CRI Annual Report 2012-2013

Center for Research Informatics

2012-2013

University of Chicago

ANNUAL REPORT

The Center for Research Informatics (CRI) was set up two years ago in August 2011

to provide services and resources to support biomedical informatics. The CRI views

biomedical informatics very broadly to include bioinformatics, clinical informatics,

translational informatics, and health care informatics. As is detailed in this report,

during the past two years, the CRI has set up a Clinical Research Data Warehouse and

a Bioinformatics Core, updated the BSD’s high-performance computing cluster, and

made secure and compliant storage and computing resources available to every BSD

researcher.

The Office of the CRIO has also set up a governance structure, bringing together BSD

and UCM leadership and experts in information systems, patient privacy, and a variety

of research fields to guide us in making long-term decisions that serve our researchers,

comply with all relevant laws and policies, and protect our patients’ data.

In addition, the Office of the CRIO has supported initiatives such as setting up a secure

and compliant computing infrastructure so that researchers can more quickly and easily

analyze large-scale genomic datasets.

As we move forward and continue to grow, it is important that we hear from faculty

so that we can provide the services, resources, and education that are important to

you. I am very interested in hearing from every BSD researcher to make sure that your

needs are met. You can contact me directly or talk to any member of the BSD Research

Informatics Oversight Committee (you can find their names on the CRI website and on

page 74 of this report).

We look forward to hearing from you.

Robert Grossman, Ph.D.

Message from the BSD Chief Research Informatics Officer

Who We Are

Clinical and Translational Informatics

Bioinformatics Core

Systems and Security

Training and Education

Faculty Oversight and Governance

Looking Ahead

Our Partners

40

2

12

26

53

59

67

65

Center for Research InformaticsAnnual Report 2012-13

TABLE OF CONTENTS

Appendix 69

WHO WE ARE

As a physician scientist and informaticist, I know firsthand the problems facing basic

researchers, translational medicine specialists, and clinicians. Deficiencies in any part of

the pipeline can have serious downstream effects. A productive translational research

operation requires a solid and secure infrastructure, easy access to powerful analytical

tools and high-performance computing, expertise in complex study design and data

analysis, and the ability to create and implement platforms for collecting, storing,

studying, and presenting research data. When the Center for Research Informatics was

established two years ago, the path from the bench to the bedside at the University of

Chicago was fragmented and inefficient, serving neither basic scientists nor clinicians

well. In the short time since, the CRI has grown into an active and versatile group of

professionals, capable of executing on a wide range of technologies to enable world-

class biomedical research.

To support these endeavors, we have built an industrial-grade, HIPAA-compliant secure

infrastructure, able to store and compute over even the largest and most complex

datasets. Every research group, from the basic sciences to clinical faculty, has access

to the storage and computing resources provided by the CRI. The Bioinformatics Core

takes on the most intricate and complicated data analysis tasks, working closely with

investigators to advise on data collection, perform complex computations, and render

advanced interpretation of the results. Nearly one hundred groups have taken advantage

of the Core so far, and the number of grants and papers directly resulting from our

assistance is growing every day. Our Clinical and Translational Group provides state-of-

the-art custom application development for investigators in need of specialized data

collection or other assistance with their clinical studies.

The crowning achievement of the Center’s first two years has been the design, building,

and implementation of a robust Clinical Research Data Warehouse. Starting with just

a data feed from the Centricity billing system, the CRDW now boasts data from over

600,000 patients in an easily searchable system that allows researchers to quickly

determine cohort size for their studies. The CRI has the BSD’s only system capable of

performing complex queries to study quality and other important clinical metrics.

Looking ahead, we have many exciting plans for the CRI. In 2014, we will release a

feature-rich system for accessing de-identified patient data in the CRDW. We will

implement a full-text searchable system for querying pathology and radiology reports.

We will further expand our computational infrastructure, doubling our HPC power

A Letter from the Director

Who We Are

CRI Annual Report 2012-134

and increasing our storage capacity. We continue to develop, test, and roll out new

bioinformatics methods, making these available to researchers through our core service

offerings and as self-service workflows on our Galaxy platform.

We hope that everyone in the BSD will take advantage of the array of resources offered

by the CRI. We look forward to continuing our mission of providing advanced informatics

support to enable world-class biomedical research throughout the BSD.

Samuel Volchenboum, MD, PhD

Director and Associate CRIOSamuel Volchenboum, MD, PhD

our leadership

Sam has been a part of the CRI since May 2012 in his role as Associate Chief Research Informatics Officer, leading our faculty outreach and education efforts. In April 2013 he was appointed Director of the CRI and now leads our operations and strategic planning. In addition to his work in the CRI, Sam serves the Department of Pediatrics as Assistant Professor, is an Associate Director of the Institute for Translational Medicine, and is a Faculty Fellow in the Computation Institute. His research includes using proteomics to study neuroblastoma, a pediatric solid tumor; developing software to facilitate real-time mass spectrometry peptide identification; and creating tools to improve provider communication and patient care.

Who We Are

cri.uchicago.edu 5


Who We Are

The Center for Research Informatics

(CRI) was created in 2011 to support the

University of Chicago Biological Sciences

Division (BSD) research community. We

offer state-of-the-art, standards-com-

pliant technologies for the acquisition,

management, and storage of clinical,

translational, and basic research data.

Our resources and services are open to

all members of the BSD; users include

students, postdoctoral fellows, tech-

nicians, staff, faculty, researchers, and

collaborators. In addition, we support

research and education in informatics

and work with the Institute for Trans-

lational Medicine (ITM), Clinical and

Translational Science Awards (CTSA)

program, and other partners on joint

initiatives. Finally, we are strong advo-

cates for informatics within our research

communities.

Since 2011, when the Office of the CRIO was created to guide research informatics efforts across the BSD, the Center for Research Informatics has grown into a robust service organization. In our first year, we developed a mission, hired several of the Direc-tors who would lead our major initiatives, and began work on key projects. Since early 2012, we’ve seen several important projects come to fruition: a functioning and growing Clinical Research Data Warehouse, with faculty data requests being evaluated by our Data Use Committee and fulfilled by our staff; a Bioinformatics Core providing pipelines, consulting, training, and other services; and an improved, HIPAA-compliant computing and storage infrastructure for researchers.

As we work to improve and expand our existing services, we will continue to reach out to faculty to increase user adoption and develop new initiatives. We look forward to seeing where the next year of our timeline will bring us.

August 2011

The CRI is created as a central organization for informatics service,

research, and education.

Robert Grossman

is appointed CRIO.

February 2011

The Office of the CRIO is created with a charge of overseeing and directing

research informatics across the BSD.

About the CRI

How We’ve Grown: A Timeline

cri.uchicago.edu 7

Who We Are

The CRI’s services and resources are

provided by three core groups. The


team manages our Clinical Research

Data Warehouse (CRDW), provides

custom programming for initiatives in

clinical research, and supports data

management for clinical trials. The

Bioinformatics Core provides analy-

sis pipelines, consulting services, and

other expertise for researchers working

with genomic data. The Systems and

Security team maintains and improves

our scientific computing infrastructure,

provides technical support to users, and

ensures our technical compliance with

appropriate security regulations. All

three of these groups, along with our

administration, governance committees,

and strategic partners, work together

toward our goal of enabling world-class

research in a secure environment.

Don Saner joins the CRI as

Director of Clinical and Translational

Informatics.

October 2011

The BSD Research Informatics Governance Structure is approved

by the BSD Dean’s Office.

Hannah Lawrence

joins the CRI as Executive

Administrator.

The CRI’s mission is to provide informatics resources and services to BSD faculty, to

support high-quality biomedical and clinical research, and to promote research and

education in informatics.

OUR MISSION


Who We Are

Jorge Andrade joins the CRI as Director of

Bioinformatics.

May 2012

Sam Volchenboum is appointed Associate

Chief Research Informatics Officer.

February 2012

The IRB protocol for the CRDW is approved, and the

system goes live for BSD researchers.

