Cloud computing in biomedicine intel talk

Intel Health & Life Sciences | Make it Personal

Ketan ParanjapeGeneral Manager, Life SciencesIntel Corporation

www.intel.com/healthcare/bigdata

http://www.intel.com/healthcare/bigdata


HP Offers 'That Cloud Thing Everyone Is Talking About'

https://www.youtube.com/watch?v=9ntPxdWAWq8

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https://www.youtube.com/watch?v=9ntPxdWAWq8


*National Institute of Standards and Technology (NIST)

Cloud Computing:A model for enabling convenient, on-demand network access to a shared pool of configurable computing resources (e.g., networks, servers, storage, applications, and services) that can be rapidly provisioned and released with minimal management effort or service provider interaction*

Definition


Anatomy of a CloudA Cloud is…

Really just one or more data centers…

Hosting a number of servers…

Supporting a number of virtualized environments

Accessed by network-connected clients


Corporate Firewall

• Virtualized data centers outside a company’s firewall

• Service providers make resources available to companies on-demand over the internet

• Third-party manages infrastructure

• Economies of scale maximized

• Example: Azure, AWS, Force, Heroku, Rackspace Cloud, vCloud

Cloud Computing 101 – Deployment ModelsPublic Cloud


Corporate Firewall

Cloud Computing 101 – Deployment ModelsPrivate Cloud

• Cloud infrastructure is used by just one organization

• May need to buy, build, manage hardware

• Data centers are virtualized – and located inside a company’s firewall

• Example: VMW’s vSphere-based private clouds, RAX Hosted Private Cloud

http://en.wikipedia.org/wiki/Virtualization


Corporate Firewall

Cloud Computing 101 – Deployment ModelsHybrid Cloud

• Combined use of private and public cloud -- where these are networked together

• When a burst of activity exceeds one cloud’s capability (e.g. private cloud), some activity is shifted to another

• Subset of the hybrid cloud remains internal (e.g. sensitive intellectual property)

• Subset of the hybrid cloud is public (e.g. SaaS offering such as travel services)

• Example: VMW’s vCloud Service Director


Introducing the “Cloud Stack”

There are three key types of cloud offerings – referred to as the “Cloud Stack”

Clo

ud

Sta

ck

Cloud computing means that infrastructure, applications, and business processes can be delivered to you as a service, over the Internet (or your own network)

Software-as-a-Service (SaaS)

SaaS: Cloud application services, whereby applications are delivered over the Internet by the provider, so that the applications don’t have to be purchased, installed, and run on the customer’s computers --Examples of this are Salesforce.com’s CRM solution, Google Docs, etc.

Platform-as-a-Service(PaaS)

PaaS: Cloud platform services, whereby the computing platform (operating system and associated services) is delivered as a service over the Internet by the provider – Examples here are Windows Azure, some of AWS’ solutions (Elastic Beanstalk), Force, Heroku

Infrastructure-as-a-Service(IaaS)

IaaS: Cloud infrastructure services, whereby a virtualized environment is delivered as a service over the Internet by the provider. The infrastructure can include servers, network equipment, and software -- A couple examples of IaaS “workloads” include storage and compute


Cloud solutions have some common characteristics

1 Elasticity + Scalability: The cloud is elastic – so resource allocation can get bigger or smaller depending on a users’ demand

‒ Elasticity enables scalability – so that the cloud can scale up for peak demand and down for lighter demand (e.g. allows for scale when an application in the cloud adds users, etc.)

2 On Demand, Self-Service Provisioning: Users can “provision” or add cloud services easily + quickly

‒ Users request an amount of computing, storage, software, etc. from the cloud provider

‒ Once used (or no longer needed), resources can be automatically de-provisioned

4 Broad Network Access: Capabilities / offerings are deployed over a network and be accessed from multiple platforms or locations – not just a dedicated thin client (e.g. not just from 1 computer) – Gmail is an example

5 Billing + Service Usage Metering: Usage is monitored, controlled + reported – and users pay only for what they use (e.g. in the same way you pay for utilities); could be chargeback through cost center on private cloud

3 Resource Pooling: Different cloud resources (e.g. portions of servers) are dynamically assigned / reassigned according to consumer demands

Cloud Computing Characteristics


Regulatory Compliance

• Part 11, HIPAA, System Validation etc.

• Time stamping, version control, GXP process documents, batch records, traceability, acess-control etc.

