Publications

Below is a list of related publications by the partners of the BioExcel consortium. We strive to publish as Open Access, or to provide green open access preprints where gold open access is not possible. Please let us know if you are unable to access any of our publications.


Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis

This paper is published in Data Science and Engineering, to appear in special issue “HPC-enabled Modelling for Big Data Problems in Life, Socio-Economical and Physical Sciences“. The Common Workflow Language is a core part of the Workflows component of BioExcel. Abstract Information integration and workflow technologies for data analysis have […]


Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

The paper Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data was published in PLoS Biology in June 2017. The authors, which includes experts from well-recognized data providers like Uniprot and EMBL-EBI, describe the lessons learnt when […]


Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 1

The paper Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 was published in the journal eLife in November 2016. Abstract By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which […]


The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes

This paper was published in the¬†Journal of Molecular Biology in February 2017. Both DISVIS and POWERFIT are key parts of the BioExcel community of services. Highlights of this paper include: Core-weighted local cross-correlation and edge-enhancing Laplace filter in PowerFit New occupancy analysis and statistics for interacting residues in DisVis Grid-based, […]


Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient largescale ensemble sampling

We are pleased to announce the publication of the paper Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient largescale ensemble sampling in the journal Future Generation Computer System. Highlights of this paper include: Hybrid dataflow and peer-to-peer computing to fully automated ensemble sampling. The platform automatically distributes […]