The CRI is an initiative developed and

managed by the Chief Research Infor-

matics Officer (CRIO) and Associate

CRIO. The Office of the CRIO is respon-

sible for advising the Dean and the Dean

for Research and Graduate Education of

the Biological Sciences Division on the

BSD’s investment in research informat-

ics, for managing research informatics

services and resources, for creating new

research informatics initiatives, and for

operating a Research Informatics Gover-

nance Structure.

Chief Research Informatics Officer Robert Grossman, PhD

As Chief Research Informatics Officer, Bob guides informatics activities and initiatives across the BSD, including providing strategic direction and oversight for the CRI. In addition to his role as CRIO, Bob is a Senior Fellow in the Institute for Genomics and Systems Biology, a Senior Fellow in the Computation Institute, and a Professor of Medicine in the Section of Genetic Medicine. His research group focuses on big data, biomedical informatics, data science, cloud computing, and related areas. Bob served as the first Director of the CRI from August 2011 to April 2013.

our leadership

cri.uchicago.edu 9

Who We Are

September 2012

The Bioinformatics Core makes its core informatics

pipelines available to researchers.

The Bioinformatics

Core begins offering services.

October 2012

The cohort discovery tool i2b2 is released to facilitate

queries of the CRDW for all BSD researchers.

The CRI’s administrative

team: Caitlin Pike, Michael Daus, and Hannah Lawrence

Who We Are

November 2012

The CRI makes available a new, HIPAA-compliant HPC cluster, storage and backup

resources, and other computing infrastructure.

April 2013

Sam Volchenboum is appointed Director

of the CRI.

Plamen Martinov joins the CRI as

Director of Systems and Security.


Executive Administrator Hannah Lawrence

As Executive Administrator of the CRI, Hannah is responsible for planning and oversight of our financial and administrative functions, including coordination across service areas, management of governance committees, communications, and project management for CRI initiatives. She works closely with our leadership team to develop short- and long-term organizational plans, manages our budget and hiring process, and provides other administrative and strategic support. Prior to joining the CRI, she served as Strategist and Planner in the Office of the Dean of the BSD. There, she was responsible for organizing the Informatics Advisory Group that ultimately led to the Dean’s decision to appoint a CRIO and create the CRI. She also served as the first administrative manager of the BSD’s Faculty Advisory Committee.

our leadership

Who We Are

Our Organization

For a detailed list of CRI employees, please see Appendix A.

cri.uchicago.edu 11

Timothy HolperManager of CRDW

Development

Brian FurnerManager of

Programming

Seong ChoiKeith Danahey

Kevin LeProgrammers

Julissa AcevedoBusiness Systems

Analyst

Luis MacielDatabase

Administrator

Tiffany CyrusProject Manager

Riyue BaoElizabeth BartomKyle Hernandez

Lei HuangJianpeng Xu

Chunling ZhangBioinformaticians

Wenjun KangScientific

Programmer

Hannah LawrenceExecutive

Administrator

Don SanerDirector of Clinicaland Translational

Informatics

Jorge AndradeDirector of

Bioinformatics

Plamen MartinovDirector of Systems

and Security

Sam VolchenboumAssociate CRIO & Director of the

CRI

Robert GrossmanChief Research

Informatics Officer

Caitlin PikeCommunication

Specialist

Michael DausAdministrative

Specialist

Andy BrookBeth Lynn EicherMichael Jarsulic

Sneha Jha Olumide Kehinde

Systems Administrators

Bruce ThompsonSecurity Analyst

Brad OrrSenior Project

Manager

CLINICAL & TRANSLATIONAL INFORMATICS



Since the CRI’s beginnings, one of the

central projects of the Clinical and Trans-

lational team has been to build, populate,

and maintain the Clinical Research Data

Warehouse. Over the past two years,

the team has seen this initiative develop

from a concept to a functioning and

growing data warehouse. The IRB proto-

col outlining its standards, governance,

and oversight was approved in February

2012, and the team began fulfilling data

requests for researchers in May 2012.

The CRDW incorporates six years’ worth

of data from electronic medical records

and patient billing, including lab values,

procedure and diagnosis codes, demo-

graphics, medications, and visit informa-

tion. The Clinical and Translational team

continues to work to expand the amount

and types of data available; they are

currently engaged in integrating radiol-

ogy and pathology notes and discharge

summaries.

The CRDW

Director of Clinical and Translational InformaticsDon Saner

our leadership

Over the past two years, Don has led his team through the process of building and developing the Clinical Research Data Warehouse. In addition, he provides informatics leadership and support for other clinical and translational research projects in conjunction with the Institute for Translational Medicine and our other partners. With over 20 years of experience at the University of Chicago, Don joined the CRI as one of our first staff members in 2011.

cri.uchicago.edu


To interact with the CRDW, research-

ers use a datamart interface. The first

datamart implemented by the CRI, i2b2,

went live for users in June 2012. i2b2, or

“Informatics for Integrating Biology and

the Bedside,” is an NIH-funded open-

source project created by a National

Center for Biomedical Computing based

at Partners HealthCare System. i2b2 is

designed for cohort identification, allow-

ing researchers to query the CRDW for

sets of patients meeting search criteria.

Applications and benefits of the i2b2

interface include:

• Helping investigators create new

research hypotheses

• Identifying potential cohorts for clin-

ical trials

• Reducing the time researchers must

spend on discovery of research

cohorts, study feasibility, and subject

recruitment

• Familiarizing researchers with the

standard terminologies and data that

reside in the CRDW

Researchers log into i2b2 using BSD or

hospital credentials and can then explore

the CRDW using an intuitive drag-and-

drop interface. Queries may be created

As of August 2013,the CRDW contains1...

1 Please note that some numbers regard-ing the data housed in the CRDW differ from those listed in the CRI’s 2012 Annual Report due to changes in how these data are measured. (1) The number of patients reported here represents only those patients who have encounter data associ-ated with them, while last year’s report included all patients regardless of encounter data. (2) Billing records where debits are canceled out by credits (for example, when a procedure is ordered but never performed) are no longer listed here. (3) This year’s report no longer includes “orphaned” records that were previously included in CRDW summary counts but cannot be returned via i2b2 or in custom data requests.

607,000patients

6.1 millionencounters

16.1 millionmedications

36.8 millionprocedures

93 millionlabs

13.9 milliondiagnoses

15

i2b2 and Data Requests


with multiple and/or logic, using search

terms based on standard terminologies.

The information returned by the system

allows researchers to determine the

number of patients meeting their crite-

ria. These results can inform subsequent

requests for full datasets with either

de-identified data or IRB-approved

protected health information. To date,

almost one hundred users have cre-

ated and executed over one thousand

searches.

Requests for CRDW data are fulfilled

by the Clinical and Translational team,

under the oversight of the Data Use and

Technical Policy Committees. Research-

ers submit requests using a simple

online form, providing information about

the scientific purpose of the requested

data. To protect the University’s data

and comply with patient privacy laws

and our IRB protocol, the Data Use Com-

mittee monitors data requests to ensure

appropriate use of CRDW data. (For

more information about this committee,

see page 63.) In addition, the CRI acts as

an Honest Broker service for researchers,

integrating data from different sources

such as the Cancer Registry and Epic and

removing identifiers when necessary to

protect patient privacy. Since May 2012,

the Clinical and Translational team has

fulfilled 92 data requests of varying size

and complexity.


92 10

Data Request Status Summary (as of August 2013)

17

not approved

completed

on hold awaiting IRB awaiting user

in progress


cri.uchicago.edu 17

As the demand for clinical data for

research purposes continues to grow,

the future of the CRDW’s develop-

ment will include the creation of a fully

de-identified datamart for research,

which will allow investigators to access

and query de-identified data within

a secure data zone. In addition, the

continued development of the CRDW

includes the incorporation of additional

data elements, which have been pri-

oritized by the Research Informatics

Governance Committee. These elements

include the Cancer Registry; radiology,

pathology, and discharge summaries;

other data elements from Epic’s Clarity

data warehouse; and the integration of

research-specific databases including

Velos and REDCap.

5

Family Medicine

Human Genetics

Medicine

Neurology

Obstetrics & Gynecology

Orthopaedics

Pathology

Pediatrics

Psychiatry

Radiology

Surgery

Total Data Requests

115302010

Who uses the CRDW? Since May 2012, our Clinical and Translational Informatics team has processed data requests from 11 different University departments.

