Meetings
BioHackSWAT4HCLS 2025
BioHackathon Europe 2024
3rd BioHackathon Germany
DBCLS BioHackathon 2024
ELIXIR INTOXICOM
Recent preprints
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An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems
Here we report the results of a project started at the BioHackathon Europe 2022. Its goals were to cross-compare and analyze the metadata centralized in the Tools Ecosystem, and linked to the EDAM ontology, as well as to explore methods for connecting tools used in registered Galaxy workflows (i.e. WorkflowHub entries) to the annotations available in bio.tools. -
Empowering the community with notebooks for bespoke microbiome analyses
MGnify is EMBL-EBI’s metagenomics resource. MGnify’s recently launched Notebook Server provides an online Jupyter Lab environment for users to explore programmatic access to MGnify’s datasets using Python or R. Here, we report several developments to the Notebook Server completed during the BioHackathon Europe 2022. The developments range from establishing an instance of the notebooks on the Galaxy platform, to adding new notebooks and Jupyter UI extensions enabling more users to perform downstream analysis tasks on MGnify’s extensive metagenomics datasets. -
CiTO support for BioHackrXiv
In this paper we present the work executed on BioHackrXiv during the international ELIXIR BioHackathon in Barcelona, Spain, 2021. -
Addressing sex bias in biological databases worldwide
Precision medicine aims at tailoring treatments to individual patient needs. In this context, artificial intelligence (AI)-based technologies are viewed as revolutionary since they have the capacity to identify key features that link genomic and phenotypic traits at the individual level. AI techniques therefore depend on the quantity and quality of patient data. When variables like sex, age, or race are ignored in sample records, it can result in biased predictions as they will not be considered in the training of the AI algorithm. To this end, the European Genome-phenome Archive (EGA) took action in 2018 and put into place a rule that requires data providers to declare the sex of donor samples uploaded into their repository to improve data quality and prevent the spread of biased results. In this work we quantified biases in sex classification over time in human data from studies deposited in EGA and the database of Genotypes and Phenotypes (dbGaP), which represents the EGA’s equivalent in the USA. The main result is that the EGA policy is effective to fight sex classification biases because there are significantly less samples classified as unknown after 2018 in this repository than in dbGaP. Additionally, we qualitatively assessed public opinion on this issue. A survey addressed to users, creators, maintainers, and developers of biological databases revealed that specialized training and additional knowledge about diversity criteria are required. Based on our findings, we raise awareness of sample bias problems and provide a list of recommendations for enhancing biomedical research practices. -
BioHackEU22 Report for Project 16: Make your own or favourite software available on your cluster with EasyBuild/EESSI
EasyBuild is a community effort to develop a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. As its name suggests, EasyBuild makes software installation easy by automating builds, making previous builds reproducible, resolving dependencies, and retaining logs for traceability. It is also one of the components of the European Environment for Scientific Software Installations (EESSI), a collaboration between different European HPC sites and industry partners, with the common goal to set up a shared repository of scientific software installations that can be used on a variety of operating systems and computer architectures. It can be applied in a full size HPC cluster, a cloud environment, a container or a personal workstation.With the deluge of data in the genomics field (e.g., clinical data) and the concomitant development of new technologies, the number of data analysis software has exploded in recent years. The fields of bioinformatics and cheminformatics follow this same trend with ever more developments to optimize and parallelize analyses. The bioinformatics field is now the main provider of new software in EasyBuild. Developers of those tools are not always professional developers, and they do therefore not always follow best practices when releasing their software. As a result, many tools are complicated to install, making them ideal candidates for porting their installation to EasyBuild so that they become more easily accessible to end users.We propose to introduce users to EasyBuild and EESSI, and to port new software to EasyBuild/EESSI (e.g., the participant’s own or favourite software), thereby making it available and discoverable to the entire EasyBuild community. In parallel we would like to build bridges between EESSI and Galaxy to make the scientific software more accessible to researchers in the domain. -
Validating Subtype Specific Oncology Drug Predictions
There is an impressive number of data and code reproducibility initiatives, both within Europe and across the world. To motivate researchers to use this amazing infrastructure, we must show the translational research community that the aforementioned initiatives are able to drive change in translational science. Here we demonstrate that using public datasets, it is reasonable to build a pipeline for proposal and validation of driver mutation and subtype-specific colorectal cancer medications. While all three molecular, clinical and chemical name harmonization were necessary, open data and code initiatives, while varied in their approaches, made this project possible. -
BioHackEU22 Project 22: Plant data exchange and standard interoperability
Status of discussions around the topic of data standard formats for plant sciences and their interoperability at the BioHackathon Europe 2022 in Paris.