[3dem] RELEASE NOTE SIMPLE2.1

[Dominika Elmlund]

Hi,
YES, we tested on most systems including Fedora. If you have the right
compilers it's going to work.
Cheers,
Dominika

On Thursday, May 26, 2016, Sergey Ryazantsev <sryazant at ucla.edu> wrote:

> Hans, hello
> Is it possible to run your software under RedHat flavor Linux?
> Sergey
>
> On 5/25/2016 9:50 PM, Hans Elmlund wrote:
>
> 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
> <javascript:_e(%7B%7D,'cvml','hans.elmlund at monash.edu');>
> simplecryoem.com
>
>
> _______________________________________________
> 3dem mailing list3dem at ncmir.ucsd.edu <javascript:_e(%7B%7D,'cvml','3dem at ncmir.ucsd.edu');>https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
> --
>
> --------------------------------------------
> Sergey Ryazantsev Ph.D.
> Phone: 310-453-0748
> E-mail: sryazant at ucla.edu <javascript:_e(%7B%7D,'cvml','sryazant at ucla.edu');>
>
>

-- 

-- 
*DOMINIKA ELMLUND PhD *
Associate Professor

*ARC Centre of Excellence for Advanced Molecular Imaging*
*Dept. of Biochemistry and Molecular Biology*
Monash University
Room 223, Level 2, Building 77, Clayton Campus
23 Innovation Walk
Clayton VIC 3800
Australia

T: +61 399050002
M: +61 (0)450899171
E: dominika.elmlund at monash.edu
simplecryoem.com
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