Peach: a simple Perl-based system for distributed computation and its application to cryo-EM data processing.

A simple distributed processing system named "Peach" was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific electron cryomicroscopy applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.

[1]  David P. Anderson,et al.  SETI@home: an experiment in public-resource computing , 2002, CACM.

[2]  M van Heel,et al.  A new generation of the IMAGIC image processing system. , 1996, Journal of structural biology.

[3]  Friedrich Förster,et al.  Computational exploration of structural information from cryo-electron tomograms. , 2004, Current opinion in structural biology.

[4]  R. Huber,et al.  Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. , 1995, Science.

[5]  S. Subramaniam,et al.  Three-dimensional electron microscopy at molecular resolution. , 2004, Annual review of biophysics and biomolecular structure.

[6]  R. Glaeser Review: electron crystallography: present excitement, a nod to the past, anticipating the future. , 1999, Journal of structural biology.

[7]  M. Heel,et al.  Single-particle electron cryo-microscopy: towards atomic resolution , 2000, Quarterly Reviews of Biophysics.

[8]  J. M. Cowley,et al.  The scattering of electrons by atoms and crystals. I. A new theoretical approach , 1957 .

[9]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[10]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[11]  Inmaculada García,et al.  High-performance electron tomography of complex biological specimens. , 2002, Journal of structural biology.

[12]  T. Earnest,et al.  From words to literature in structural proteomics , 2003, Nature.

[13]  Heymann Jb,et al.  Bsoft: Image and Molecular Processing in Electron Microscopy , 2001 .

[14]  E. Orlova,et al.  Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs. , 2004, Current opinion in structural biology.

[15]  J. Frank Single-particle imaging of macromolecules by cryo-electron microscopy. , 2002, Annual review of biophysics and biomolecular structure.

[16]  James Pulokas,et al.  Automated three-dimensional reconstruction of keyhole limpet hemocyanin type 1. , 2003, Journal of structural biology.

[17]  Walz,et al.  Electron Crystallography of Two-Dimensional Crystals of Membrane Proteins. , 1998, Journal of structural biology.