• FDA’s concern

• “If cloud services become the archive for clinical trial data, our concern would be to safeguard the system for write protection in order to prevent tampering. Auditing companies such as Google would not be practical, and the responsibility for data security would likely remain with the trial sponsors. This means that using the cloud will not change the fact that compliance and IT security are still the responsibility of the developer or trial sponsor” – Karen Riley, FDA

Miller, Rich. “Pharmaceuticals Test Drive the Cloud.” May 26 2009. Data Center Knowledge (Online). Retrieved October 28, 2009 from: http://www.datacenterknowledge.com/archives/2009/05/26/pharmaceuticals-test-drive-the-cloud

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Where in the Spectrum Are Your Cloud Workloads?


Novartis Institutes for BioMedical Research (NIBR)

• Unique research strategy driven by patient needs

• World-class research organization with about 6000 scientists globally

• Intensifying focus on molecular pathways shared by various diseases

• Integration of clinical insights with mechanistic understanding of disease

• Research-to-Development transition redefined through fast and rigorous “proof-of-concept” trials

• Strategic alliances with academia and biotech strengthen preclinical pipeline


• Requirements

• Large Scale Computational Chemistry Simulation

• Results in under a week

• Ability to run multiple experiments “on-demand”

• Challenges

• Sustained access to 50000+ compute cores

• Ability to monitor and re-launch jobs

• No additional Capital Expenditure

• Internal HPCC already running at capacity

• Job Profile

• Embarrassingly Parallel

• CPU Bound

• Low I/O, Memory and Network requirements

Accelerating the ScienceVirtual Screening

Target Molecule

CompoundMolecule

binding site

"Lock" "Keys"


The Cloud: Flexible Science on Flexible Infrastructure

• Engineering the right infrastructure for a workload:

• Software runs the same job many times across instance types

• Measures the throughput and determines the $ per job

• Use the instances that provide the best scientific ROI

• CC2 instance (Intel Xeon® ‘Sandy Bridge’) ran best for this


Metric Count

Compute Hours of Science 341,700 hours

Compute Days of Science 14,238 days

Compute Years of Science 39 years

AWS Instance Count-CC2 10,600 instances

Super Computing in the Cloud

• $44 Million infrastructure

• 10 million compounds screened

• 39 Drug Design years in 11 hours for a cost of …$4,232

• 3 compounds identified and synthesized for screening


Key Learnings/What’s Next?

• Diversity of Life Sciences brings unique challenges• Spend the time analyzing and tuning• Flexibility, Scalability and Performance • Time to rethink and retool• Challenge the Science and the Scientist• Collaboration

• Future plans• Chemical Universe : 166 Billion cpds (Extreme scale CPU)• Next Generation Sequencing in the Cloud (Extreme CPU, Mem, I/O)• “Disruptive” Technologies-Imaging (10x that of NGS!)


High Performance Cloud Computing Powers Schrödinger

Schrodinger and Nimbus Discovery virtually screens billions of molecules in a fraction of the time it would take to test them in labs.

But the solution requires an immense amount of computing power

Screen entire library of 21M ligands at higher level of accuracy would take months, even years on the internal 1500 core cluster …

http://arstechnica.com/business/2012/04/4829-per-hour-supercomputer-built-on-amazon-cloud-to-fuel-cancer-research/

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High Performance Cloud Computing Powers Schrödinger

Solution – Configured 51,132 Codes on 6742 Amazon EC2 instances (CentOSLinux) for 3 hours, 58.78 TB of RAM, Secured with HTTPS, SSH and 256-bit AES encryption, at $4828.85/hour.

(Cost to build this cluster - $20-25M)

13 years of compute in 3 hours for < $15,000

Significant reduction in false negatives because you can ask the right question$4,829-per-hour supercomputer built on Amazon cloud to fuel cancer researchhttp://arstechnica.com/business/2012/04/4829-per-hour-supercomputer-built-on-amazon-cloud-to-fuel-cancer-research/

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50K cores running for 3 hours. Grey portions are cores that finished their tasks and are ready to pick up new ones.


Summary

Cloud – Public, Private, Hybrid, IaaS, PaaS, SaaS …

Concerns with security, regulatory, compliance, networking …

What can you do next –

1. Begin with a cloud adoption assessment

2. Don’t think about replacing the data center

3. Move processes in stages – test data, security, deploy PaaS

4. Create a roadmap – don’t look for a “big bang”. Baby steps.

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Date post:	06-Aug-2015
Category:	Health & Medicine
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Cloud computing in biomedicine intel talk

Health & Medicine