[3DEM] Announcing SPARX v0.3

[Pawel Penczek]

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We are pleased to announce a release of a new single particle package 
SPARX with EMAN2 as its essential dependency.  Both components together 
with all other necessary dependencies are available through a single 
installation step:

http://macro-em.org/sparxwiki/HowToInstall

The software is introduced in:

SPARX, a new environment for Cryo-EM image processing.  Hohn, M., Tang, 
G., Goodyear, G., Baldwin, P. R., Huang, Z., Penczek, P. A., Yang, C., 
Glaeser, R. M., Adams, P. D., Ludtke, S. J., 2007.  J. Struct. Biol. 
157, 47-55.

EMAN2: An extensible image processing suite for electron microscopy. 
Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., 
Ludtke, S. J., 2007.  J. Struct. Biol. 157, 38-46.

The Transform Class in SPARX and EMAN2.  Baldwin, P. R., Penczek, P. A., 
2007.  J. Struct. Biol. 157, 250-261.

Main futures include:

•	New generation of 2D and 3D alignment protocols.

•	Ab initio structure determination programs.

•	Resampling methods for investigation of structural heterogeneity (3D 
variance).

•	Advanced code for multivariate statistical analysis (PCA, Varimax),

•	New generation of interpolation methods relaxing the need for 
oversampling the data.

•	Wiki-based interactive documentation http://macro-em.org/sparxwiki/

•	Extensive C++ library of general and EM-specific image operations with 
Python bindings, thus accessible to Python programmer.

•	All structure determination applications written as user transparent 
Python scripts http://macro-em.org/sparxwiki/HowToUseSparx

•	All major scripts parallelized for clusters of workstations using MPI.

•	The Transform Class supports all Eulerian angles conventions commonly 
used in EM, generates point-group symmetries, and provides definitions 
of asymmetric units.

•	Package reads/writes all commonly used file formats (SPIDER, Imagic, 
MRC,…)

•	New HDF5 data format.  In addition to storing image data, the file 
headers store data processing information (orientation parameters) and 
can also store any other information provided by the user.

•	Run-through example of a structure determination project.

Pawel A. Penczek, UTH
Steven Ludtke, Baylor College
Chao Yang, LBL
Paul Adams, LBL
Robert M. Glaeser, LBL
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