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<p>Dear all ,</p>
<p><span id="p286"><span id="293">Thank you</span> very much for
all your <span id="343-344">responses</span> and your <span
id="345-346">interest</span>.</span><span id="p287"> I <span
id="295">now</span> <span id="296">have</span> a <span
id="294">good</span> idea about how to <span id="361-362">do
it</span>.</span><span id="p288"> In my <span id="347-348">case</span>
I was <span id="363-364">referring</span> to the <span
id="297">whole</span> files <span id="365-366">associated</span>
to the <span id="349-350">project</span> at the first <span
id="351-352">time</span>, but it looks to <span
id="298-367-368">be</span> a valuable option to <span
id="299-369-370">make</span> an additional backup on <span
id="290" class="s-rg">EMPIAR</span> to.</span><span
id="p289"><span id="353-354">Thanks</span> also for the <span
id="355-356">informations</span> on <span id="357-358">TIFF
compression</span>, unfortunately some of the data sets <span
id="371-372">were</span> <span id="291">gain</span>
corrected during the <span id="359-360">acquisition</span>.</span><span
id="p2"></span></p>
<p>Best,</p>
<p>Julien<br>
</p>
<p>for the raw data: It was suggested to depose it on EMPIAR (to
make an aditionnal bakup and to make it available for the
communauty) the raw movies should be prefered to the
preprocessed data in order to allow else to reprocess it.</p>
<p>Regarding to the Relion projects it was suggested by most of
you to save it directly on an external hard drive and to store
it locally.In order to save some space , to remove useless jobs,
clean trash, to clean all none necessary iterations by using
"gentle clean all jobs" for relion projects and the to compress
it in tar.gz archive.</p>
<p>Regarding to compression formats it have been mentioned that
computing ressources necessary as well as compretion efficacy
are important. Benchmarking them on a small batch of data look
the best way to choose for me.</p>
<p>Thank you all For your interest.</p>
<p>Best,</p>
<p>Julien<br>
</p>
<div class="moz-cite-prefix">Le 29/08/2019 à 15:50, Ludtke, Steven
J. a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:C5E2B614-04C6-409A-91E6-9C62A4599543@bcm.edu">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class="">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div class="">
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<div dir="auto" style="color: rgb(0, 0, 0);
letter-spacing: normal; text-align: start;
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normal; word-spacing: 0px;
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after-white-space;" class="">
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<div style="color: rgb(0, 0, 0);
font-variant-caps: normal; letter-spacing:
normal; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width:
0px;"> <font class="" face="Courier"><span
style="font-size: 14px;" class="">--------------------------------------------------------------------------------------<br
class="">
Steven Ludtke, Ph.D. <<a
href="mailto:sludtke@bcm.edu" class=""
moz-do-not-send="true">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=""
moz-do-not-send="true">www.bcm.edu/biochem</a>)<br
class="">
Academic Director, CryoEM Core
(<a
href="http://cryoem.bcm.edu" class=""
moz-do-not-send="true">cryoem.bcm.edu</a>)<br
class="">
Co-Director CIBR Center
(<a
href="http://www.bcm.edu/research/cibr"
class="" moz-do-not-send="true">www.bcm.edu/research/cibr</a>)<br
class="">
<br class="">
</span></font><br class="">
</div>
</div>
</div>
</div>
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Aug 29, 2019, at 8:27 AM, Takanori
Nakane <<a
href="mailto:tnakane@mrc-lmb.cam.ac.uk" class=""
moz-do-not-send="true">tnakane@mrc-lmb.cam.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<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="">
<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=""> 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="">
<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=""> 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=""
moz-do-not-send="true">sludtke@bcm.edu</a><<a
href="mailto:sludtke@bcm.edu" class=""
