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BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

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Cossio,  Pilar       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Baruffa,  Fabio
Max Planck Computing and Data Facility, Max Planck Society;
Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities, Boltzmann Str. 1, 85748 Garching, Germany;

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Rampp,  Markus
Max Planck Computing and Data Facility, Max Planck Society;

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Hummer,  Gerhard       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Cossio, P., Rohr, D., Baruffa, F., Rampp, M., Lindenstruth, V., & Hummer, G. (2017). BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Computer Physics Communications, 210(01), 163-171. doi:10.1016/j.cpc.2016.09.014.


Cite as: https://hdl.handle.net/21.11116/0000-0001-279B-5
Abstract
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM (BioEM) formalism. By ranking structural models using posterior probabilities calculated for individual images, BioEM in principle addresses the challenge of working with highly dynamic or heterogeneous systems not easily handled in traditional EM reconstruction. However, the calculation of these posteriors for large numbers of particles and models is computationally demanding. Here we present highly parallelized, GPU-accelerated computer software that performs this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI parallelization combined with both CPU and GPU computing. The resulting BioEM software scales nearly ideally both on pure CPU and on CPU+GPU architectures, thus enabling Bayesian analysis of tens of thousands of images in a reasonable time. The general mathematical framework and robust algorithms are not limited to cryo-electron microscopy but can be generalized for electron tomography and other imaging experiments.