40 50 60 70



The CRI maintains an instance of caTis-

sue, a robust open-source biobanking

management system used by labs to

organize freezers and track samples. In

addition to the standard deployment

of caTissue, the CRI has worked with

Dr. Michael Maitland, who manages

the Cancer Center’s biofluids core, to

add customizations created by Indiana

University. These customizations, called

caTrack, permit tracking the chain of

custody for all samples using barcode

labels and handheld barcode readers,

which then synchronize with caTissue

when placed in docking stations. This

system permits tracking of a sample’s

origin, when it was drawn, and where it

was initially stored.

Biobanking Management

Highlighted Accomplishments from 2012-13

• Expanded the CRDW by incorporating data elements from Epic and Clarity as well as the Cancer Registry

• Released i2b2 and began fulfilling data requests

• Established data request guidelines and policies to protect patient information

• Developed a Data Use Committee review process for data requests

• Expanded the team by hiring a business systems analyst, a database administrator, and a project manager

• Launched a REDCap users group

• Rewrote Dr. David Meltzer’s Hospitalist Protocol application and wrote a dashboard and alerting system for his Continuity of Care program

our contributions

Brian Furner, Keith Danahey, and Tim Holper


cri.uchicago.edu 19

Beyond maintaining the CRDW and

fulfilling data requests, the Clinical and

Translational team works directly with

research groups to provide custom

research application development for

their clinical research projects.

One such project is 1200 Patients, a

personalized medicine initiative jointly

sponsored by the CRI and the Center for

Personalized Therapeutics. This pharma-

cogenomics project seeks to develop a

new medical system model for person-

alized care in which patients’ genetic

information can be incorporated into the

decision-making process of prescribing

medications.

Patients who have consented to partic-

ipate in the project are genotyped in a

Custom Programming:1200 Patients and TRIDOM



CLIA-certified lab. Their genetic informa-

tion is then stored in a relational database

along with curated pharmacogenomic

data from published studies. During clinic

visits, a physician dashboard displays a

“30-second summary” synthesized from

the information in the database relevant

to the patient’s genomic profile. Physi-

cians can use these summaries to inform

their choices in prescribing medication—

by pre-identifying patients who are likely

to experience severe side effects, for

example, or by predicting when a patient

may need alternative dosing.

Clinical and Translational Informatics team members Tiffany Cyrus, Brian Furner, Don Saner, Luis Maciel, Julissa Acevedo, Tim Holper, Kevin Le, and Keith Danahey


cri.uchicago.edu 21

Our Goals for 2013-14our future

• Improve internal efficiency, including time, data repository, bug tracking, reporting, and status tracking, by implementing team project management software

• Implement a standard procedure for processing project requests that includes defining business requirements and scope of work, providing a time estimate, and receiving client approval

• Create a dashboard with metrics for the CRDW, REDCap, and Velos to increase the visibility of the data in each system

• Enhance the skill set of each team member through professional training

• Develop and maintain tools for data collection and reporting, including continuing to develop in-house systems to support custom applications and datamarts

• Improve internal knowledge and collaboration across the team through biweekly presentations

As new technologies allow the practice

of medicine to become increasingly

personalized, the 1200 Patients project

contributes to this progress by improv-

ing doctors’ ability to make patient-

specific medication decisions. The CRI

helps enable this important initiative

by providing custom programming and

database design as well as data import

and overall technical management.

TRIDOM (Translational Research Initia-

tive in the Department of Medicine) is

a biobanking protocol started in 2005

that stores DNA, plasma, and serum for

consented patients who are scheduled



for a standard-of-care blood draw.

The CRI contributed to this project

by leading a rewrite of the database

that maintains consent and sample

information and generates operational

reports. In addition, the CRI partnered

with eSphere, which makes the Human

Tissue Resource Center’s biobanking

software, to create an automated feed

to the TRIDOM database. To date, TRI-

DOM has enrolled over 8,800 patients

and has banked samples for more than

5,900 of these patients, resulting in a

total of over 58,000 samples.

300

1200

1500

900

600

0

REDCap adoption has progressed at a steady rate since 2011.

total projects

total users

July

Augu

st

Sept

embe

r

Oct

ober

Nov

embe

r

Dec

embe

r

Janu

ary

Febr

uary

Mar

ch

April

May

June July

Augu

st

Sept

embe

r

Oct

ober

Nov

embe

r

Dec

embe

r

Janu

ary

Febr

uary

Mar

ch

April

May

June July

Augu

st

2011 2012 2013


cri.uchicago.edu 23

Clinical Trials Management

The Clinical and Translational team

supports clinical trials management by

operating two data management solu-

tions, REDCap and Velos eResearch.

The University of Chicago has been a

member of the REDCap consortium

since 2010. This self-managed, secure,

web-based application, developed by

the Vanderbilt University Clinical and

Translational Science Awards (CTSA),

supports data collection strategies for

research studies with tools for build-

ing and managing online surveys and

databases. The University of Chicago’s

instance of REDCap currently supports

more than 700 users from across the

BSD and houses over 600 projects.

As the number of REDCap users con-

tinues to grow, the CRI has worked to

provide opportunities for education and

collaboration. A REDCap users group

provides the community with an ongo-

ing meeting space for discussion, new

feature announcements, tips and tricks,

and real-time help. The CRI also offers

individual and small group REDCap

tutorial sessions for those in need of

more personalized guidance (for more

detail, see page 56).

Velos eResearch is a clinical trials

management system that integrates

study administration and clinical data

management. The system supports

many aspects of running a clinical trial,

including:

• Patient recruitment and scheduling

• IRB and study monitoring

• Project planning and study design

• Protocol compliance

• Web-based data capture on a

per-protocol basis

• Data safety monitoring and adverse

event reporting

Velos is now supporting over 1,500 pro-

tocols for more than 550 investigators

at the University. The CRI is currently

working with the vendor to complete a

hardware migration and upgrade that

will improve the user experience.

faculty spotlight

David Meltzer

David Meltzer, MD, PhD, is Chief of the Section of Hospital Medicine, Director of the Center for Heath and the Social Sciences, and an Associate Professor of Medicine, Economics, and Public Policy Studies at the University of Chicago. He also serves as the co-leader of the Institute for Translational Medicine’s Training Cluster, as well as the co-director of the ITM’s academic arm, the Committee for Clinical and Translational Science.

Dr. Meltzer’s research ex-plores problems in health economics and public policy, focusing on the theoretical foundations of medical cost-effectiveness analysis and the cost and quality of hospital care. In the past year, the CRI’s Clin-ical and Translational team has worked with Dr. Meltzer in support of two of his proj-ects: the Hospitalist Project and the Comprehensive Care Program (CCP) initiative.

The Hospitalist Project, which is supported in part by the Clinical and Translational Science Awards, has been in operation for over 16 years and has enrolled over 100,000 patients. The



aims of this multi-site project are to study the quality and cost of care among hospitalized patients at the University of Chicago and Mercy Hospital, to examine whether there are significant differences in outcomes and costs for patients cared for by hospitalists compared to those cared for by other inpatient attending physicians, and to develop a research infrastructure that allows collaboration among multiple investigators and institutions.

Patients enrolled in the Hospitalist Project are administered two separate interviews, one during their hospitalization and one 30 days after discharge. The results are recorded during the patient encounter using iPads connected to a custom-written web application. This information is stored in an SQL server database, from which it can be exported with a custom-built reporting system into SAS and Stata for analysis. This year, the CRI’s Clinical and Translational team updated the database and web-based interface for this project.

The CCP initiative is a randomized study started in 2012 with the aim of testing novel care delivery systems for improving the quality and reducing the cost of health care. The study’s hypothesis is that improving continuity in the doctor-patient relationship by having a single physician see patients at high risk of hospitalization in both inpatient and outpatient settings will improve outcomes and lower costs by reducing unnecessary emergency department visits, hospital admissions, and readmissions.

