[3dem] RELEASE NOTE SIMPLE2.1

Hans Elmlund hans.elmlund at monash.edu
Wed May 25 21:50:17 PDT 2016


Dear Structural Biologists:

We announce the release of a new version of our program package *SIMPLE
(v2.1)* for single-particle cryo-EM *ab initio* 3D reconstruction.

Please note that the webpage has moved to www.simplecryoem.com.

*New features include:*

** PRIME2D:* A Stochastic Hill Climbing Approach for Simultaneous 2D
Alignment and Clustering of cryo-EM images (DOI:
http://dx.doi.org/10.1016/j.str.2016.04.006) which
  (1) generates improved 2D class averages from large single-particle
cryo-EM datasets
  (2) can be used in conjunction with PRIME3D to obtain a reliable 3D
starting model in a rapid and unbiased fashion
  (3) overcomes inherent limitations in widely used clustering approaches
  (4) is many times faster than other widely used approaches

** PRIME3D:* ~150-fold speedup as compared to the previously released
version. This was accomplished using new theory for fast rotational
matching of polar Fourier transforms based on Hadamard products calculated
using a re-organised and highly parallelizable data structure. The paper is
not yet published, but we decided to nevertheless release the code since we
anticipate that the massive speedup of PRIME3D will have major impacts for
our users. For example, less than 10,0000 particles downscaled to around
100x100 pixels can feasibly be processed on a modern laptop equipped with
an Intel i5 or i7 processor. We executed an *ab initio* 3D reconstruction
run using PRIME3D on half a million images downscaled to 64x64 pixels in
less than 5 hours on a cluster with 224 CPU cores (Intel(R) Xeon(R) CPU
E5-2670 0 @ 2.60GHz).

** MRC file format support.* The file handling classes are shared with the
Frealix program for helical reconstruction.

** Improved manuals* and easier to use command line-based front-end.

** Extended automatic unit test suite *(executed via the optional "make
check").

*Our next release (SIMPLE 3.0) is planned for January 2017 and will
include:*

* GPU accelerated motion correction
* GPU accelerated PRIME2D/3D
* GPU accelerated multiparticle 3D reconstruction

We thank our beta testers for their constructive feedback. If you need help
installing SIMPLE, optimising its execution for your computer architecture
or experience any problems or bugs please use the contact form on the
webpage (www.simplecryoem.com) to file a help ticket. We will endeavour to
respond within two days.

Happy image processing!

*The SIMPLE team:*
Sarah N Le
Cyril F Reboul
Frederic Bonnet
Dominika & Hans Elmlund

-- 
*HANS ELMLUND PhD *
Associate Professor

*ARC Centre of Excellence for Advanced Molecular Imaging*
*Dept. of Biochemistry and Molecular Biology*
Monash University
Room 228, Level 2, Building 77, Clayton Campus
23 Innovation Walk
Clayton VIC 3800
Australia

T: +61 399029310
M: +61 (0)45271213
E: hans.elmlund at monash.edu
simplecryoem.com
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