<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Somehow, just buying the $40K storage doesn’t cut it. And who decides on what gets saved? I’d rather discuss who decides what actually gets collected.</div><div dir="ltr"><br></div><div dir="ltr">1TB tier-one storage currently is €130 a year at EMBL Heidelberg considering total cost of storage, including backups (tape & tape robot etc.) and that’s underpriced considering power, IT personnel costs etc.</div><div dir="ltr">And synchrotron budgets still make EM look like the cheapest stuff around, until you want to buy another EM...</div><div dir="ltr"><br></div><div dir="ltr">Wim</div><div dir="ltr"><br>On 29. Aug 2019, at 15:50, Ludtke, Steven J. <<a href="mailto:sludtke@bcm.edu">sludtke@bcm.edu</a>> wrote:<br><br></div><blockquote type="cite"><div dir="ltr">
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I agree that my estimate was sort of a worst case scenario. However, 1 TB/structure is also not realistic, as most structures I'm aware of involve many days of Krios data collection, and are closer to 10 TB than 1 TB. If we estimate 50 projects/week, and set
a range of 1-10 TB/project, that would be
<div class="">2.5 - 25 PB of data per year. While this is feasible bandwidth-wise, it is still not a trivial amount of storage. While EMPIAR is talking about going 'peta-scale', I'm not sure they meant 25 PB/year. </div>
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<div class="">I do agree with you that making the centers responsible for long-term data archival would be quite reasonable, there are certainly still some issues. In that situation you would probably, again, be talking about archiving all of the data produced
by the center, or at least all of the "useful" data. If the center had 3 krios, and ~50 % of the data were "useful", each center would have to archive ~2 TB/day, or <1 PB/year. </div>
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<div class="">Of course, storage costs fall with time, over the long term, averaging a 2-fold cost reduction every 14 months, so while 25 PB sounds like a lot right now, in 5 years it should be extremely feasible. While data production rates also increase with
time, there are some physical limits there which we are beginning to approach. Given that 1 PB of raw RAID 6 storage only costs ~$40 k now, it seems like a $40 M center ought to be able to allocate enough budget to do this sort of archival. If you look at
the NYSBC's recent paper on JPG compression, though, it seems they are far from anxious to take on this role other than perhaps saving degraded JPG versions of the aligned averages.</div>
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<font face="Courier" class=""><span style="font-size: 14px;" class="">--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D. <<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a>> Baylor College of Medicine <br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology (<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)<br class="">
Academic Director, CryoEM Core (<a href="http://cryoem.bcm.edu" class="">cryoem.bcm.edu</a>)<br class="">
Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)<br class="">
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<div class="">On Aug 29, 2019, at 8:27 AM, Takanori Nakane <<a href="mailto:tnakane@mrc-lmb.cam.ac.uk" class="">tnakane@mrc-lmb.cam.ac.uk</a>> wrote:</div>
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<div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Hi,</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
back of the envelope:<br class="">
2000 images/day * 500 MB/compressed counting movie * 100 krios ~ 100<br class="">
TB/day<br class="">
</blockquote>
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">But
datasets that result in published maps are only a</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fraction
of what were collected. Most of the scope time</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">is
spent on sample screening and optimisation, and</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">these
preliminary datasets don't have to be made public.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">There
are 52 new maps released in EMDB this week.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Some
maps came from a single dataset by classification.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">If
1 TB per map, it is 52 TB/week, not 100 TB/day.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">By
the way, some X-ray synchrotrons and XFELs are implementing data</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">policy,
where all raw data will be stored on site and made public after</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">a
certain embargo period. It would be nice if CryoEM facilities follow</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">this
trend.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
You mean the "final" particle stack, or movies, when you say raw data ?<br class="">
The latter might be too large for EMPIAR ?<br class="">
</blockquote>
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">I
recommend raw movies, so that others can reprocess for the beginning</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">with
possibly improved strategies and programs than initially processed.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Of
course, having cleaned particle coordinates and stacks is useful,</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">because
some users are interested only in later steps of processing.</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Best
regards,</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Takanori
Nakane</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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EMPIAR is great, and while they say they will take whatever people<br class="">
provide, if all of the raw data (even if it were limited to 'good' data)<br class="">
from all of the Krios around the world were archived in EMPIAR, there<br class="">
would be massive bandwidth and storage issues. When used as it is now,<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">as</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
an archive for important reference data sets, it's great, but I'm not<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">sure</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
it's a viable strategy for archiving everything produced in the CryoEM<br class="">
community.<br class="">
back of the envelope:<br class="">
2000 images/day * 500 MB/compressed counting movie * 100 krios ~ 100<br class="">
TB/day<br class="">
even a dedicated 10 Gb network running flat out couldn't keep up.<br class="">
