Download resources page - Division of Biomedical Informatics

Cincinnati Children’s Hospital
November 2011
Informatics Core Resources to Support Research
Personal Computers: All investigators have hospital provided computers (minimum
- HP or Mac laptop or desktop with an Intel processor and 4GB memory), replaced
every three years with an upgraded model by the Hospital. All computers are
networked to CCHMC’s secure intranet and, via a firewall, to the Internet.
Computers are linked to the Hospital’s main system for authentication and remote
software install, as well as access to data storage. Each user is provided with a
personal charge-free quota of 10GB and divisional shared storage quota of 100GB
with a change-back for storage above this limit. Files on the servers or shared
storage are backed up nightly. CCHMC maintains licenses for all major statistical
packages, word processing, data presentation, and bibliographic software.
The Division of Biomedical Informatics (BMI) at CCHMC employs 12 faculty and 42
technical staff. It provides informatics support to programs of the Research
Foundation.
Data Center: The research data center is operated by BMI and is housed in a portion
of CCHMC’s state-of the- art 15,000 square foot, highly secure, institutional data
center that meets Tier 4 standards for reliability (redundant power and cooling
systems, remote site backup, etc.) and provides redundant, high bandwidth, fiber
connectivity between the University of Cincinnati and CCHMC networks, as well as
with Internet2. The secure environment permits compliance with numerous federal
and state regulations (e.g. HIPAA, NIH, DOD) as well as with security requirements
attached to many data access agreements. It has scalable storage capacity, which is
essential because of the regulatory requirements governing the length of time data
must be retained/archived. State of the art firewalls and systems for identity
management and access control are incorporated into management of the Data
Center, including interfaces between the Hospital and Research IT networks and
equipment. There is a dedicated staff of security experts who oversee both the
research and clinical systems.
Hardware:
• A 350+ CPU Linux cluster for parallel computation, including multi-core
AMD Opteron and Intel Xeon based servers with 4-64 GB or memory
• A Citrix farm of MS Windows servers serving remote desktop capabilities to
individual workstations
• A VMWare cluster of 450+ virtual machines running Windows and Linux
operating systems for testing and development environments as well as to
provide backup and redundant services.
• Dedicated mysql, MS SQL and Oracle database servers
• Dedicated redundant web servers
• A terabyte-scale storage facility, with currently over 500TB usable space,
with daily incremental and weekly full backups.
• Centralized authentication (LDAP and AD) servers, serving unique
usernames and passwords to all investigators
• Basic developer tools (compilers, debuggers, graphical developments
environments) and parallel computing software (MPI, PVM) are available.
Security: Significant resources including personnel, software, and hardware are
invested in ensuring data, facilities, and systems are secure. CCHMC employs
multiple layers of security at the policy, network, system, and application levels to
continuously monitor, respond, and improve security within environment. Security
measures include organizational security policies, in-line monitoring of activity for
attacks, multiple layers of firewalls both internally and externally, central
authentication and authorization, regular testing of systems and applications for
vulnerabilities, and regular risk assessments of the environment using current
standards (NIST 800-53, contracts, etc). These measures are continuously
evaluated and updated as risks to change to address changing threats and
requirements for the environment and to improve security of data hosted within the
CCHMC environment.
Data Storage: The Research Data Storage (RDS) system (600TB) in the Data Center
was designed to provide data storage for all research divisions. RDS provides
centralized, backed-up storage and has staff onsite 24x7. Several types of storage
are available: Institutionally supported enterprise storage -- i.e., personal, divisional
shared and project drives; Web-based storage systems for specific research data
types, e.g. genotype, microarray, flow cytometry. Other specialized storage includes
that required by the i2b2 Research Data Warehouse hosted on Oracle, storage for
VMWare clusters, cluster scratch space, and home directories for DMZ LDAP
accounts.
i2b2: BMI has implemented an enhanced version of the i2b2 (Informatics for
Integrating Biology and the Bedside) Research Patient Data Warehouse. i2b2 is a
scalable informatics data warehouse framework that enables the use of existing data
for cohort discovery research. i2b2 enjoys a wide international adoption by the
CTSA network, academic health centers, and industry. All of the data contained in
the hospital’s clinical information systems is available to the data warehouse. It
presently contains records on approximately 1 million patients. It has been
accruing data from the hospitals electronic health record (EHR), Epic, during its
implementation over the last 4 years. Approximately 60,000 new patients are
added each year, and information on existing patients is updated as they are cared
for in the institution. From the data warehouse investigators can retrieve: age, sex,
race, ethnicity, height, weight, temperature, blood pressure, medications, diagnoses,
laboratory values, and clinical notes (includes family and social history), and
discharge summaries. De-identified, limited, and fully identified data sets can be
made available, depending on investigator needs and IRB permissions. CCHMC
currently uses ICD9 diagnosis and CPT procedure codes as standard billing
terminology. We will migrate to ICD10 by the October 1, 2013 transition deadline.
Diagnosis records are coded using Intelligent Medical Objects, which lists over
200,000 problems and maps to standard terminologies like ICD- 9/10 and SNOMEDCT. CCHMC has piloted the use of the HL7 CCD to exchange summary documentation
with other area hospitals. It has an ongoing NLP (natural language processing)
project to map medical concepts within text documents to UMLS terminology.
Software: BMI offers centralized administration of >100 software packages, licensed
and open-source. A few examples include: for data capture and storage –
InfoPath/SharePoint, REDCap, OpenClinica, Oracle, FileMaker Pro, MS SQL Server,
MySQL, Toad; for statistical computing and numerical analysis – SAS, PSPP, JMP, JMP
Genomics, Matlab, Nquery, SPSS, R, SUDAAN; for genome wide association studies –
dprime, snpgwa, dandelion, IMPUTE, Plink/gPlink, Progeny, SOLAR; machine
learning – ILOG/CPLEX, Weka.
Software Development: The BMI software development group can assist
investigators in a number of areas, including: developing small- and large-scale
electronic data collection systems for research studies using languages such as C#,
.NET, Flash and PHP ; evaluating, hosting and customizing licensed and open-source
research software; designing databases and writing database queries; developing
research web sites compliant with industry and corporate standards. Technologies
include: Microsoft InfoPath/SharePoint; ASP/ASP.NET; Microsoft SQL Server;
PHP/MySQL; Oracle; Java/J2EE. Hosting: Servers are available in the Data Center
for hosting MySQL, Microsoft SQL Server, Oracle and FileMaker databases. Web
server configurations include Apache/Tomcat, IIS, SharePoint and Drupal.
High performance computing: BMI maintains a Linux-based computational cluster
in the Data Center that currently has over 350 processing cores and is
heterogeneous with both large-memory SMPs as well as low cost processing nodes.
Collaboration tools: Several options are available including a wiki, web-based
calendar, equipment booking system, mailing lists, Drupal and Microsoft SharePoint.
Biobank Core Facility: A substantial institutional commitment has been made to the
development of an institutional biobank, supervised by the Department of
Pathology. It contains tissues, DNA, serum, plasma, and cells. Staffing includes 2 FTE
for sample processing, 0.5 FTE for the director, and informatics support from BMI.
Physically, the Biobank occupies space in the R building adjacent to the main
Pathology department. A monitored alarm system for the freezers (-80 and liquid
nitrogen) and emergency generators to protect against power failure are supplied
by the Hospital. For sample tracking and management, the Biobank utilizes
“Biomaterial Tacking and Management” (BTM; Daedalus Inc, Cambridge, MA). BTM
is linked to the i2b2 data warehouse, allowing investigators to search for the
existence of samples using the i2b2.