BioExcel News

Since late 2015 when the BioExcel Centre of Excellence (CoE) for Computational Biomolecular Research ( www.bioexcel.eu ) was first established, the CoE has been supporting biomolecular researchers in their computational research. BioExcel works on improving the usability of technologies for biomolecular researchers and also the efficiency and scalability of important software packages for biomolecular research (like HADDOCK and GROMACS). In addition, BioExcel provides training to help life sciences researchers make good use of the available software and e-infrastructures and to help them to be aware of the “best practices” for the relevant combinations of software and hardware.

Following the success of the first BioExcel conference – which was held online in 2021 as a collaboration with the European Molecular Biology Organization (EMBO) – BioExcel is running its second conference this summer on “Advances in Biomolecular Simulations”.

In the autumn, BioExcel will also organise the second event of the BioExcel Ambassador Program, the Atlantic Edition (involving Portugal, Spain, France and Ireland). The workshop will have lectures/tutorials on the four BioExcel core application (GROMACS, PMX, HADDOCK and BioBB library) and on AlphaFold (thanks to the recent agreement between BioExcel and the European Bioinformatics Institute, also known as EBI). The conference will be held at the University of Coimbra in collaboration with Portuguese and French National Competence Centres (NCCs).

BioExcel Webinar Series

The BioExcel webinars (see bioexcel.eu/category/webinar ) feature notable developments in the field of computational biomolecular research. Amongst other speakers this spring, BioExcel has hosted:

Mathieu Linares (PDC) who, together with Robin Skånberg from Linköping University, spoke about the VIAMD software for visual analysis of molecular dynamics,

Magnus Lundborg (KTH) revealed the new features and developments in the latest GROMACS 2024 release, and

the COLVARS development team who discussed the use of enhanced-sampling in collective variable space with the Colvars library, which is available in standard GROMACS 2024 releases.

In addition, at the time of writing, it is planned that on the 28th of May, Adam Hospital from BioExcel will speak about “Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows”.