Workshop: GROMACS in Riga

Benson Muite, University of Tartu

GROMACS is a free and open source parallel molecular dynamics software. It is used by a wide variety of people, particularly for biomolecular and chemistry simulations. It is one of the most efficient open source molecular dynamics packages with a strong community influenced development model and a wide userbase. Continue reading “Workshop: GROMACS in Riga”

Containers for bioinformatics: a hands-on workshop

Brian Skjerven and Marco De La Pierre, Pawsey Supercomputing Centre

In the past year, staff at the Pawsey supercomputing centre in Perth, Australia, have been investigating the deployment of containers on HPC resources to address several major issues researchers face when migrating workflows to HPC: complex software stacks and dependencies, cross-platform portability, reproducibility of results, and difficulties in collaboration. A solution has been devised, which involves a combination of Docker and Shifter container engines, where the former allows building as well as deployment on cloud systems, and the latter deployment on HPC clusters. Continue reading “Containers for bioinformatics: a hands-on workshop”