1 experiences and lessons learned from past grid projects chuck kesler [email protected] november...

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Experiences and Lessons LearnedExperiences and Lessons Learnedfrom Past Grid Projectsfrom Past Grid Projects

Chuck KeslerChuck Kesler

[email protected]@mcnc.orgNovember 2004November 2004

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AgendaAgenda

Experience from the NC BioGridExperience from the NC BioGrid

What we learned; what can be done betterWhat we learned; what can be done better Business environmentBusiness environment Technical environmentTechnical environment Cultural environmentCultural environment Regulatory environmentRegulatory environment

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The NC BioGrid PartnershipThe NC BioGrid Partnership

NC Biotech CenterNC Biotech Center Provided the catalyst through the Provided the catalyst through the

NC Genomics & Bioinformatics NC Genomics & Bioinformatics ConsortiumConsortium

MCNCMCNC Provided the funding and Provided the funding and

dedicated staffdedicated staff

SunSun Donated infrastructure hardwareDonated infrastructure hardware Established Sun Center of Established Sun Center of

Excellence in BioinformaticsExcellence in Bioinformatics

IBMIBM Donated human capital Donated human capital

(application developers)(application developers)

Triangle UniversitiesTriangle Universities Focal point for the collaborationFocal point for the collaboration Brought early adopters to the tableBrought early adopters to the table Created collaborative working Created collaborative working

groupsgroups

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NC BioGrid AccomplishmentsNC BioGrid AccomplishmentsIn the Summer of 2002, installed a In the Summer of 2002, installed a dedicated testbed for evaluating grid dedicated testbed for evaluating grid middleware and developing grid middleware and developing grid applications for bioinformaticsapplications for bioinformatics

Testbed spanned multiple administrative Testbed spanned multiple administrative domains with systems located at MCNC, domains with systems located at MCNC, NC State, UNC-CH & Duke, and included NC State, UNC-CH & Duke, and included representative heterogenity of hardware representative heterogenity of hardware and OS platforms found at those sitesand OS platforms found at those sites

Employed “best of breed” approach to Employed “best of breed” approach to grid middleware deploymentgrid middleware deployment

Working groups met up to twice a month Working groups met up to twice a month during 2002-2003during 2002-2003

Created several pilot applications using Created several pilot applications using the testbedthe testbed

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Job SchedulingJob Scheduling Platform LSFPlatform LSF Sun Grid EngineSun Grid Engine

User PortalUser Portal CHEF / OGCECHEF / OGCE MyProxyMyProxy

Grid Middleware:Grid Middleware:Best-of-Breed ApproachBest-of-Breed Approach

Compute GridCompute Grid Globus V2 (NMI)Globus V2 (NMI) Avaki V2Avaki V2

Data GridData Grid Avaki Data Grid V4Avaki Data Grid V4 GridFTP (Globus)GridFTP (Globus)

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Data GridData Grid

Avaki 4.0 Data GridAvaki 4.0 Data Grid Federation of data providers across the WANFederation of data providers across the WAN

Provides a global name space for user home directories, Provides a global name space for user home directories, shared project spaces, databases, and applicationsshared project spaces, databases, and applicationsAbility to have results from canned SQL queries show up Ability to have results from canned SQL queries show up as files in the global name spaceas files in the global name space

Variety of access methodsVariety of access methodsWeb-based user interfaceWeb-based user interfaceNFS and CIFS through local “data grid access servers” to NFS and CIFS through local “data grid access servers” to provide access at the native OS levelprovide access at the native OS level

Simple deploymentSimple deploymentNo kernel mods requiredNo kernel mods requiredEach site can run a “share server” to distribute their local Each site can run a “share server” to distribute their local home and project directories to the gridhome and project directories to the gridWeb-based management interface Web-based management interface

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Compute GridCompute Grid

Globus Toolkit –global gridGlobus Toolkit –global grid NSF Middleware Initiative (NMI) V2 (Globus NSF Middleware Initiative (NMI) V2 (Globus

2.4.3)2.4.3)Provides “gatekeeper” functionality for submitting Provides “gatekeeper” functionality for submitting jobs through to the local cluster managerjobs through to the local cluster managerProvides GridFTP support for file transferProvides GridFTP support for file transferProvides MDS to track grid resource characteristicsProvides MDS to track grid resource characteristicsPlanned migration to Globus 3.2Planned migration to Globus 3.2

