[3dem] SPHIRE release

[Stefan Raunser]

Dear EM-community,

We are happy to bring our new software package SPHIRE to the world of cryo-EM. We announced SPHIRE (SParx for HIgh Resolution Electron Microscopy) at this year’s GRC conference in Hong Kong and, in response to the interest of the community we deliver now the early version of the package.
SPHIRE embodies a single-particle pipeline supported by ten modules of the previous SPARX system that are accessible through an easy-to-use GUI (Graphical User Interface). It is designed for easy immersion into cryo-EM with the stress on validation and reproducibility of results by using concepts of statistical resampling and provides powerful algorithms that encompass all steps of a typical cryo-EM project. Advanced users have the luxury of easy access to all process parameters through ‘advanced’ tabs and can easily customize the code, which is written in transparent Python!

THE TESTS
During the last months we worked day and night to extensively test the workflow. We used our in-house datasets and also processed a number of EMPIAR datasets (e.g. TRPV1 (ID: 10005), T20S proteasome (ID: 10025), beta-galactosidase (ID: 10061)) and are happy to report that in all cases we were able to reproduce published results.

 The SPHIRE pipeline comprises the following major steps:
- Frame movie alignment, supported by a graphical drift assessment tool.
- CTF estimation and its error assessment tool providing utilities for automated sorting out of inferior data.
- Reproducible 2-D classification.
- Validated ab initio 3-D reconstruction yielding a perfect starting point for 3-D refinement.
- Efficient 3-D structure refinement utilizing maximum likelihood methodology.
- Tools for assessing data heterogeneity, including computation of local variance, local resolution providing the necessary validation for our 3D sorting program.

THE INFO
To find out more about SPHIRE and its team please consult
http://sphire.mpg.de

The SPHIRE team is accessible almost 24/7 via mailing list. To subscribe please visit:
https://listserv.gwdg.de/mailman/listinfo/sphire

where you can also browse through the archive of already discussed subjects.
In order to facilitate smooth immersion into the SPHIRE world, we prepared an extensive step-by-step tutorial that is supported by a test dataset. Both can also be downloaded from the SPHIRE homepage.

THE RELEASE
And now the most important part, the release. We have decided to release SPHIRE as a public beta version and here is why:
Despite the substantial testing, as a developer team we are only able to test a limited number of datasets so it is reasonable to expect the unexpected. We hope for the community input that will allow us to find problems we did not anticipate and solve them quickly. This phase will be followed by a stable release of SPHIRE within the next year.

THE FUTURE
We believe that increasing the number of cryo-EM software packages will benefit our community by providing alternative solutions to challenges of cryo-EM structure determination. We sincerely hope SPHIRE will meet your expectations.  More importantly, we hope for community feedback, however enthusiastic or critical it may be, to stimulate us for the future developments to carry us into the next quarter of the century.


Your SPHIRE development team

 [cid:D58434BF-44E4-43F0-81A3-928977BCAE42 at client.mpi-dortmund.mpg.de]




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