The CRI has supported this effort by creating a custom dashboard that serves as a central location for CCP staff and physicians to record study information on patients and integrate this information with data from electronic medical records. In addition to the dashboard, the CRI has implemented a notification system that sends pages and emails to the appropriate CCP physicians and staff when a patient enrolled to the CCP protocol visits the emergency department or is admitted to the hospital.


cri.uchicago.edu 25

SYSTEMS & SECURITY


The Systems and Security team began

with just two members and a limited

infrastructure set up by the Initiative in

Biomedical Informatics. It has now grown

to include five full-time employees who

support and manage the development

of infrastructure in multiple data centers.

The team has grown our computing envi-

ronment considerably since its inception

with generous support from the Institute

for Translational Medicine and the BSD.

The purpose of the Systems and Secu-

rity team is to provide core services and

scientific computing resources with the

highest quality of customer service, in

order to enable BSD faculty to conduct

advanced biological research in a com-

pliant environment while simultaneously

protecting intellectual property and sen-

sitive information.


Director of Systems and SecurityPlamen Martinov

our leadership

Plamen joined the CRI leadership team as Director of Systems and Security in April 2013 and manages the team of engineers responsible for the development and operations of our secure computing infrastructure. He leads our efforts to ensure compliance with security regulations and provides regular reports to the Research Informatics Compliance Review and Technical Policy Committees. Prior to joining the CRI, Plamen was Lead Data Security Engineer for Chicago Biomedicine Information Systems.

About Us


cri.uchicago.edu 29

The CRI’s resources, which have been

upgraded and expanded over the past

year, include:

• 1,024-core high-performance com-

puting (HPC) cluster (2.2 GHz AMD

Opteron 6274)

• Large Memory Linux supercomputer

with 1 TB of RAM, 8 Intel® Xeon®

E7-8870 2.4 GHz processors (160

cores)

• 700-TB ultra-high-density NAS for

data storage that can scale up to 20

PB, available for both labshares and

individuals

• Virtual Server Infrastructure with

the capacity to support up to 1,500

virtual servers on Windows or Linux

platforms

• Centralized and automated data

backup and encryption with the

capability to back up 2.1 PB of data

• Galaxy web-enabled biomedical data

analytics tool that is fully integrated

with the CRI’s HPC cluster

Infrastructure

Storage & Backup By the Numbers

files backed up

total labshare capacity

total backup capacity

virtual infrastructure total storage

854,597,057

1.7 petabytes

2.5 petabytes

110 terabytes



Genetics

Health Studies

Cellular Screening Center

Laboratory for Advanced Computing

Cardiology

Pediatrics

Clinical & Translational Informatics

Bioinformatics Core

Clinical Cancer Genetics

Childhood Cancer & Blood Diseases

Medicine Administration

Radiology, HIRO

Academic & Administrative Applications

CRI Infrastructure

10 6050403020

Who uses our virtual machines? Our VMs in Kenwood Data Center serve 11 different BSD groups, in addition to supporting CRI activities.

Total VMs

125

The Systems and Security team main-

tains the computing infrastructure that

supports not only the CRI’s activities but

also research for faculty across the BSD.

These new HIPAA-compliant resources

went live in November 2012 and are

available to all members of the BSD.

To date, our resources are supporting a

total of 479 active users: 279 users of our

storage resources, 162 users of our HPC

cluster, and 38 Galaxy users. Kenwood

Data Center houses 125 virtual machines,

with 350 TB of storage in use and 595 TB

of data backed up.

cri.uchicago.edu 31


Highlighted Accomplishments from 2012-13our contributions

• Made a new HPC cluster and large memory servers available to all BSD researchers

• Launched a VMware farm and began provisioning virtual machines for researchers

• Migrated labshares from outdated equipment to a new state-of-the-art data center

• Introduced the CRI help desk and created an online technical help portal to direct users to the correct sources of information

• Hired Plamen as Director and expanded the team by hiring four systems administrators and a security analyst

• Created detailed security procedures to demonstrate HIPAA compliance

• Worked with the Compliance Review Committee to establish policies and procedures for patient privacy and data security

• In collaboration with the Bioinformatics Core, released the CRI’s implementation of Galaxy



Kenwood Data CenterThe CRI’s advanced computing resources

are housed in the state-of-the-art Ken-

wood Data Center on the University of

Chicago campus. The CRI has made sub-

stantial investments in superior, resilient

technology at Kenwood, improving the

security, reliability, and recoverability

of system resources through the mod-

ernization of data center services and

standard architecture.

A primary focus of the Systems and Secu-

rity team over the past year has been the

migration of users’ data from outdated

equipment in the Prudential Data Center

to the newer, better-equipped Kenwood

Data Center. The closing of Prudential

and the move to Kenwood will allow us

to shift our investments to more efficient

and standardized computing platforms

and technologies. The targets for com-

pleting this move include:

• Virtualizing and migrating more than

80 servers

• Migrating 80 labshares and 300

home directories

• Adding an additional 1,024-core HPC

cluster

• Adding two 1-TB Large Memory

Servers

Migration has proceeded carefully over

the course of a year to achieve the goals

of protecting the integrity of all data

and ensuring clear communication with

users. As of August 2013, 64 labshares

(55 TB) out of a total of 75 (79 TB) have

been migrated. All home directories have

been migrated to new servers, and the

team is on track to migrate 10 servers per

month. The completion of this project is

expected by the end of 2013.

Kenwood Data Center is equipped to

house systems that are compliant with

federal guidelines, including HIPAA and

the Federal Information Security Man-

agement Act (FISMA). Moving all CRI

resources to this facility helps us to pro-

tect patient privacy and keep our data

secure.

650

600

550

500

450

400

350

300

250

200

150

100

50

0

iBi Clus

ter

iBi Big

Memory

Large M

emory

Labsha

res

Home D

irecto

ries

Storag

e

Server

Backup

HPC

2,368

Total Data Center Users

Kenwood

Prudential


cri.uchicago.edu 33



Who uses our labshare storage resources? More than 30 different departments and groups across

the University store data on CRI-provided labshares.

Ben MayBiochemistry & Molecular Biophysics

BioinformaticsBiomedical Sciences Cluster

Cancer ResearchCell & Molecular BiologyCellular Screening Center

Center for Clinical Cancer GeneticsChicago Booth School

Childhood Cancer & Blood DiseasesEcology & Evolution

Endocrinology, Diabetes, & MetabolismEvolutionary Biology

Genetic MedicineGenetics & Clinical Cytogenetics

Health StudiesHematology/Oncology

Human GeneticsInstitutional Biosafety

Internal MedicineLaboratory - Human Genetics

MedicineMolecular Genetics & Cell Biology

NeurobiologyNeuroscience

Obstetrics & GynecologyPathology

Pulmonary/Critical CareRheumatology

Science & EducationSurgery

0 10,000 GB

20,000 GB

30,000 GB

80,000 GB

Total Storage Used

151,791 GB

cri.uchicago.edu 35


To complement our improved computing

infrastructure, the Systems and Security

team has made several important steps

over the past year to enhance customer

service and technical support for users

of our resources.

The CRI’s help desk was opened in sum-

mer 2012 with phone and email support

staffed by employees who either resolve

or triage issues. Concurrently, we intro-

duced a new, easier-to-use system for

submitting trouble tickets. Including

Technical Support

Systems and Security team members Beth Lynn Eicher, Sneha Jha, Plamen Martinov, Olumide Kehinde, Dan Sullivan, Brad Orr, Mike Jarsulic, and Bruce Thompson



working through the initial backlog of

unresolved tickets, the support staff

has now resolved almost ten thousand

issues. The CRI also created a web portal

to make it easier for users to find sources

of technical help.

In addition, the Systems and Security

team hosted several events throughout

the year to educate users about CRI

resources and specific issues. See IT Live!

seminars in November and December

highlighted our HPC cluster, Galaxy, and

i2b2, with each seminar focused on a live

demonstration of one resource. In March

and April, the team hosted HPC Lunch

& Learn events tailored to existing and

potential HPC users, both to introduce

our newest resources and spread the

word about our migration to Kenwood.

For more detail, see pages 57-58.