MCNC provides infrastructure servicesMCNC provides infrastructure servicesCertificate Authority (initially based on the Globus Certificate Authority (initially based on the Globus SimpleCA)SimpleCA)GIIS (master resource directory for the grid)GIIS (master resource directory for the grid)

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BioGrid Web PortalBioGrid Web Portal

CHEF/OGCE – a grid portal frameworkCHEF/OGCE – a grid portal framework Implements web-based interfaces for Implements web-based interfaces for

managing job submissions, file access, and managing job submissions, file access, and online meetingsonline meetings

Originally developed as a distance learning toolOriginally developed as a distance learning tool

MyProxy – security credential MyProxy – security credential repositoryrepository Provides the portal with a mechanism for Provides the portal with a mechanism for

accessing and using Globus security accessing and using Globus security credentialscredentials

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Portal ExamplePortal Example

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NC BioGrid Proof of Concept NC BioGrid Proof of Concept ApplicationsApplications

Parameter Space Study with BLASTParameter Space Study with BLAST BLAST compares a target gene sequence against a BLAST compares a target gene sequence against a

known genome to find similaritiesknown genome to find similarities Grid BLAST distributed 1,000+ target sequences across Grid BLAST distributed 1,000+ target sequences across

the grid for comparisonthe grid for comparison

IBM Extreme Blue ProjectIBM Extreme Blue Project Built a grid interface to BioPerl libraries Built a grid interface to BioPerl libraries

UNC-CH/IBM QSAR ApplicationUNC-CH/IBM QSAR Application Grid-enabled version of a drug compound screening Grid-enabled version of a drug compound screening

applicationapplication Finds compounds that have promising biological activity Finds compounds that have promising biological activity

characteristics that should receive further researchcharacteristics that should receive further research

The MCNC Enterprise GridThe MCNC Enterprise Grid 128-CPU cluster and 32-CPU Linux SMP environment 128-CPU cluster and 32-CPU Linux SMP environment

with Globus interfacewith Globus interface

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32-CPU SGI AltixLinux SMP Server

128-CPU IBM LinuxCluster (64 nodes)

8-TB Storage

LSF Master Job Scheduler

Grid Gatekeeper / Interactive Nodes

Global Grid Resource DB

(GIIS)

Users

Campus Grids

The MCNC Enterprise GridThe MCNC Enterprise Grid

AvakiDataGrid

Data G

rid A

ccess Servers

(8 total, i.e. 1 p

er 8 no

des)

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What did we learn?What did we learn?What do we do better next time?What do we do better next time?

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Critical Success FactorsCritical Success Factors

Technical EnvironmentTechnical Environment Insure the technology fits the problemInsure the technology fits the problem

Cultural EnvironmentCultural Environment Satisfy the disparate needs of stakeholdersSatisfy the disparate needs of stakeholders

Business EnvironmentBusiness Environment Create transforming competitive advantagesCreate transforming competitive advantages

Regulatory EnvironmentRegulatory Environment Adhere to government or industry regulationsAdhere to government or industry regulations

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Today’s Discussion...Today’s Discussion...

Technical EnvironmentTechnical Environment Insure the technology fits the problemInsure the technology fits the problem

Cultural EnvironmentCultural Environment Satisfy the disparate needs of stakeholdersSatisfy the disparate needs of stakeholders

Business EnvironmentBusiness Environment Create transforming competitive advantagesCreate transforming competitive advantages

Regulatory EnvironmentRegulatory Environment Adhere to government or industry regulationsAdhere to government or industry regulations

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The Business Environment:The Business Environment:Using Grids for Competitive Using Grids for Competitive

AdvantageAdvantage

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Transforming the Business Transforming the Business EnvironmentEnvironment

Two Possible Competitive Advantages Two Possible Competitive Advantages from Gridsfrom Grids Virtual OrganizationsVirtual Organizations Knowledge ManagementKnowledge Management

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CAPABILITIESCAPABILITIES

““VIRN” Test for Competitive VIRN” Test for Competitive AdvantagesAdvantages

SustainableSustainableCompetitiveCompetitiveAdvantageAdvantage

KnowledgeKnowledge

VVALUABLEALUABLEExploits opportunities,Exploits opportunities,

Neutralizes threatsNeutralizes threats

RRAREAREPossessed by fewPossessed by few

DIFFICULT TO DIFFICULT TO IIMITATEMITATECausally ambiguousCausally ambiguousor socially complexor socially complex

