Meetings
BioHackSWAT4HCLS 2025
BioHackathon Europe 2024
3rd BioHackathon Germany
DBCLS BioHackathon 2024
ELIXIR INTOXICOM
Recent preprints
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VIB Hackathon on spatial omics tools and methods
During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The topics were organized in five workgroups and included benchmarking, pipelines, spatial transcriptomics, spatial proteomics, spatial multi-omics and cell-cell communication. Most tools and methods were considered in the context of the Python ecosystem for spatial (SpatialData) and single-cell (scverse) data analysis. -
Phenological Diversity Trends with Remote Sensing Datacubes
During the 2024 B-Cubed Hackathon, we extended the R package “rasterdiv” by incorporating Time-Weighted Dynamic Time Warping (TWDTW) to the package’s pre-existing paRao() function for the calculation of parametric Rao’s Quadratic Diversity (Rao’s Q) index. This expands the user’s ability to biodiversity trends when using time series of Earth Observations. Biodiversity indices like Shannon’s H do not consider spatio-temporal dynamics, and others (e.g. Rao’s Q) only incorporate geographic distance between observations, often leaving phenological variation overlooked.Through integrating TWDTW into the paRao() function, users can assess different facets of an ecosystem’s biodiversity by incorporating phenological differences among its plant communities. This is also valuable to distinguish between natural habitats that follow a seasonal phenological trend and artificial land cover types, which may lack phenological changes. Previous studies have also found that the time weighting ability of TWDTW enables the discernment of different floral community types which could otherwise be misclassified as the same with traditional Dynamic Time Warping (DTW).To evaluate the efficacy of TWDTW within the paRao() function, we compared the ability of TWDTW Rao’s Q index against other biodiversity indices at classifying the different plant communities in a disturbed grassland in Calabria, Italy. Our study used a Plant Phenological Index (PPI) time series from the Sentinel-2 satellite network. The results indicated that accounting for phenological cycles can filter out artefacts and better distinguish habitats with differing plant species diversity. This improves the ability to assess ecosystem changes through space and time, providing a more comprehensive understanding of biodiversity dynamics, and the ability to gauge the resilience of different vegetation patches.We conclude that the inclusion of plant phenology in biodiversity assessment is necessary, and that our modifications to paRao() will be valuable to facilitate the accurate detection and description of ecosystem trends in response to our changing environment. -
How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources
Galaxy hosts a vast array of tools, tutorials, and workflows, with the exact number of workflows remaining uncertain. To address the challenge of enhancing tool visibility within this expansive ecosystem, a pipeline called the Galaxy Tool Metadata Extractor was created during the BioHackathon Europe 2023. This pipeline aggregates Galaxy tool suites from various sources, automatically extracts metadata such as bio.tools identifiers and EDAM ontology, and presents the information in an interactive table. Users can filter this table to find tools relevant to their research community. Throughout development, it was noted that many tools lack EDAM annotations. An effort of the microGalaxy community was started to update 50+ microbial-related Galaxy tools, link them to their respective bio.tools entries, and collectively peer-review the results. However, that was far from enough to properly annotate all Galaxy tools and other types of Galaxy resources like training material and workflows. In addition to tools, the community offers other resources that are not properly annotated using ontologies like EDAM. Annotating all mentioned resources would improve their findability but also allow for aggregation and display of resources covering similar topics. To facilitate this work and work on a proof-of-concept for other communities, the microGalaxy community organized an online hackathon in April 2024. During this hackathon, 41 new bio.tools have been created, 85 Galaxy tool suites linked to bio.tools and EDAM terms, and 33 tutorials annotated with EDAM terms. Some microbial-related Galaxy tools have been improved. In addition, new features and improvements have been added to Galaxy Tool Metadata Extractor. The hackathon was successful with outcomes beyond the initial expectations. -
SPARQL services for InterMine databases
InterMine is an open source data warehouse system that can be used to create biological databases that can be accessed via web query tools. There are many public InterMine instances that are currently deployed worldwide and they share a core data model pertaining to common biological entities. Besides the core data model, each instance of InterMine typically has an extended data model to cover data specific to that particular deployment. The data is organised according to the graph-based data model but exists in a relational store (Postgres). The goal of this project was to explore the possibility of translating InterMine data from relational form to a graph form using Resource Description Framework (RDF) as the exchange format. This could provide a route to exposing data from InterMine instances as RDF triples and thus making it possible to query the data using the SPARQL Protocol and RDF Querying Language (SPARQL). -
Synergising ELIXIR resources for training in systems biology
Systems biology (SB) is a new ELIXIR community, that aims to utilise the ELIXIR ecosystem, such as the Training eSupport System (TeSS) and bio.tools, a registry of software tools and data resources for life sciences. One of the main initial objectives of the SB community is to create an SB-themed domain hosted by TeSS, encompassing SB-related ELIXIR services and events, in a fully automated way.Most content in TeSS is sourced through automated aggregation (“scraping”) of external sources containing resources marked up with semantic metadata, like Bioschemas. Currently, TeSS cannot recognize references to bio.tools identifiers from a Bioschemas-annotated resource, so the number of resources linked to bio.tools is relatively low.In this project, we will focus on selected SB disciplines from the priority areas of the ELXIR SB community to integrate and cross-link related ELIXIR products - training events, training materials, computational and bioinformatics tools, databases and services from the bio.tools registry.This will be achieved using suitable ontologies identified by the SB community and by careful curation of SB-related materials. We aim to extend this work to other ELIXIR products such as lists of trainers, related ELIXIR Innovation and Industry events and publications. This will serve as a pilot project leading to broader integration with other SB disciplines, and will be of interest to several other ELIXIR communities. -
Enhancing the image analysis community in Galaxy
Project 6 during the 2023 BioHackathon Europe in Barcelona focused on “Enhancing the image analysis community in Galaxy.” Despite Galaxy’s strong presence in genomics and proteomics, its image analysis tools and workflows are currently scattered. This project aimed to gather efforts in image analysis across fields to build a robust interdisciplinary community. -
Secure data-out API - enabling encrypted htsget transactions
The European Genome-phenome Archive (EGA) is a service for archiving and sharing personally identifiable genetic and phenotypic data, while the The Genomic Data Infrastructure (GDI) project is enabling access to genomic and related phenotypic and clinical data across Europe. Both projects are focused on creating federated and secure infrastructure for researchers to archive and share data with the research community, to support further research.This project proposal is focusing on the data access part of the infrastructure. The files are encrypted in the archives, using the crypt4gh standard. Currently, there exist data access processes, where the files are either decrypted on the server side and then transferred to the user or re-encrypted server-side and provided to the user in an outbox.Htsget as a data access protocol also allows access to parts of files, but there’s currently no production-level client tools that support access to encrypted data. Our goal is to create a client tool that can access encrypted data over the htsget protocol. It should also work with the GA4GH Passport and Visa standard so we can then enhance the security of our data access interfaces. We will also modify htsget-rs, a Rust htsget server, and crypt4gh-rust as required to support the aforementioned standards. Finally, there will be an effort to implement this feature in already existing tools, like samtools and IGV.