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<p>Thank you, Steve, for this detailed calculations that give an
upper bound of what is needed. As part of some European project,
we are designing and implementing a data management policy in
which the data acquired by the microscope is immediately copied to
some temporary storage server. This is in part motivated by the
need to make public data that has been funded by public money. At
this point it is given a unique identifier that is used along the
process to track the acquisition. This copy of raw data can be
accompanied by derived data (aligned micrographs, CTFs,
coordinates, image processing workflow, ...), which is not that
large compared to the size of the raw data. After a period of
time, typically 3 years, we could check whether this data has
resulted in a deposited EMDB entry. In this case, the data is
automatically moved from the temporary repository to EMPIAR. If it
has not resulted in a successful structure, then the user is
contacted and, upon approval, the data can be deleted. This
strategy limits the storage needs at EMPIAR, the storage needs of
the temporary repository (limited to 3 years), and accounts for
the fact that not all acquisition end in successful
reconstructions. The temporary repository can be local to the
institution, or more global (within the European project we are
making a pilot with EMPIAR itself).</p>
<p>Kind regards, Carlos Oscar<br>
</p>
<div class="moz-cite-prefix">El 29/08/2019 a las 15:50, Ludtke,
Steven J. escribió:<br>
</div>
<blockquote type="cite"
cite="mid:C5E2B614-04C6-409A-91E6-9C62A4599543@bcm.edu">
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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>
<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="">
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<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>
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<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);
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class="">Hi,</span><br style="caret-color: rgb(0, 0,
0); font-family: Courier; font-size: 14px;
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none; white-space: normal; word-spacing: 0px;
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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;
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none;" class="">
<blockquote type="cite" style="font-family: Courier;
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start; text-indent: 0px; text-transform: none;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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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;
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none; float: none; display: inline !important;"
class="">Takanori Nakane</span><br
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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="">
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moz-do-not-send="true">3dem@ncmir.ucsd.edu</a><<a
href="mailto:3dem@ncmir.ucsd.edu" class=""
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href="mailto:3dem@ncmir.ucsd.edu" class=""
moz-do-not-send="true">mailto:3dem@ncmir.ucsd.edu</a>><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">3dem@ncmir.ucsd.edu</a>
<a class="moz-txt-link-freetext" href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a>
</pre>
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<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano e-mail: <a class="moz-txt-link-abbreviated" href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>
Biocomputing unit <a class="moz-txt-link-freetext" href="http://i2pc.es/coss">http://i2pc.es/coss</a>
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510
28049 MADRID (SPAIN) Fax: 34-91-585 4506
------------------------------------------------------------------------
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