Bruce Thompson and Beth Lynn

Eicher in Kenwood Data Center


cri.uchicago.edu 37

Fabrice Smieliauskas, PhD, is a health economist whose research interests cen-ter on the operation of markets for medical technologies. His work includes studies of financial conflicts of interest in medicine and of disparities in the adoption and abandonment of new medical technologies. Dr. Smieliauskas primarily uses SAS and Stata to perform statistical analyses for his research.

The focus of Dr. Smieliauskas’s ongoing work is the evidence base for new medical technologies. He is analyzing the response of payers and providers to evidence that a common medical treatment is of limited value to patients, as well as the response to state and federal policies that mandate coverage of drugs for “off-label” indica-tions not approved by the FDA. He is also developing a unique comprehensive data-base on clinical cancer trials in order to address several open research questions, including the effects of a variety of gov-ernmental and institutional policies on the rate and direction of cancer innovation.

Dr. Smieliauskas’s research has been enabled in part by the CRI’s Large Mem-ory Server. Before moving his work to the CRI’s infrastructure, he encountered problems using servers that were not capable of handling the large memory requirements of his research. He was deterred from other potential options by high user fees and inability to handle sensitive data in compliance with HIPAA. “By contrast,” he noted, “the new CRI server is able to handle confidential data securely, essential to much of the research at the BSD.”

Dr. Smieliauskas also spoke positively about the support provided by the Sys-tems and Security team, saying, “The server administrative team is friendly and responds promptly to user needs and requests. I also have great con-fidence in CRI management and their desire and ability to continue adding capacity and computing capabilities as they grow.”

faculty spotlight

Fabrice Smieliauskas

Plamen Martinov and Olumide Kehinde in Kenwood Data Center



Data Security and Compliance

Secure handling of sensitive human sub-

ject data is of the utmost importance to

the CRI’s Systems and Security team. The

CRI is the primary computing resource

for BSD researchers working with

electronic protected health information

(ePHI). For this reason, it is essential that

our infrastructure and security policies

comply with relevant federal guidelines,

including HIPAA.


cri.uchicago.edu 39


• Redesign and implement secure, stable, and sustainable computing infrastructure and resources at Kenwood Data Center

• Complete the Prudential-to-Kenwood data center move by migrating or discontinuing all resources, while maintaining the integrity of all user data

• Update and deliver improved customer service policies, procedures, services, and automation

• Improve communication internally and within the user community

• Enhance the skill set of each team member and of the team as a whole

To this end, the Research Informatics

Compliance Review Committee, made

up of IT security professionals from

other IT organizations across the Uni-

versity, spent several months drafting,

editing, and approving a set of policies

and procedures for data protection. This

committee is also responsible for con-

ducting regular audits to ensure com-

pliance to these important standards.

(For more information on this commit-

tee, see page 63.) In addition, the CRI

retains experts in FISMA and HIPAA as

consultants.

BIOINFORMATICS CORE

Bioinformatics Core

The analysis that transforms high-

throughput raw data into biologically

meaningful information can present a

challenge to clinical, translational, and

basic researchers alike. To make it easier

for BSD investigators to take full advan-

tage of high-throughput technologies in

their research, the Bioinformatics Core

has developed a set of pipelines for the

analysis of Next-Generation Sequencing

and Microarray data.

These automated pipelines quickly

absorb and process large amounts of raw

data and produce meaningful analysis

results. They are executed on the CRI’s

high-performance computing (HPC)

cluster, which provides the significant

Bioinformatics Analysis Pipelines


Director of BioinformaticsJorge Andrade, PhD

our leadership

As the technical director responsible for planning and oversight of the Bioinformatics Core, Jorge works closely with CRI leadership to develop and deliver bioinformatics services and expertise. Jorge joined the CRI in May 2012 and brings extensive experience in the pharmaceutical industry and scientific research community, most recently at the Beijing Genome Institute, where he was an Associate Director.

Bioinformatics Core

computational power necessary for

working with such large quantities of

data. Researchers interested in using

one of the CRI’s pipelines for their data

analysis can request this on the CRI

website. The Core currently offers a

total of 12 production-ready pipelines

for a variety of platforms and analyses.

In addition, the Bioinformatics Core

maintains a catalog of publicly-available

and commercial software tools, refer-

ence datasets, and databases for use by

the BSD research community. A com-

plete list of these resources is available

on the CRI’s website.

cri.uchicago.edu 43

Illumina pipelines for RNA-Seq, ChIP-Seq, Exome Sequencing, Whole Genome Re-Sequencing (WGRS), Consensus Genotyping, and De-Novo Assembly

SOLiD pipelines for RNA-Seq, WGRS, ChIP-Seq, and De-Novo Assembly

One pipeline for Illumina and Affymetrix Expression Arrays

One pipeline for Affymetrix and Exiquon miRNA Arrays

For more information on what each of these pipelines offers, see Appendix B.

The Core currently offers production-ready pipelines for the following platforms and analyses:

Bioinformatics Core


Kenan Onel, MD, PhD, is an Associate Professor of Pediatrics in the Section of Hematology/Oncology and Director of the Pediatric Familial Cancer Clinic. He is an expert on pediatric and other familial genetic cancer syndromes. The Onel Lab uses genomic platforms and systems biology strategies to investi-gate how genetics contribute to cancer risk and response to therapy.

The lab studies families with high-penetrance cancer-predispos-ing conditions, but no known can-cer-predisposing gene mutations, in order to discover new genes that may, when mutated, predispose individuals to cancer. Recently, they have begun to advance this research by taking advantage of the CRI’s Next-Generation Sequencing offerings. Dr. Onel reports, “The Bioinformatics Core has been in-strumental in pushing forward our work because of their expertise in handling genomic data.”

Dr. Onel’s lab used the CRI’s Galaxy instance to develop a pipeline for exome analysis. In addition, they worked with the CRI’s team of bio-informaticians to develop a power-ful command-line pipeline utilizing multiple aligners and callers, allowing a robust analysis over a large number of family studies. The Onel Lab and the CRI bioinformaticians continue to meet weekly to discuss progress.

According to Dr. Onel, “The analysts have been intellectually engaged in the projects and extremely professional. They have helped us develop methods for analysis of family data that we could not have done on our own.”

faculty spotlight

Kenan Onel

cri.uchicago.edu 45

Bioinformatics Core

For researchers interested in self-

service data analysis, the CRI maintains

a customized version of Galaxy, an

open-source bioinformatics workflow

management and system integration

tool. The CRI’s Galaxy instance is inte-

grated with our advanced computing

infrastructure, allowing researchers

to take advantage of our HPC and

large-scale storage resources within a

self-service data analysis environment.

Galaxy can substantially facilitate the

use of common bioinformatics tools by

non-bioinformaticians and those without

extensive computing expertise.

Highlighted Accomplishments from 2012-13our contributions

• Developed, tested, and implemented 12 production-ready pipelines, some of which are currently in use for the NIH-funded Bionimbus Protected Data Cloud contract

• Expanded the Core to a team of seven scientists

• Hosted monthly training seminars which have drawn over 350 total participants

• Developed a project management and invoicing system now used as a template by other BSD Cores

• Launched the CRI’s implementation of Galaxy

Self-Service Data Analysis: Galaxy

Bioinformatics Core


A selection of completed analysis projects illustrates the diversity of the research facilitated by the Bioinformatics Core:

Genome assembly and annotation of the Siberian hamster genome, using SOLiD sequences generated at the University of Chicago Genomics Core facility

ChIP-Seq data analysis for a project studying how hyperglycemia induces epigenetic changes that lead to renal injury

A gene expression profile analysis of the rat brain in response to perimenopausal hormonal signals

RNA-Seq analysis of differential gene expression between two types of melanoma tumors

Quality trimming of large sets of Illumina sequences for a study of nasal microbiota of people with chronic allergies

Exome-wide analysis of 60 samples from four cohorts for research on the genetic components of several cancer types

The CRI’s implementation of the Galaxy

framework includes workflows for several

Next-Generation Sequencing pipelines

to enable users to perform, reproduce,

and share complete analyses.