NNON-SUBSTITUTABLEON-SUBSTITUTABLENo strategic equivalentsNo strategic equivalents

CultureCulture

InfrastructureInfrastructure

RESOURCESRESOURCES ADVANTAGESADVANTAGES

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Knowledge ManagementKnowledge Management

KnowledgeKnowledge

CultureCulture



Grids help firms Grids help firms analyze massive analyze massive amounts of data amounts of data more quickly and more quickly and cost effectively, cost effectively,

leading to a better leading to a better insight into the insight into the marketplace, marketplace, keeping the keeping the

product pipeline product pipeline full, and lower full, and lower

development costsdevelopment costs






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Haeckel’s Hierarchy ofHaeckel’s Hierarchy ofOrganizational KnowledgeOrganizational Knowledge

DATADATA

INFORMATIONINFORMATION

INTELLIGENCEINTELLIGENCE

KNOWLEDGEKNOWLEDGE

WISDOMWISDOM

Data + Context =Data + Context =

Information + Inference =Information + Inference =

Intelligence + Certitude =Intelligence + Certitude =

Knowledge + Synthesis =Knowledge + Synthesis =


Source: http://www-1.ibm.com/ibm/palisades/ assets/pdf/Knowledge_Dev.pdf

2020

Leveraging Data forLeveraging Data forCompetitive AdvantageCompetitive Advantage

DATADATA



KNOWLEDGEKNOWLEDGE

WISDOMWISDOM





ITIT

HumansHumans

The Information Age...The Information Age...

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DATADATA



KNOWLEDGEKNOWLEDGE

WISDOMWISDOM





ITIT

HumansHumans

The Information Age...The Information Age...

Context created through Context created through classification of data, classification of data,

sorting, statistics, etc...sorting, statistics, etc...

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DATADATA



KNOWLEDGEKNOWLEDGE

WISDOMWISDOM





ITIT

HumansHumans

The Internet Age...The Internet Age...

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DATADATA



KNOWLEDGEKNOWLEDGE

WISDOMWISDOM





ITIT

HumansHumans

The Internet Age...The Internet Age...

Inference enabled by Inference enabled by the network, which the network, which

allows the federation of allows the federation of data and workflowsdata and workflows

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DATADATA



KNOWLEDGEKNOWLEDGE

WISDOMWISDOM





ITIT

HumansHumans

The Grid Age...The Grid Age...

2525


DATADATA



KNOWLEDGEKNOWLEDGE

WISDOMWISDOM





ITIT

HumansHumans

The Grid Age...The Grid Age...Grids enable deep analysis Grids enable deep analysis through easy aggregation through easy aggregation

of people, data, and of people, data, and computing resourcescomputing resources

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Virtual OrganizationsVirtual Organizations

KnowledgeKnowledge

CultureCulture



Enables flexible Enables flexible workforces to be workforces to be built just-in-time, built just-in-time,

using the best using the best resources, resources,

wherever they wherever they physically are physically are

located; this allows located; this allows companies to focus companies to focus their own staffing their own staffing

on their on their organizational core organizational core

competenciescompetencies






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In a traditional workforce, the In a traditional workforce, the worker must serve the system;worker must serve the system;

In a knowledge workforce, the In a knowledge workforce, the system must serve the worker.system must serve the worker.

Peter Drucker,Peter Drucker,

Managing in the Next SocietyManaging in the Next Society

(2002)(2002)

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The Regulatory Environment:The Regulatory Environment:Understanding the impact of Understanding the impact of

industry regulationsindustry regulations

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Service ProvidersService Providers


TECHNICALTECHNICAL

CULTURALCULTURAL

BUSINESSBUSINESS

LEGAL &LEGAL &REGULATORYREGULATORY

How can a grid resource How can a grid resource provider protect themselves provider protect themselves against illegal activities that against illegal activities that

their users may perform, their users may perform, particularly if those users may particularly if those users may

“belong” to another “belong” to another organization?organization?

