Cloud computing in biomedicine intel talk

Intel Health & Life Sciences | Make it Personal
Ketan Paranjape
General Manager, Life Sciences
Intel Corporation
www.intel.com/healthcare/bigdata

HP Offers 'That Cloud Thing Everyone Is
Talking About'
https://www.youtube.com/watch?v=9ntP
xdWAWq8
2

*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 Cloud
A 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 Models
Public Cloud

Corporate Firewall
Private 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

Corporate Firewall
Hybrid 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”
CloudStack
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 Science
Virtual Screening
Target
Molecule
Compound
Molecule
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/
17

High Performance Cloud Computing Powers
Schrödinger
Solution – Configured 51,132 Codes on
6742 Amazon EC2 instances (CentOS
Linux) 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 research
http://arstechnica.com/business/2012/04/4829-per-hour-supercomputer-built-on-amazon-cloud-to-fuel-cancer-research/
18
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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Cloud computing in biomedicine intel talk

Cloud computing in biomedicine intel talk

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