Available workflows in Galaxy include:

• RNA-Seq: Sample Level for quality

control, mapping, and statistics for

paired-end Illumina reads (individual

samples)

• RNA-Seq: Project Level Merge for

merging multiple samples and gen-

erating a differentially expressed

list, for both single- and paired-end

Illumina reads

• Exome Sequencing Analysis for qual-

ity control, mapping, and recalibra-

tion for both single- and paired-end

Illumina reads

The CRI’s Galaxy platform became

available to researchers in November

2012, concurrent with the release of our

updated HPC and storage resources. It

now supports around 40 active users

and is maintained and updated with

new tools, workflows, and pipelines in

collaboration with the CRI’s Systems and

Security team.

cri.uchicago.edu 47

Bioinformatics Core

Bioinformatics Core team members Jorge Andrade, Wenjun Kang, Riyue Bao, Jianpeng Xu, Chunling Zhang, and Lei Huang

Bioinformatics Core

For researchers who are looking for

personalized analysis, including cus-

tom-built pipelines, the Bioinformatics

Core provides consulting and custom-

ized services. Our bioinformaticians’

expertise extends to areas beyond those

of our standard pipelines, including pro-

teomics and genome-wide association

studies.

Collaboration and Custom Analysis

Ben MayBiochemistry

Molecular BiologyEcology & Evolution

External OrganizationsHealth Studies

Human GeneticsMedicine

MicrobiologyMolecular Genetics

NeurobiologyNeurology

Obstetrics & GynecologyOrganismal Biology

PathologyPediatrics

Radiation OncologySocial Sciences

Surgery

Total Project Requests

995 3025201510

Who uses the Bioinformatics Core? Since May 2012, the Core has received project requests from 18 different University departments and several external organizations.


Bioinformatics Core

When a researcher submits an online

project request form, the Core returns a

proposal, including the scope of deliver-

ables, a timeline for completion, and the

estimated cost. The execution of each

project is guided by frequent discussion

between researchers and bioinformati-

cians, and updates are provided regularly.

When a project is complete, results are

delivered in the form of a written report

and presentation.

Since May 2012, the Core’s bioinfor-

maticians have completed a total of 53

projects, with many more in progress. An

average of seven new project requests

are submitted each month. These proj-

ects, conducted for researchers from

over 25 different University departments

and sections, vary widely in both scope

and subject matter (for examples, see

sidebar on page 46).

Sept. 2012

Oct. 2012

Nov. 2012

Dec. 2012

Jan. 2013

Feb. 2013

Mar. 2013

Apr. 2013

May 2013

June 2013

July 2013

in progress

completed

submitted

The Bioinformatics Core has completed 53 projects since May 2012, with 24 currently in progress and new requests submitted each month.

Total Projects

Completed

53

10 6050403020

cri.uchicago.edu 49


Bioinformatics Core

Director of Bioinformatics Jorge Andrade

The Bioinformatics Core supports the

creation of research grants in several

ways, with the goal of fully developing

and integrating the bioinformatics com-

ponents of each grant and increasing

its competitiveness for funding. CRI

bioinformaticians can collaborate with

researchers directly on the bioinformat-

ics components of their grants, or they

can provide cost analysis services and

letters of support. In addition, standard

language is available to be added to

grants, documenting the accessibility

of the necessary tools and expertise to

complete the bioinformatics research

indicated. The Core has so far contrib-

uted to the writing and submission of 13

research grants, and has established this

as an area of focus for future growth.

One more important part of the Core’s

mission is to provide training opportuni-

ties that will help investigators develop

bioinformatics expertise within their own

laboratories. To this end, the CRI hosts a

free monthly training seminar open to all

members of the BSD, covering a differ-

ent topic in bioinformatics analysis each

month. For more detail and a list of past

topics, see pages 54-55.

Other Services: Grant Analysis and Training

cri.uchicago.edu 51

Bioinformatics Core


• Recruit and hire two additional Bioinformatics Scientists

• Improve efficiency by reducing the standard turnaround time of projects in the following production pipelines: Exome-Seq, RNA-Seq, and Microarray expression arrays

• Increase customer satisfaction by producing high-quality and customer-oriented services (to this end, the Core has already introduced a feedback survey to gather information on potential areas of improvement)

• Improve existing pipelines by performing comparative analysis of tools, and develop new pipelines to accommodate new technologies, protocols, and data types

• Continue to author and coauthor scientific publications

• Increase interest in the Core by developing advertising materials and meeting with department chairs

• Increase the Core’s funding through chargebacks, grant inclusion, and expanding internal and external collaboration

Bioinformatics Core


Ernst Lengyel, MD, PhD, is a Professor of Obstetrics/Gynecology, specializing in advanced surgical treatments for patients with ovarian cancer. The Lengyel Lab is dedicated to studying the biology of ovarian cancer metastasis and finding new drugs for its treatment.

One of the scientific goals of the Lengyel Lab is to understand the mecha-nisms of a common problem in the treatment of ovarian cancer: that most

patients will develop a resistance to carboplatin and taxol chemotherapy. To study this, the lab sought to identify the miRNA expression profiles of chemore-sistant versus chemosensitive patients. They worked with the CRI’s Bioinfor-matics Core to obtain and analyze these genomic data.

With the assistance of the CRI’s bioin-formaticians, the lab mined the Cancer Genome Atlas (TCGA) and distinguished unique patient groups of chemosen-sitive and chemoresistant patients. They then performed six analysis sets, and were able to identify seven miRNA genes upregulated in chemoresistant

disease and three in very chemosensitive disease. These findings have since been validated in an independent cohort of patients.

The Lengyel Lab’s findings, enabled in part by the CRI, have prognostic and functional implications that may aid in developing therapies to target these miRNA in chemoresistant patients. Dr. Lengyel said, “Without the CRI we would not have had the expertise to take advantage of the TCGA ovarian cancer data.”

faculty spotlight

Ernst Lengyel

TRAINING & EDUCATION



An integral part of the CRI’s mission is providing training and education for our users so that they become comfortable and confident both with our resources and with other technologies for biological computing.

The Bioinformatics Core presents a free

training seminar with a different topic

each month, taught by PhD bioinforma-

ticians. These seminars cover the use

and application of a variety of publicly

and commercially available software

and tools for bioinformatics analysis—R,

Bioconductor, and Galaxy, for example.

In some cases, the training is directly

tied in to CRI resources such as our

HPC cluster. As investigators bring this

education back to their laboratories,

bioinformatics expertise can be further

developed throughout the BSD. Since

these seminars began in May 2012, they

have attracted over 350 participants.

A post-training survey, introduced in

February 2013, requests opinions from

users after each seminar in an effort to

improve future sessions and cover the

topics most important to researchers.

Of those responding to the survey in

February through July 2013, 96 percent

found their course worthwhile, with 80

percent choosing “very” or “extremely”

worthwhile. The CRI’s bioinformaticians

have received high marks, with 96 per-

cent of respondents calling their instruc-

tors “very knowledgeable.” Overall, 92

percent of respondents reported satis-

faction with the course they attended.

Survey participants also provided sug-

gestions and requests for future seminar

topics, helping the Bioinformatics Core

to continue to design valuable training

opportunities that meet the needs of our

research community.

Bioinformatics Training


cri.uchicago.edu 55

Introduction to Linux Command Line for Bioinformatics

Introduction to Linux Command Line for Bioinformatics

Analyzing Illumina ChIP-Seq Data with the CRI

Introduction to CRI’s HPC Cluster for Bioinformatics Computing

Analysis of Illumina and Microarray Data with R and Bioconductor

Analysis of Microarrays with R and Bioconductor

Galaxy: Web-Based Bioinformatics Analysis and RNA-Seq Workflow Management

Analysis of Microarray Data with R and Bioconductor

Introduction to R

Analyzing Illumina RNA-Seq Data with the CRI

Analyzing Illumina Whole Exome Data with the CRI

Analyzing Illumina RNA-Seq Data with the CRI

Introduction to R and Execution on HPC

7/2013

6/2013

5/2013

4/2013

3/2013

2/2013

1/2013

11/2012

9/2012

8/2012

7/2012

6/2012

5/2012

24

37

32

34

12

25

22

31

40

41

16

12

25

date topic attendance

Past training seminars have covered a range of systems and software programs useful for bioinformatics analysis.