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DMCADMCABackgroundBackground

Attempts to bring copyright law into the Attempts to bring copyright law into the Internet AgeInternet Age

In “traditional” copyright law, the copyright owner is In “traditional” copyright law, the copyright owner is granted exclusive rights to reproduce, display, perform, granted exclusive rights to reproduce, display, perform, transmit, or otherwise distribute the work, as well the transmit, or otherwise distribute the work, as well the rights to prepare derivative works rights to prepare derivative works

ISP’s, search engines, and web sites can easily infringe ISP’s, search engines, and web sites can easily infringe upon traditional copyright protectionsupon traditional copyright protections

Case in point: Google caching web pages that it has Case in point: Google caching web pages that it has indexed, and allowing them to be re-displayed to users indexed, and allowing them to be re-displayed to users violateviolate

Another case in point: The ISP whose users use the ISP’s Another case in point: The ISP whose users use the ISP’s infrastructure to illegally re-distribute copyrighted infrastructure to illegally re-distribute copyrighted material could be held liable for contributing to the material could be held liable for contributing to the infringing activitiesinfringing activities

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DMCADMCAProvisionsProvisions

Two primary considerations (for our Two primary considerations (for our purposes, at least)purposes, at least) Provisions that restrict, except under certain Provisions that restrict, except under certain

fair use conditions, circumvention of anti-fair use conditions, circumvention of anti-copying and access control mechanisms (Titles copying and access control mechanisms (Titles I and II); and,I and II); and,

““Safe harbors” that provide a means for online Safe harbors” that provide a means for online service providers to indemnify themselves service providers to indemnify themselves from the actions of their users (Title II).from the actions of their users (Title II).

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DMCADMCASafe HarborsSafe Harbors

Under certain conditions, service providers Under certain conditions, service providers can be held harmless for the following:can be held harmless for the following:

Transitory communications, such as when data is being Transitory communications, such as when data is being transferred between systems in the grid;transferred between systems in the grid;

System caching, such as when transient data is System caching, such as when transient data is temporarily stored on a grid system to prevent it from temporarily stored on a grid system to prevent it from having to be re-transmitted across the network;having to be re-transmitted across the network;

Storage of information on grid systems at the direction Storage of information on grid systems at the direction of users; and,of users; and,

Information location tools, such as registries that keep Information location tools, such as registries that keep track of data and resources on the grid.track of data and resources on the grid.

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DMCADMCAService Provider QualificationsService Provider Qualifications

A service provider must meet the following A service provider must meet the following tests to qualify for the safe harbors:tests to qualify for the safe harbors:

Establish and reasonably implement a policy of Establish and reasonably implement a policy of removing or disabling the distribution of infringing removing or disabling the distribution of infringing content upon notification of infringement by copyright content upon notification of infringement by copyright holders, and terminating in appropriate circumstances holders, and terminating in appropriate circumstances the accounts of grid user who are repeat infringers; and,the accounts of grid user who are repeat infringers; and,

Accommodate and not interfere with “standard technical Accommodate and not interfere with “standard technical measures” that copyright owners use to identify or measures” that copyright owners use to identify or protect copyrighted works. protect copyrighted works.

Must not have prior knowledge that the grid user was Must not have prior knowledge that the grid user was infringing copyrightsinfringing copyrights

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PharmaceuticalsPharmaceuticals


TECHNICALTECHNICAL

CULTURALCULTURAL

BUSINESSBUSINESS


21 CFR Part 11: How can the 21 CFR Part 11: How can the FDA insure that pharmas FDA insure that pharmas are properly protecting are properly protecting

electronic records electronic records associated with new drug associated with new drug

applications?applications?

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21 CFR Part 1121 CFR Part 11BackgroundBackground

Applies to the pharmaceutical Applies to the pharmaceutical industryindustry Currently, only required in development, Currently, only required in development,

clinical trials, and manufacturingclinical trials, and manufacturing Does not currently apply to drug discovery, but Does not currently apply to drug discovery, but

may apply in the futuremay apply in the futureSee Vioxx, Baycol, etc...See Vioxx, Baycol, etc...

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21 CFR Part 1121 CFR Part 11PurposePurpose

Define a framework in which Define a framework in which pharmaceutical companies can make pharmaceutical companies can make submissions to the FDA with submissions to the FDA with electronic records without electronic records without compromising public healthcompromising public health Before this, massive amounts of hardcopy Before this, massive amounts of hardcopy

paperwork had been required to submit New paperwork had been required to submit New Drug Applications (NDA) to the FDADrug Applications (NDA) to the FDA

21 CFR Part 11 allowed companies to increase 21 CFR Part 11 allowed companies to increase the efficiency of the submission process by the efficiency of the submission process by reducing time to market and costs. reducing time to market and costs.

