Together with their international colleagues ELIXIR Netherlands works towards shared solution at ELIXIR BioHackathon 2023

Members of the Dutch ELIXIR community made significant contributions to several of them, including some led by the Dutch participants. 

Highlights of Dutch participation in the different BioHackathon projects include: 

• Assessing quality and privacy metrics of synthetic health data for benchmarking: the variant callers use case (Project 2) 
  This project is co-lead by Núria Queralt Rosinach (LUMC) together with colleagues Styliani-Chrisitina Fragkouli (ELIXIR Greece) and Alberto Labarga (ELIXIR Spain). The team generated synthetic genomes using two different tools and in parallel worked on defining evaluation metrics that capture the characteristics of real-world data needed for benchmarking variant calling methods. 
• New benchmarks for bioinformatics workflow bake offs (Project 4) 
  This project is co-lead by Vedran Kasalica (Netherlands eScience Center) and Magnus Palmblad (LUMC). It advanced on several fronts, including aggregation of software-level benchmarks to relevant workflow benchmarks and mapping of EDAM operations to defined benchmarks in proteomics and genomics. New people were successfully onboarded and detailed discussions could be held with several members of the OpenEBench team, based in Barcelona. 
• The Bioschemas annotation of plants and chemicals resources was improved (Project 7) 
  This project is led by the ELIXIR Germany and Italy, with the ELIXIR Netherlands team adding Protein and MolecularEntity annotations to WikiPathways in a new, richer data dump. 
• Cell type-specific and druggable pathway models and maps (Project 9) 
  This project is co-lead by Martina Summer-Kutmon (Maastricht University) and was able to implement a workflow that integrates different data sources and diagrams to build cell-type specific and druggable pathway modules and maps that can be used for downstream modeling and analysis. Some work is still needed on the visualizations and to make the workflow robust, but overall a great achievement. 
• Lesson plans to advance life sciences data steward & researcher FAIR skills (Project 11) 
  This project is co-lead by Martijn Kersloot (Amsterdam UMC), Mijke Jetten (Health-RI), and colleagues from ELIXIR Sweden, Norway and France. The team polished the plans and significantly updated the website and repository. The RD Rome Summer School was mapped into a FAIR lesson plan. Generalizing this training program from Rare Diseases into a learning path could be the blueprint for a Dutch national “autumn school” yearly training for FAIR data stewards, project and data managers. 
• Creating the ELIXIR Data Stewardship/Management (DS/DM) Handbook - a guide for DS/DM to manage their life sciences RDM efforts (Project 12) 
  This project is co-lead by Mijke Jetten (Health-RI), with colleagues from ELIXIR UK, Norway and the ELIXIR Hub. They formulated a strategy, did a benchmarkagainst similar resources and created a mock-up for the handbook. Continuous work is planned in the RDM Community Implementation Study. 
• Added functionality to BioDataFuse, a tool designed to improve the interoperability of experimental data (Project 17) 
  This project is co-lead by Tooba Abbassi-Daloii (Maastricht University) and progressed significantly, improving the interoperability of experimental data and adding support for additional data sources. Several new people were onboarded to the project, and a continuation has been pitched to the organizers of the next Japanese BioHackathon. 

The delegation of ELIXIR-NL looks back on a successful BioHackathon

• Martina Summer-Kutmon (Maastricht University): ''We were able to connect to other projects like #17 and #30 and had a lot of motivated people join our project that we didn’t know before. Fantastic experience!'' 
   
  Magnus Palmblad (LUMC) adds: ''There were so many awesome projects, and it was amazing to see so many people hacking late into the night. The BioHackathon is unique in it allows a focused sprint within projects and productive interaction with relatedprojects''.  
   
  Vedran Kasalica (NLeSC) concludes: ''Being face-to-face allowed us to interact with many amazing projects. The open atmosphere was encouraging collaborations between teams during the whole week. It’s a unique opportunity to have face-to-face discussions with the members of the whole ELIXIR Europe community''. 
  
  Do you want to know more about ELIXIR-NL or get involved? Please find our more at ELIXIR-NL.