Other CRI Training

The CRI provides individual and small-

group training sessions upon request for

researchers who need assistance with

using REDCap for their studies. Julissa

Acevedo, the CRI’s Business Systems

Analyst, holds an average of eight train-

ing and demo sessions per month for

groups of one to three researchers at a

time.

In addition, the CRI hosted several events

over the past year with the goal of shar-

ing information about our computing

resources with existing and potential

users.

Three See IT Live! seminars were held in

November and December, aligning with

the release of new CRI resources. Each

seminar was centered on a live demon-

stration of the featured resource and

included an overview of the CRI, instruc-

tions on obtaining an account, and an

opportunity to meet our technical staff

and ask questions, as well as free refresh-

ments. These events were open to all

members of the BSD and were attended

by a total of 32 participants.

What bioinformatics training participants had to say...

“Very approachable and helpful instructors.” (June 2013)

“I thought it was really cool and I learned a lot about how to navigate around a Linux system. Great job!” (June 2013)

“Very helpful.” (April 2013)

“Well organized, very knowledgeable, and well presented.” (March 2013)

“Very good training class, need more like this.” (February 2013)


cri.uchicago.edu 57

See IT Live! sessions highlighted the

following resources:

Galaxy: Learn how to access Galaxy, a

web-based portal providing data stor-

age, data management, and analytical

tools integrated with our computing

resources

i2b2: Learn how to use our de-identified

datamart to identify cohorts and request

data for your research

HPC Cluster: Learn how to optimize and

run jobs on our new high-performance

computing cluster

Jorge Andrade presents a bioinformatics training seminar



Don Saner presents at the CRI’s first HPC Lunch & Learn

event

In addition to the HPC Cluster session

of See IT Live!, the CRI’s Systems and

Security team hosted two Lunch & Learn

events in the spring to further educate

HPC users about our available resources

and to provide an overview of the data

center migration from Prudential to

Kenwood. Each event included a discus-

sion of available resources in Kenwood,

the rationale and timeline for moving out

of Prudential, and a question and answer

session. These events were advertised to

both potential and current users and were

attended by a total of 32 participants.

FACULTY OVERSIGHT & GOVERNANCE



The CRI’s strategic decision-making and

long-term planning are led by a gover-

nance structure set up by the Office of the

CRIO. These committees guide research

informatics activities across the entire

BSD, ensuring that informed long-term

decisions for the Division are reached in

a transparent and accountable way.

Governance Structure

Research Informatics Executive Governance

Committee

Research Informatics Governance Committee

Research Informatics Technical Policy

Committee

Research Informatics Data Use Committee

Research Informatics Compliance Review

Committee


cri.uchicago.edu 61

The five committees outlined below

bring together senior BSD and University

of Chicago Medicine (UCM) leadership,

information systems experts, patient

privacy experts, and faculty represent-

ing basic science, clinical research,

and translational research. Decisions

from these committees guide us in

establishing policies and procedures,

prioritizing new initiatives, safeguarding

patient information, and complying with

BSD policies and applicable federal and

state laws.

For a full list of governance committee

membership, see Appendix C.

Research Informatics Executive Governance Committee

Dr. Kenneth Polonsky, Dean and Executive Vice President for Medical

Affairs

To provide high-level strategic decisions for all research informatics

activities across the BSD, integrating the needs of faculty, clinicians,

and BSD and hospital leadership

BSD and UCM executive leadership

Chair

Mission

Members




Dr. Robert Grossman, Chief Research Informatics Officer

To establish priorities and policies for research informatics across

the BSD, including those for the development and use of the CRDW

and the comprehensive computing resources provided to BSD

faculty

Senior faculty and staff leadership from across the BSD and UCM

Chair

Mission

Members

Research Informatics Technical Policy Committee

Dr. Robert Grossman, Chief Research Informatics Officer

To provide oversight and governance for the technical aspects of

research informatics across the BSD and to ensure appropriate

safeguards for ePHI used in research

Staff and faculty with expertise in informatics and information

technology security

Chair

Mission

Members


cri.uchicago.edu 63


Dr. Dana Edelson, Assistant Professor of Medicine

To review, approve, monitor, and prioritize requests for CRDW data

release to individual investigators and to approved datamarts and

systems, including i2b2 and any subsequently-developed datamarts

Staff and faculty with expertise in regulatory issues, compliance,

and data management

Chair

Mission

Members

Research Informatics Compliance Review Committee

Tyler DeNormandie, Information Systems Manager and Senior

Systems Engineer, Health Studies and Family Medicine

To advise the CRI Systems and Security group on best practices for

ensuring compliance with BSD policies and to help ensure the CRI’s

implementation of appropriate safeguards for ePHI used in research

Information technology security experts representing the major IT

organizations at the University and UCM

Chair

Mission

Members


Informatics Oversight Committee

Guidance and oversight for research

informatics throughout the BSD are

provided by the Informatics Oversight

Committee, made up of faculty leaders

representing both basic science and clin-

ical departments. The recommendations

of this committee guide us in ensuring

that the direction and activities of the CRI

are in line with the needs of the research

faculty we serve. This committee reports

to the Research Advisory Committee,

a BSD/UCM Committee that reports to

the Dean for Research and Graduate

Education.

The Informatics Oversight Committee is

chaired by Dr. John Cunningham, Chief

of the Section of Pediatric Hematology/

Oncology. For a full list of members, see

Appendix D.

Faculty Oversight

Research Advisory Committee

Office of the CRIO


cri.uchicago.edu 65

The Center for Research Informatics is grateful for the support of our strategic

partners and collaborators across the University of Chicago. These partners

enable the collaborative work that has made the CRI successful in our first years

of operations.

OUR PARTNERS

Biological Sciences Division bsd.uchicago.edu

Chicago Biomedicine Information Systems help.bsd.uchicago.edu

Comprehensive Cancer Center cancer.uchicago.edu

Computation Institute ci.uchicago.edu

Our Partners


Human Imaging Research Office hiro.bsd.uchicago.edu

Institute for Genomics & Systems Biology igsb.anl.gov

Institute for Translational Medicine itm.uchicago.edu

Institutional Review Board humansubjects.uchicago.edu

IT Services itservices.uchicago.edu

Office of Clinical Research bsdocr.bsd.uchicago.edu

The Center for Research Informatics has achieved many important goals over the past

two years. The establishment of the Clinical Research Data Warehouse, the design and

implementation of a state-of-the-art high-performance computing and storage infra-

structure that can house protected health information, and the development of a solid

and robust Bioinformatics Core are all providing the foundation of support for a large

number of research programs throughout the BSD. Many grants, papers, and research

projects owe part of their success to the services delivered by the CRI. Providing ser-

vices and training to enable high-quality scientific research was our goal when we were

established, and we are happy to have achieved this level of success in the short period

of time since the CRI was founded.

Building on these accomplishments, we plan to improve and expand our offerings in

several ways over the coming years:

Our Clinical Research Data Warehouse now serves BSD faculty by offering cohort dis-

covery tools able to search over millions of patient encounters. The next phase for the

CRDW will include the development of a de-identified datamart and tools for analyzing

de-identified data in a secure manner. We will further enhance the CRDW by including

full-text search functionality for pathology and radiology notes.

We are starting now to work with researchers to use data from the CRDW to build pre-

dictive models that produce alerts to improve hospital operations and quality of care.

From identifying patients at risk for readmission to the hospital to predicting which

patients may suffer a cardiac arrest while inpatient, we are leading the way for clinical

researchers to design, develop, and use complex alerts in their practice. We are working

closely with CBIS to ensure that we will be able to implement alert notifications within

the Epic electronic medical record.

LOOKING AHEAD

cri.uchicago.edu 67

Institute for Genomics & Systems Biology igsb.anl.gov

IT Services itservices.uchicago.edu

Office of Clinical Research bsdocr.bsd.uchicago.edu

In the next year we will further expand our high-performance computational resources

to provide increased capacity, functionality, and performance with the goal of ensur-

ing that all faculty have access to agile and advanced computing. Coupled with these

efforts, we will expand our training and educational offerings to enable more faculty to

leverage these computing tools to enhance their research.