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21 CFR Part 1121 CFR Part 11Applicable RegulationsApplicable Regulations

Section 11.10(a) – Validation of systems to insure accuracy, Section 11.10(a) – Validation of systems to insure accuracy, reliability, consistency of intended performance, and the ability to reliability, consistency of intended performance, and the ability to detect invalid or altered records; detect invalid or altered records;

Section 11.10(b) – Generation of accurate and complete copies of Section 11.10(b) – Generation of accurate and complete copies of records in both human readable and electronic form, suitable for records in both human readable and electronic form, suitable for inspection and copying;inspection and copying;

Section 11.10(c) – Employment of procedures and controls that Section 11.10(c) – Employment of procedures and controls that insure the authenticity, integrity, and confidentiality of electronic insure the authenticity, integrity, and confidentiality of electronic records, including digital signatures that cannot be repudiated records, including digital signatures that cannot be repudiated and protection of electronic records that enables their accurate and protection of electronic records that enables their accurate and timely retrieval during the required retention period;and timely retrieval during the required retention period;

Section 11.10(d) – Limiting system access to authorized Section 11.10(d) – Limiting system access to authorized individuals; andindividuals; and

Section 11.10(e) – Creation of secure, computer-generated, time-Section 11.10(e) – Creation of secure, computer-generated, time-stamped audit trails that are kept as long as the subject electronic stamped audit trails that are kept as long as the subject electronic records are stored.records are stored.

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21 CFR Part 1121 CFR Part 11RequirementsRequirements

System validationSystem validation Documentation of system hardware, OS and Documentation of system hardware, OS and

application setup and modifications so that application setup and modifications so that computational results can be recreated at a computational results can be recreated at a future date if necessaryfuture date if necessary

All grid participants must commit to standard All grid participants must commit to standard operational practices insure systems are operational practices insure systems are validatedvalidated

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Authentication and non-repudiationAuthentication and non-repudiation Users must be uniquely identifiedUsers must be uniquely identified Data and programs should be digitally signedData and programs should be digitally signed In a grid, all participants must agree upon a In a grid, all participants must agree upon a

Certificate Authority that implements a Certificate Authority that implements a mutually acceptable Certification Practice mutually acceptable Certification Practice StatementStatement

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Authorization and access controlAuthorization and access control Least privilege access model should be Least privilege access model should be

employedemployed Grid must translate between global identity Grid must translate between global identity

and local identity, mapping access rights and local identity, mapping access rights appropriatelyappropriately

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Audit trailsAudit trails Must track transactions across all nodes in the Must track transactions across all nodes in the

gridgrid Requires combining accounting records from Requires combining accounting records from

across the gridacross the gridDifficulty increases with heterogeneityDifficulty increases with heterogeneity

Timestamps must be consist to insure an Timestamps must be consist to insure an accurate representation of activitiesaccurate representation of activities

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Public CompaniesPublic Companies


TECHNICALTECHNICAL

CULTURALCULTURAL

BUSINESSBUSINESS


SOX: If a grid is used to SOX: If a grid is used to process financial info process financial info that is material to the that is material to the

performance of the firm, performance of the firm, how can the results be how can the results be

verified?verified?

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Sarbanes-Oxley (SOX) ActSarbanes-Oxley (SOX) ActBackground and PurposeBackground and Purpose

Instituted in response to corporate Instituted in response to corporate scandals to make corporate officers scandals to make corporate officers and board members accountable for and board members accountable for financial reportingfinancial reporting Applies to all public companiesApplies to all public companies

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Sarbanes-Oxley (SOX) ActSarbanes-Oxley (SOX) ActRequirementsRequirements

Section 404 defines the need for IT Section 404 defines the need for IT controlscontrols Must insure the integrity, authenticity, and Must insure the integrity, authenticity, and

non-repudiation of information concerning non-repudiation of information concerning assets and transactionsassets and transactions

Requirements are similar to those seen for 21 Requirements are similar to those seen for 21 CFR Part 11, so it similar solutions may be CFR Part 11, so it similar solutions may be employedemployed

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HealthcareHealthcare


TECHNICALTECHNICAL

CULTURALCULTURAL

BUSINESSBUSINESS


HIPAA: How can the privacy of HIPAA: How can the privacy of individuals be protected if individuals be protected if

data that identifies patients is data that identifies patients is used on a grid that includes used on a grid that includes

external resources?external resources?

