Biocomputing Unit, Spanish National Center for Biotechnology
The cryo-electron microscopy (cryo-EM) is very quickly evolving method with growing popularity in structural biology. It allows to study specimen in its natural environment (e.g. no crystalization is needed), thus is highly relevant in many applications. The progress in electron detectors and image processing in few recent years allows cryo-EM to image specimens on nearly atomic resolution. However, the post-processing of images gathered from electron microscopes is highly computationally demanding, as the noise-to-signal ratio is very poor, the 3D specimen needs to be reconstructed from 2D images of unknown orientations and there may be several conformations of specimen observed.
A widely used tool for processing cryo-EM data is Xmipp, developed by Biocomputing Unit, Spanish National Center for Biotechnology. As the image reconstruction is highly computationally demanding, we speed-up the software to use computing facility more efficiently (activity under project World-wide E-infrastructure for structural biology - West-Life). Image reconstruction in Xmipp uses image fitting, which is basically embarrassingly parallel. Thus, main opportunity of further speedup of Xmipp is leveraging SIMD computations. Currently, we have implemented vectorized version of performance critical parts of Xmipp, improving their speed more than 2x on classic CPUs. In the future, we plan to optimize it for accelerators, namely Xeon Phi and GPGPUs.
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