[3dem] CryoSPARC v3 and cryoSPARC Live Announcement
Ali Punjani
alipunjani at cs.toronto.edu
Thu Mar 4 11:53:18 PST 2021
Dear 3DEM / CCPEM,
We are happy to announce the general availability of cryoSPARC v3 and cryoSPARC
Live! Click here to download and install.
<https://urldefense.com/v3/__https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q6WDfXBiQ$ >
CryoSPARC <https://urldefense.com/v3/__https://cryosparc.com/__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q5oEDYvZA$ > is used today by scientists at hundreds
of academic institutions and many industry labs to power and accelerate
single-particle cryo-EM workflows. Thanks to tremendous support and
feedback from cryo-EM scientists, our growing team
<https://urldefense.com/v3/__https://structura.bio/*team__;Iw!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q6pwlzklA$ > has been working to rapidly develop cryoSPARC
and we have an ambitious roadmap ahead. Our overall aim is to help expand
the frontiers of SPA and realize a vision of cryo-EM as a robust,
high-throughput, scalable tool that is central to enabling new science and
biological advances across basic research and drug discovery.
To that end, we are very proud to announce that cryoSPARC Live
<https://urldefense.com/v3/__https://cryosparc.com/live__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q42sYrd2g$ > is available for all - and is free of charge
for non-profit academic research <https://urldefense.com/v3/__https://guide.cryosparc.com/licensing__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q53Nn6DpQ$ >.
[image: cryoSPARC-Live-only-550.gif] <https://urldefense.com/v3/__https://cryosparc.com/live__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q42sYrd2g$ >
Many cryo-EM scientists have imagined a future where 3D structures can be
solved right at the microscope and where processing results can provide
real-time feedback into data collection. CryoSPARC Live enables that future
today - and has been in production use at dozens of major cryo-EM
facilities and industry labs since its initial private release in May
2019. Read
what users have to say. <https://urldefense.com/v3/__https://cryosparc.com/live*testimonials__;Iw!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q6dqtZvbg$ >
-
Live performs real-time preprocessing, particle picking, streaming 2D
classification and 3D refinement faster than data collection
<https://urldefense.com/v3/__https://guide.cryosparc.com/live/about-cryosparc-live__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q77HXflAw$ >. This means 2D
classes and 3D refined structures update every few minutes as new particle
images are collected.
-
It is the fastest <https://urldefense.com/v3/__https://guide.cryosparc.com/live/performance-metrics__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q6YEH1xmg$ >,
simplest way for all users to process new cryo-EM data, real-time or not.
Outputs can be used directly in cryoSPARC or other tools for advanced
processing.
-
On our development roadmap, Live is the platform that will enable full
processing automation and data-driven decision making during collection.
-
In cryoSPARC v3, Live has been redesigned, fine-tuned and optimized
based on extensive feedback. Our team is very happy to contribute a mature,
engineered, commercial product to the community to help accelerate cryo-EM
science.
-
Stay tuned for an upcoming webinar in April!
In addition to building Live, we are continuously improving cryoSPARC
algorithms, features, workflow and performance.
CryoSPARC v3 <https://urldefense.com/v3/__https://cryosparc.com/updates__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q5IcUiNFA$ > is faster than ever. On our test
workstation
<https://urldefense.com/v3/__https://guide.cryosparc.com/setup-configuration-and-management/hardware-and-system-requirements*example-hardware-systems__;Iw!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q7GY2kmKA$ >
:
-
4.5 minutes for 2D classification of 250K particles into 50 classes
on a single
GPU (box size 256; EMPIAR-10288)
-
8.2 minutes for 2D classification of 250K particles into 100 classes on
a single GPU (box size 256; EMPIAR-10288)
-
7.5 minutes for 3D refinement of 105K particles to 3.0Å resolution
on a single
GPU (box size 360; EMPIAR-10028)
-
650 movies per hour per GPU Live processing (K2-counting, TIFF, 40
frames)
-
420 movies per hour per GPU Live processing (K3-counting, TIFF, 40
frames)
-
303 movies per hour per GPU Live processing (Falcon 4, EER 2x usampled,
40 frames)
And includes new methods advances:
-
Non-uniform Refinement (Nature Methods 2020)
<https://urldefense.com/v3/__https://www.nature.com/articles/s41592-020-00990-8__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q43tgAYpA$ >, used widely to
improve map quality for membrane proteins. Updated and improved in v3, and
used extensively for SARS-CoV-2 spike protein structures
-
3D Variability Analysis (JSB 2021)
<https://urldefense.com/v3/__https://doi.org/10.1016/j.jsb.2021.107702__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q4A_nfgnA$ >, enables high-resolution
continuous conformational changes to be resolved even in small proteins,
used notably for several recent studies of GPCR conformational landscapes
-
Helical refinement tools (new in v3)
<https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q79_OiyDQ$ >
including filament picking and symmetry search methods
As part of the v3 launch, we have created a new cryoSPARC Guide
<https://urldefense.com/v3/__https://guide.cryosparc.com/__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q4U9EwGyQ$ >. It is perfect for beginners as well as
experts, with extensive videos, tutorials, case studies, and fully
searchable details about each job type.
The cryoSPARC Discussion Forum <https://urldefense.com/v3/__https://discuss.cryosparc.com/__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q6E6u8hNw$ > has grown
to be a vibrant, helpful and friendly community with 1000+ active users and
100+ new topics per month. All questions are welcome and fruitful
discussions with community members and our team are common.
Lastly, our team is hiring! Join our mission-driven, fast-moving
organization and help us develop new methods and tools that can power both
fundamental academic life science research and ambitious drug discovery
projects searching for life-changing medicines. We are looking for methods
developers, software engineers, cryo-EM scientists with expertise in
computational tools, and high-performance computing experts. Work at the
frontier of structural biology and see your work used by thousands of
scientists daily. Please reach out to careers at structura.bio.
Thank you!
The cryoSPARC Team <https://urldefense.com/v3/__https://structura.bio/*team__;Iw!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q6pwlzklA$ >
Structura Biotechnology Inc.
Note: CryoSPARC v3.0 was made available in December 2020, and as of this
announcement, v3.1.0 is available with several stability and performance
enhancements. For more information, please see:
https://urldefense.com/v3/__https://cryosparc.com/updates__;!!Mih3wA!VCoTVOe3ZOofudB5dMFErJpMSJFXAslt1l_liwDqFJtnrAnJjd8UA-W80q5IcUiNFA$
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