to Wikidata, Wikimedia Commons, and Wikipedia. In this report, we describe the methodology and outcomes of this event, including the collection of 109 biodiversity observations and their subsequent verification and integration into Wikimedia platforms. We highlight the challenges and best practices for running a WikiBlitz, particularly around licensing and data quality, and demonstrate how tools such as iNaturalist2Commons and Wikidata queries can enhance the reuse of citizen science data. Finally, we provide a step-by-step tutorial to support future WikiBlitz events, ensuring broader participation and sustainable knowledge-sharing across platforms. -
BioHackEU24 report: Bioschemas for Mortals
We report here on the progress of project #10: “Bioschemas for Mortals” from BioHackathon Europe 2024. The goal of this project is to reimagine, reframe and supplement the existing Bioschemas guidance available. We identified patterns of use, commonly undertaken tasks and user personas and roles. This information will be used to identify what is needed by less technical users, ultimately providing specific code examples that can be copy/pasted, documented examples for different web setups, customised guidance for different personas, and to address usability and content accessibility. We will also use the learnings from the Bioschemas hackathons to progress more quickly on the domain-agnostic schemas.sci site. -
BioHackEU24 report: Creating user benefit from ARC-ISA RO-Crate machine-actionability & Increasing FAIRness of digital agrosystem resources by extending Bioschemas
As part of the BioHackathon Europe 2024, we here report on the progress that both project 19 and project 24 have made during the event. For the purpose of this report we will present the abstract of both projects and then dive deeper on what work was done during the BioHackathon. -
Enhancing multi-omic analyses through a federated microbiome analysis service
Multi-omics datasets are an increasingly prevalent and necessary resource for achieving scientificadvances in microbial ecosystem research. However, they present twin challenges to researchinfrastructures: firstly the utility of multi-omics datasets relies entirely on interoperability ofomics layers, i.e. on formalised data linking. Secondly, microbiome derived data typically leadto computationally expensive analyses, and so rely on the availability of high performancecomputing (HPC) or cloud infrastructures. These challenges can be better met by combining the resources of multiple groups, services and infrastructures. In this BioHackathon Europe 2024 project, we envisioned a “federated microbiome analysis service” and worked on three tracks of development towards it: mapping metagenomics metadata standards to Schema.org and Bioschemas terms, rendering Nextflow workflow executions as RO-Crates, and tooling for creating, viewing and interlinking human-readable RO-Crate previews. -
1st SpatialData Developer Workshop
This pre-print is aimed at sharing the results of the “1st SpatialData workshop,” an in-person event organized by the SpatialData team and funded by the Chan Zuckerberg Initiative (CZI) that brought together expertise from different fields, including methods developers of a variety of tools for single-cell and spatial omics. The purpose is to explore new directions to advance the field of spatial omics. By leveraging multiple programming languages, including Python, R, and JavaScript, the event focuses on four central hackathon tracks: R interoperability: This track aims to enhance the integration and compatibility of R and Python with the SpatialData Python framework by using the language-agnostic SpatialData Zarr file format (which follows, when possible, the NGFF specification). Visualization interoperability: This track is dedicated to improving the seamless integration of visualization tools across different systems and programming languages via a tool-agnostic view configuration. Scalability and benchmarking: Participants will identify, benchmark, and address computational bottlenecks within the SpatialData framework. Ergonomics and user-friendliness: This track focuses on enhancing the usability and accessibility of the SpatialData framework for both first-time users and third-party developers. These tracks aim to foster collaboration and innovation, driving advancements in the analysis and infrastructure of spatial omics and imaging data.