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HIPAAHIPAABackground and PurposeBackground and Purpose

Applies to the healthcare industryApplies to the healthcare industry Therapeutic and research areas, basically Therapeutic and research areas, basically

wherever there are patient recordswherever there are patient records Overseen by DHHSOverseen by DHHS

Two TitlesTwo Titles Title I – Requires insurance portability (not Title I – Requires insurance portability (not

applicable to our discussion)applicable to our discussion) Title II – Administrative simplificationTitle II – Administrative simplification

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HIPAAHIPAATitle II PurposeTitle II Purpose

To protect and enhance the rights of consumers by To protect and enhance the rights of consumers by providing them access to their health information providing them access to their health information and controlling the inappropriate use of that and controlling the inappropriate use of that information;information;

To improve the quality of health care in the U.S. by To improve the quality of health care in the U.S. by restoring trust in the health care system among restoring trust in the health care system among consumers, health care professionals, and the consumers, health care professionals, and the multitude of organizations and individuals multitude of organizations and individuals committed to the delivery of care; andcommitted to the delivery of care; and

To improve the efficiency and effectiveness of health To improve the efficiency and effectiveness of health care delivery by creating a national framework for care delivery by creating a national framework for health privacy protection that builds on efforts by health privacy protection that builds on efforts by states, health systems, and individual organizations states, health systems, and individual organizations and individuals.and individuals.

4848

HIPAAHIPAATitle II StrategyTitle II Strategy

Protection of privacy;Protection of privacy;

Protection of security; and,Protection of security; and,

Standardization of electronic data Standardization of electronic data interchange (EDI) in health care interchange (EDI) in health care transactions.transactions.

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HIPAAHIPAATitle II Privacy RequirementsTitle II Privacy Requirements

Protect patient identifiable Protect patient identifiable informationinformation Information can be “de-identified” or sanitizedInformation can be “de-identified” or sanitized Process of sharing information has to approved Process of sharing information has to approved

by an Institutional Review Board (IRB)by an Institutional Review Board (IRB) In a grid, each organization likely has its own In a grid, each organization likely has its own

IRB, and each IRB is free to interpret HIPAA IRB, and each IRB is free to interpret HIPAA rules as strictly as they see fitrules as strictly as they see fit

Grid participants should coordinate their Grid participants should coordinate their approaches to their IRBs as much as possible approaches to their IRBs as much as possible (see BIRN project)(see BIRN project)

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Financial ServicesFinancial Services


TECHNICALTECHNICAL

CULTURALCULTURAL

BUSINESSBUSINESS


GLB: How can individual GLB: How can individual financial records be protected, financial records be protected,

if a financial services uses a if a financial services uses a grid for portfolio analysis grid for portfolio analysis

(basically a parameter space (basically a parameter space study problem)? study problem)?

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Gramm-Leach-Bliley ActGramm-Leach-Bliley ActBackground and PurposeBackground and Purpose

A.K.A. Financial Modernization ActA.K.A. Financial Modernization Act Provides a framework for using electronic Provides a framework for using electronic

records in the financial industryrecords in the financial industry Overseen by the FTCOverseen by the FTC

Two Primary RegulationsTwo Primary Regulations Financial Privacy RuleFinancial Privacy Rule Safeguards RuleSafeguards Rule Again, parallels can be drawn to HIPAA, etc...Again, parallels can be drawn to HIPAA, etc...

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Questions or Comments?Questions or Comments?

Please feel free to contact me:Please feel free to contact me:

Chuck KeslerChuck Kesler

Director, Grid & Data Center ServicesDirector, Grid & Data Center ServicesMCNCMCNC

[email protected]@mcnc.org

1 experiences and lessons learned from past grid projects chuck kesler [email protected] november...

Documents

grid applications

grid middleware deployment

local data grid access

grid resource characteristics

testbed slide

nc state

nc biogrid accomplishments

bioinformatics testbed