The CRI is fully invested in advancing world-class research within the Biological Sciences

Division. Our successes thus far and our ambitious plan going forward demonstrate our

commitment to this goal.

Looking Ahead


A CRI weekly planning meeting

APPENDIX


Appendix

Appendix A: CRI Staff List

Samuel Volchenboum, MD, PhD

Director & Associate CRIO

Administration

Hannah Lawrence

Executive Administrator

Michael Daus

Administrative Specialist

Caitlin Pike

Communication Specialist

Bioinformatics Core

Jorge Andrade, PhD

Director of Bioinformatics

Riyue Bao, PhD

Bioinformatician

Elizabeth Bartom, PhD

Bioinformatician

Kyle Hernandez, PhD

Bioinformatician

Lei Huang, PhD

Bioinformatician

Wenjun Kang, MS

Scientific Programmer

Jianpeng Xu, PhD

Bioinformatician

Chunling Zhang, PhD

Bioinformatician


Don Saner

Director of Clinical and Translational

Informatics

Julissa Acevedo

Business Systems Analyst

Seong Choi

Programmer

Tiffany Cyrus

Project Manager

Keith Danahey

Database/Systems Administrator and

Programmer

Brian Furner

Manager of Programming

Timothy Holper

Manager of CRDW Development

Kevin Le

Programmer/Analyst

Luis Maciel

Database Administrator


Plamen Martinov

Director of Systems and Security

Andy Brook

Senior Systems Administrator

Beth Lynn Eicher


Michael Jarsulic


Sneha Jha

Systems Administrator

Olumide Kehinde


Brad Orr

Senior Project Manager

Bruce Thompson

Security Analyst

cri.uchicago.edu 71

Appendix

Appendix B: Bioinformatics Core Pipelines

Illumina

RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Expression Quantification, Differentially Expressed Genes, Pathways, and Gene Ontology Analysis

ChiP-Seq: Raw Data QC, Filtering, Mapping, Peak Calling, Peak Differential Analysis, Peak Related Genes Analysis, Gene Ontology Analysis, and Annotation

Exome Sequencing: Raw Data QC, Filtering, Mapping, Genotyping, SNP Detection, InDel Detec-tion, and Annotation

Whole Genome Re-Sequencing (WGRS): Raw Data QC, Filtering, Mapping, Genotyping, SNP Detection, InDel Detection, SV (Somatic SV) Detection, CNV Analysis, and Annotation

Consensus Genotyping Pipeline: Genotyping, SNP Detection & InDel Detection using three different methods (Samtools, GATK, and Atlas-2), comparison of variant calls, list of consensus call variants, and list of method specific calls

De-Novo Assembly: Raw Data QC, Merging, Clipping, Filtering, Contigs Assembly, Scaffold Assembly, Assemble Statistics, and Downstream Analysis

SOLiD

RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Expression Quantification, Differentially Expressed Genes, Pathways, and Gene Ontology Analysis

Whole Genome Re-Sequencing (WGRS): Raw Data QC, Filtering, Mapping, Genotyping, SNP Detection, InDel Detection, SV (Somatic SV) Detection, CNV Analysis, and Annotation

ChiP-Seq: Raw Data QC, Filtering, Mapping, Peak Calling, Peak Differential Analysis, Peak Related Genes Analysis, Gene Ontology Analysis, and Annotation

De-Novo Assembly: Raw Data QC, Merging, Clipping, Filtering, Contigs Assembly, Scaffold Assembly, Assemble Statistics, and Downstream Analysis

Illumina and Affymetrix Expression Arrays

Filtering, Data Summarization and Normalization, Sample/Gene/Probe-based QC, Differentially Expressed Genes, Functional Annotation, and Pathway Enrichment Analysis

Affymetrix and Exiquon miRNA Arrays

Filtering, Data Summarization and Normalization, Sample/Gene/Probe-based QC, Differentially Expressed miRNAs, Predict miRNA Targeted Genes, Functional Annotation, and Pathway Enrichment Analysis


Appendix

Appendix C: Research Informatics Governance Committees

Kenneth Polonsky (Chair) Dean and Executive Vice President for Medical Affairs

Conrad Gilliam Dean for Research and Graduate Education

Robert Grossman Chief Research Informatics Officer, BSD

Sharon O’Keefe President, UCM

Eric Yablonka Vice President and Chief Information Officer, CBIS

Name Title and Affiliation(s)

Research Informatics Executive Governance Committee

Robert Grossman (Chair) Chief Research Informatics Officer, BSD

Sameer Badlani Chief Medical Information Officer, UCM

John Cunningham Chief, Section of Pediatric Hematology/Oncology

Chris Daugherty Chair, Institutional Review Board

Dana Edelson Assistant Professor of Medicine

Conrad Gilliam Dean for Research and Graduate Education

Marilyn Hanzal Associate General Counsel, Legal Affairs

Catherine Ostapina Senior Compliance Advisor & Director, Office of Corporate Compliance

Lainie Ross Professor of Pediatrics, Medicine, and Surgery

Julian Solway Associate Dean for Translational Medicine

Walter Stadler Associate Dean for Clinical Research

Samuel Volchenboum Director, CRI

Eric Yablonka Vice President and Chief Information Officer, CBIS



cri.uchicago.edu 73

Appendix

Robert Grossman (Chair) Chief Research Informatics Officer, BSD

Paul Chang Professor of Radiology; Vice Chair of Radiology Informatics

Tyler DeNormandie Information Systems Manager and Senior Systems Engineer, Health Studies

Roger Engelmann Image Analysis Software Developer, Human Imaging Research Office

Rajan Gopalakrishnan Director for Informatics and Information Technology, Comprehensive Cancer Center

John Moses Director of Enterprise Architecture and New Technologies, UCM

Prasanna Nippani Assistant Director of Information Technology, UCM

Don Saner (Co-Chair) Director of Clinical and Translational Informatics, CRI



Research Informatics Technical Policy Committee



Dana Edelson (Chair) Assistant Professor of Medicine

Samuel Armato Associate Professor of Radiology

Rajan Gopalakrishnan Director for Informatics and Information Technology, Comprehensive Cancer Center

Nick Gruszauskas Technical Director, Human Imaging Research Office

Contessa Hsu Application Manager, UCM

Millie Maleckar Director of Regulatory Compliance for Human Subjects, Institutional Review Board

Prasanna Nippani Assistant Director of Information Technology, UCM

Don Saner Director of Clinical and Translational Informatics, CRI

Phil Schumm Senior Biostatistician, Health Studies; Director, Research Computing Group

Cassie Simon Assistant Director, UCM Cancer Registry

Appendix


Tyler DeNormandie (Chair) Information Systems Manager and Senior Systems Engineer, Health Studies

James Clark Network Security Officer, IT Services

Andrew Kramski Infrastructure Security Engineer, UCM

Plamen Martinov Director of Systems and Security, CRI

Catherine Ostapina Senior Compliance Advisor & Director, Office of Corporate Compliance

Daniel Sullivan Web Developer and Infrastructure Architect Specialist, CBIS

Bruce Thompson Security Analyst, CRI


Research Informatics Compliance Review Committee

Appendix D: Faculty Oversight


John Cunningham (Chair) Chief, Section of Pediatric Hematology/Oncology

Michael Glotzer Professor of Molecular Genetics and Cell Biology

Robert Grossman Chief Research Informatics Officer, BSD

Michelle Le Beau Director, Comprehensive Cancer Center

Marsha Rosner Chair, Ben May Department for Cancer Research

Robert Rosner Professor of Astronomy/Astrophysics and Physics

Matthew Stephens Professor of Human Genetics and Statistics

Ronald Thisted Professor of Statistics, Health Studies, and Anesthesia/Critical Care


Informatics Oversight Committee

© The University of Chicago, 2013. All rights reserved.

Written and designed by Caitlin Pike.

Photography by Robert Kozloff.

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CRI Annual Report 2012-2013

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