GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design.

We assess costs and efficiency of state-of-the-art high-performance cloud computing and compare the results to traditional on-premises compute clusters. Our use case is atomistic simulations carried out with the GROMACS molecular dynamics (MD) toolkit with a particular focus on alchemical protein-ligand binding free energy calculations. We set up a compute cluster in the Amazon Web Services (AWS) cloud that incorporates various different instances with Intel, AMD, and ARM CPUs, some with GPU acceleration.

EAGER: efficient ancient genome reconstruction.

Background: The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.

Results: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples.