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<p>Hi Chip,</p>
<p>my name is Laura and I work in the Centro Nacional de
Biotecnología in Madrid, where we develop the software Scipion.</p>
<p>We have explored and use cryo-EM processing in the cloud for many
years already, we have some info <a moz-do-not-send="true" href="https://urldefense.com/v3/__https://scipion-em.github.io/docs/release-3.0.0/docs/developer/scipion-on-the-cloud.html__;!!Mih3wA!ARQ_pdLIz3yHTBfQnqy6MQVRQehsrMsaQFt_7kF24VFusw0xNfbVYLgNiKMNolDIhCD39fEtAt1qiGArgIJOgrM$">here</a>
but I can tell you also what we have been doing.</p>
<p>We have some AMIs with our software in AWS but we mainly use it
for training cause it is really expensive to launch powerful
hardware types to process cryo-EM and we only do it if we dont
have our own resources. <br>
</p>
<p>What we sometimes use to process real data is the European Open
Science Cloud (EOSC) resources cause we have some agreements with
(OpenStack) sites in EU. We launch those virtual servers or
clusters using the <a moz-do-not-send="true" href="https://urldefense.com/v3/__https://www.grycap.upv.es/im/index.php__;!!Mih3wA!ARQ_pdLIz3yHTBfQnqy6MQVRQehsrMsaQFt_7kF24VFusw0xNfbVYLgNiKMNolDIhCD39fEtAt1qiGArB4r-v5M$">Infrastructure
Manager</a> that uses ansible/docker recipes/images to set them
up.</p>
<p>If you are interested we can discuss it or I can try to answer
more specific questions related to instances, transfers and so on.</p>
<p>best regards</p>
<p>Laura<br>
</p>
<blockquote type="cite"
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<div dir="ltr" class="gmail_attr">---------- Forwarded message
---------<br>
From: <strong class="gmail_sendername" dir="auto">Chip
Lesburg</strong> <span dir="auto"><<a
href="mailto:chip@odysseytx.com" moz-do-not-send="true">chip@odysseytx.com</a>></span><br>
Date: Tue, Aug 30, 2022 at 5:54 PM<br>
Subject: [3dem] cryo-EM data processing in the cloud/AWS<br>
To: <a href="mailto:3dem@ncmir.ucsd.edu"
moz-do-not-send="true">3dem@ncmir.ucsd.edu</a> <<a
href="mailto:3dem@ncmir.ucsd.edu" moz-do-not-send="true">3dem@ncmir.ucsd.edu</a>><br>
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<br>
<br>
<div class="msg-2931539232983831695">
<div link="#0563C1" vlink="#954F72"
style="word-wrap:break-word" lang="EN-US">
<div class="m_-2931539232983831695WordSection1">
<p class="MsoNormal">Hi 3DEM-ers,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I wonder if anyone has experience
processing cryo-EM data in the cloud, specifically
using AWS infrastructure? There are a few online
resources describing this, listed below. I am hoping
to learn from others’ experiences, including
considerations and unexpected pitfalls.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">How does your choice of cloud
CPU/GPU instance compare with on-premises computer
hardware you may have access to? How do you transfer
raw movies from the microscope facility to your own
storage area in the cloud (direct network transfer,
first transfer to a disk array, etc.)?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><a
href="https://urldefense.com/v3/__https://aws.amazon.com/blogs/hpc/tag/cryo-em/__;!!Mih3wA!CMWEZwXyRqadyg_1XwJ40k5jk4WfLCJUR4bXgU5Fpic1vMN-Qyx2b--g4gT-aRJs-vb4U6_V7xmYwN6qAA$"
target="_blank" moz-do-not-send="true">https://aws.amazon.com/blogs/hpc/tag/cryo-em/</a></p>
<p class="MsoNormal"><a
href="https://urldefense.com/v3/__http://cryoem-tools.cloud/__;!!Mih3wA!CMWEZwXyRqadyg_1XwJ40k5jk4WfLCJUR4bXgU5Fpic1vMN-Qyx2b--g4gT-aRJs-vb4U6_V7xkYBBJREQ$"
target="_blank" moz-do-not-send="true">http://cryoem-tools.cloud/</a></p>
<p class="MsoNormal"><a
href="https://urldefense.com/v3/__https://sites.google.com/site/emcloudprocessing/__;!!Mih3wA!CMWEZwXyRqadyg_1XwJ40k5jk4WfLCJUR4bXgU5Fpic1vMN-Qyx2b--g4gT-aRJs-vb4U6_V7xl13NL_gg$"
target="_blank" moz-do-not-send="true">https://sites.google.com/site/emcloudprocessing/</a></p>
<p class="MsoNormal"><a
href="https://urldefense.com/v3/__https://guide.cryosparc.com/deploy/cryosparc-on-aws__;!!Mih3wA!CMWEZwXyRqadyg_1XwJ40k5jk4WfLCJUR4bXgU5Fpic1vMN-Qyx2b--g4gT-aRJs-vb4U6_V7xmRZbOEcg$"
target="_blank" moz-do-not-send="true">https://guide.cryosparc.com/deploy/cryosparc-on-aws</a></p>
<p class="MsoNormal"><a
href="https://urldefense.com/v3/__https://nramm.nysbc.org/wp-content/seminars/2017/slides/nramm_workshop_2017_cianfrocco.pdf__;!!Mih3wA!CMWEZwXyRqadyg_1XwJ40k5jk4WfLCJUR4bXgU5Fpic1vMN-Qyx2b--g4gT-aRJs-vb4U6_V7xnqEA2JNg$"
target="_blank" moz-do-not-send="true">https://nramm.nysbc.org/wp-content/seminars/2017/slides/nramm_workshop_2017_cianfrocco.pdf</a></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Chip</p>
<p class="MsoNormal"><b> </b></p>
<p class="MsoNormal">P.S. cross-posted to the CCP-EM
mailing list</p>
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<div>Prof. Jose-Maria Carazo<br>
Biocomputing Unit, Head,</div>
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<div>Spanish National Center for Biotechnology, CNB-CSIC</div>
<div>Darwin 3, Universidad Autonoma de Madrid</div>
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