moz-do-not-send="true">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=""
moz-do-not-send="true">www.bcm.edu/biochem</a><<a
href="http://www.bcm.edu/biochem" class=""
moz-do-not-send="true">http://www.bcm.edu/biochem</a>>)<br
class="">
Academic Director, CryoEM Core<br class="">
(<a href="http://cryoem.bcm.edu/" class=""
moz-do-not-send="true">cryoem.bcm.edu</a><<a
href="http://cryoem.bcm.edu/" class=""
moz-do-not-send="true">http://cryoem.bcm.edu</a>>)<br
class="">
Co-Director CIBR Center<br class="">
(<a href="http://www.bcm.edu/research/cibr"
class="" moz-do-not-send="true">www.bcm.edu/research/cibr</a><<a
href="http://www.bcm.edu/research/cibr" class=""
moz-do-not-send="true">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="" moz-do-not-send="true">tnakane@mrc-lmb.cam.ac.uk</a><<a
href="mailto:tnakane@mrc-lmb.cam.ac.uk" class=""
moz-do-not-send="true">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=""
moz-do-not-send="true">sludtke@bcm.edu</a><<a
href="mailto:sludtke@bcm.edu" class=""
moz-do-not-send="true">mailto:sludtke@bcm.edu</a>><<a
href="mailto:sludtke@bcm.edu" class=""
moz-do-not-send="true">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=""
moz-do-not-send="true">www.bcm.edu/biochem</a><<a
href="http://www.bcm.edu/biochem" class=""
moz-do-not-send="true">http://www.bcm.edu/biochem</a>><<a
href="http://www.bcm.edu/biochem" class=""
moz-do-not-send="true">http://www.bcm.edu/biochem</a>>)<br
class="">
Academic Director, CryoEM Core<br class="">
(<a href="http://cryoem.bcm.edu/" class=""
moz-do-not-send="true">cryoem.bcm.edu</a><<a
href="http://cryoem.bcm.edu/" class=""
moz-do-not-send="true">http://cryoem.bcm.edu/</a>><<a
href="http://cryoem.bcm.edu<http://cryoem.bcm.edu/>" class=""
moz-do-not-send="true">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="" moz-do-not-send="true">www.bcm.edu/research/cibr</a><<a
href="http://www.bcm.edu/research/cibr" class=""
moz-do-not-send="true">http://www.bcm.edu/research/cibr</a>><<a
href="http://www.bcm.edu/research/cibr" class=""
moz-do-not-send="true">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="" moz-do-not-send="true">julien.bous@etu.umontpellier.fr</a><<a
href="mailto:julien.bous@etu.umontpellier.fr"
class="" moz-do-not-send="true">mailto:julien.bous@etu.umontpellier.fr</a>><<a
href="mailto:julien.bous@etu.umontpellier.fr"
class="" moz-do-not-send="true">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="">
3dem mailing list<br class="">
<a href="mailto:3dem@ncmir.ucsd.edu" class=""
moz-do-not-send="true">3dem@ncmir.ucsd.edu</a><<a
href="mailto:3dem@ncmir.ucsd.edu" class=""
moz-do-not-send="true">mailto:3dem@ncmir.ucsd.edu</a>><<a
href="mailto:3dem@ncmir.ucsd.edu" class=""
moz-do-not-send="true">mailto:3dem@ncmir.ucsd.edu</a>><br
class="">
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href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=-Yu84q3MdcWvESYXpaK7NQdEWch6tE1eG9IVNTjLay4&s=NSrJg_YgFffwLELO1auXSC6yYLEsGHVoNV5TI_1eBqM&e="
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class="">
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moz-do-not-send="true">3dem@ncmir.ucsd.edu</a><<a
href="mailto:3dem@ncmir.ucsd.edu" class=""
moz-do-not-send="true">mailto:3dem@ncmir.ucsd.edu</a>><br
class="">
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href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwIDJg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=NIpw6RIeeyKxoYDz2eZPHOcIZvNm9VytdzBFUEtQ-10&s=UG1BMTIotgpZVcqSlW0cd0tfnpxgEo9l3RLHUfU2ODc&e="
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class="">3dem mailing list</span><br
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</blockquote>
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<br class="">
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<pre class="moz-quote-pre" wrap="">_______________________________________________
3dem mailing list
<a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu" moz-do-not-send="true">3dem@ncmir.ucsd.edu</a>
<a class="moz-txt-link-freetext" href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem" moz-do-not-send="true">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a>
</pre>
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