CryoEM: From Biomedical impact to Cloud deployment Laura del Cao - - PowerPoint PPT Presentation

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Dec 03, 2022 309 likes •673 views

CryoEM: From Biomedical impact to Cloud deployment Laura del Cao Jess Cuenca CNB CSIC, Madrid How can one see a virus ? 250 nm Confocal optical microscope 0.1 nm (1 ) X-ray crystallography From small amounts 0.5 nm of

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CryoEM:

From Biomedical impact to Cloud deployment

Laura del Caño Jesús Cuenca CNB – CSIC, Madrid

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How can one “see” a virus?

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Confocal

ptical

microscope

250 nm

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0.1 nm (1 Å)

X-ray crystallography

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From small amounts

f diluted samples,

it is possible to solve... … without 3D crystals. ...the structure

f large and flexible

macromolecular complexes...

0.5 nm (5 Å)

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“Structural and molecular basis for Ebola virus neutralization by protective human antibodies” Misasi et al. Science 351(6279), 1343-1346. (2016)

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BIM correction CTF estimation Particle Picking 2D Classification 3D classification 3D Refinement Estimate resolution Initial Model

Preprocessing Postprocessing

Validation

MOVIES MICROGRAPHS CTF COORDINATES 2D CLASSES VOLUME 3D CLASSES REFINED VOLUME

Single Particle Analysis (SPA)

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Cluster Edition Cloud Edition Desktop Edition Web Tools

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Desktop Edition

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Web Tools

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box

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Scipion cluster edition

Cluster Edition Universität Basel (Switzerland) EPFL (Switzerland) IMM (France) Politecnico de Torino (Italy) CIC-Biogune (Spain) NCPS (Shanghai) Utah University (USA) Columbia University (USA)

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Towards Scipion

n the

Cloud

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SAN

Real servers farm

Virtualization layer

VM VM VM VM VM Virtual servers farm

IaaS (Infrastructure) Distributed resources: lots of servers and storage across datacenters (across the world) Elastic computing: dynamic scaling to handle peaks Resource pooling: real infrastructure is share by all the IaaS users Billing: variable cost (as function of resource use)

Brick Brick Libraries Low-level middleware Operating system

PaaS (Platform) Standard software framework Built-in scalability and failover Predefined deployment cycle Billing SaaS (Software) Central installation Web access: easy & on demand Billing

User data Application

CLOUD SCENARIOS

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“Lower barriers for scientists to access modern e-Science solutions from micro to macro scales”. Grid & cloud based infrastructures. Cryo-EM in the cloud: bringing clouds to the data.

A Competence Center to Serve Translational Research from Molecule to Brain.

Objective Task 2

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ENMR.eu VO

Deployment for CryoEM processing

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Sara HPC Cloud

Deployment for CryoEM processing

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Deployment for Instruct training

Sara HPC Cloud

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“Bring the world of complex data analysis in Structural Biology to a simple Web browser-based Virtual Research Environment.” Integration of existing Cryo-EM web services, Scipion Web Tools, on the VRE. World-wide E-infrastructure for structural biology

Objective Task 2

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ENMR.eu VO

Scipion Web Tools Deployment

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Install and test Scipion on AWS EC2 platform. Create Scipion AMI (not public yet). Test StarCluster (Elastic Cloud images)

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Our experience

The cloud paradigm is quite different from legacy HPC, but we were able to deploy successfully

Remote visualization Cloud architecture for legacy HPC (1.0) Images for cloud (beta)

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Challenges

Elastic cloud Image publishing to independent repositories Image contextualization Big data transfers Fault-Tolerant High Performance filesystems Security

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Our vision: Scipion Ubiquity

“1-click instances” in research and commercial clouds: simple provisioning for Scipion showcase & training SaaS: Scipion Web Tools Ready for every client profile / infrastructure: traditional HPC facilities (“owners”) research clouds (paper per use) commercial clouds (pay per use)

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Further info

“Structural and molecular basis for Ebola virus neutralization by protective human antibodies” Misasi et al. Science 351(6279), 1343-1346. (2016) “Structures of protective antibodies reveal sites of vulnerability on Ebola virus”. Murin et al. PNAS 111(48), 17182–17187. (2014) “Camouflage and Misdirection: The Full-On Assault of Ebola Virus Disease”. Misasi et al. Cell 159(3), 477-486. (2014) “Electron counting and beam-induced motion correction enable near-atomic- resolution single-particle cryo-EM”. Li et al. Nature Methods 10, 584-590. (2013)

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Further info

Scipion - http://scipion.cnb.csic.es/ INSTRUCT - http://www.structuralbiology.eu/ MoBrain project - https://mobrain.egi.eu Westlife project - http://about.west-life.eu StarCluster - http://star.mit.edu/cluster/ Infrastructure Manager - http://www.grycap.upv.es/im/ Elastic Cloud Computing (EC3): http://servproject.i3m.upv.es/ec3

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Acknowledgements

Miguel Caballer (UPV) Enol Fernandez (EGI.eu) Boris Parak (CESNET) Nuno Ferreira (SURFsara)

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i2pc.cnb.csic.es Follow us on Twitter: @InstructI2PC Laura del Caño ldelcano@cnb.csic.es Jesús Cuenca-Alba jcuenca@cnb.csic.es