--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D. <<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a><<a href="mailto:sludtke@bcm.edu" class="">mailto:sludtke@bcm.edu</a>>><br class="">
Baylor College of Medicine<br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology<br class="">
(<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a><<a href="http://www.bcm.edu/biochem" class="">http://www.bcm.edu/biochem</a>>)<br class="">
Academic Director, CryoEM Core<br class="">
(<a href="http://cryoem.bcm.edu/" class="">cryoem.bcm.edu</a><<a href="http://cryoem.bcm.edu/" class="">http://cryoem.bcm.edu</a>>)<br class="">
Co-Director CIBR Center<br class="">
(<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a><<a href="http://www.bcm.edu/research/cibr" class="">http://www.bcm.edu/research/cibr</a>>)<br class="">
On Aug 29, 2019, at 7:04 AM, Takanori Nakane<br class="">
<<a href="mailto:tnakane@mrc-lmb.cam.ac.uk" class="">tnakane@mrc-lmb.cam.ac.uk</a><<a href="mailto:tnakane@mrc-lmb.cam.ac.uk" class="">mailto:tnakane@mrc-lmb.cam.ac.uk</a>>> wrote:<br class="">
Hi,<br class="">
Most people just opt for the "hard drive on a shelf" method for<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">completed</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
projects, which has advantages (cheap/simple) and disadvantages (what<br class="">
happens if the drive dies)...<br class="">
After publication of your structures, I recommend raw data to be<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">deposited</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
in EMPIAR.<br class="">
Not only is it useful for reproducibility, education and method<br class="">
development,<br class="">
it also serves as an additional layer of backup. You might drop your<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">disk,</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
water might leak from the ceiling, etc. Having backups in a physically<br class="">
distant<br class="">
place is a good practice.<br class="">
Best regards,<br class="">
Takanori Nakanori<br class="">
Julien,<br class="">
are you referring to the raw data, or are you trying to archive all of<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">the</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
files associated with a project?<br class="">
Counting-mode movies are generally stored and archived as compressed<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">tiff</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
stacks, though if they are collected on a Falcon, there are issues with<br class="">
this, as good compression is achieved only pre-normalization (or<br class="">
post-normalization if you decide you are willing to switch back to an<br class="">
integer format).<br class="">
If you want to perfectly archive everything exactly as it is<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">(losslessly),</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
some compression algorithms may do very slightly better than others, but<br class="">
pretty much any of the commonly used algorithms will do about the same.<br class="">
Usually the slower ones will do slightly better, but you have to decide<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">if</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
it's worth the CPU time the compression takes. By definition, the<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">noisier</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
the data is, the less compressible it is, unless you are willing to<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">invoke</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
"lossy" compression and throw away some of the bits of pure noise.<br class="">
Most people just opt for the "hard drive on a shelf" method for<br class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">completed</span><br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
projects, which has advantages (cheap/simple) and disadvantages (what<br class="">
happens if the drive dies)...<br class="">
--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D.<br class="">
<<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a><<a href="mailto:sludtke@bcm.edu" class="">mailto:sludtke@bcm.edu</a>><<a href="mailto:sludtke@bcm.edu" class="">mailto:sludtke@bcm.edu</a>>><br class="">
Baylor College of Medicine<br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology<br class="">
(<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a><<a href="http://www.bcm.edu/biochem" class="">http://www.bcm.edu/biochem</a>><<a href="http://www.bcm.edu/biochem" class="">http://www.bcm.edu/biochem</a>>)<br class="">
Academic Director, CryoEM Core<br class="">
(<a href="http://cryoem.bcm.edu/" class="">cryoem.bcm.edu</a><<a href="http://cryoem.bcm.edu/" class="">http://cryoem.bcm.edu/</a>><<a href="http://cryoem.bcm.edu<http://cryoem.bcm.edu/>" class="">http://cryoem.bcm.edu<http://cryoem.bcm.edu/></a>>)<br class="">
Co-Director CIBR Center<br class="">
(<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a><<a href="http://www.bcm.edu/research/cibr" class="">http://www.bcm.edu/research/cibr</a>><<a href="http://www.bcm.edu/research/cibr" class="">http://www.bcm.edu/research/cibr</a>>)<br class="">
On Aug 29, 2019, at 6:30 AM, Julien Bous<br class="">
<<a href="mailto:julien.bous@etu.umontpellier.fr" class="">julien.bous@etu.umontpellier.fr</a><<a href="mailto:julien.bous@etu.umontpellier.fr" class="">mailto:julien.bous@etu.umontpellier.fr</a>><<a href="mailto:julien.bous@etu.umontpellier.fr" class="">mailto:julien.bous@etu.umontpellier.fr</a>>><br class="">
wrote:<br class="">
Dear Community,<br class="">
I have a question about the best way to store my data once SPA projects<br class="">
are achieved. Can you advise me about which compression format is to<br class="">
prefer?<br class="">
Thank you for your interest,<br class="">
Julien<br class="">
_______________________________________________<br class="">
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</blockquote>
<br style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=N9gZrj6tzrxb1__Ie82LVKoonNvUYYAINYAiKVJq_Ak&s=ilFAU6frbYTGpAsrBgmIjwKDDWViAU0wjU8X3H_OFSE&e=" style="font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=N9gZrj6tzrxb1__Ie82LVKoonNvUYYAINYAiKVJq_Ak&s=ilFAU6frbYTGpAsrBgmIjwKDDWViAU0wjU8X3H_OFSE&e=</a><span style="caret-color: rgb(0, 0, 0); font-family: Courier; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span></div>
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</div></blockquote><blockquote type="cite"><div dir="ltr"><span>_______________________________________________</span><br><span>3dem mailing list</span><br><span><a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a></span><br><span><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a></span><br></div></blockquote></body></html>