Bioinformatics Program

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Bioinformatics Program Projects

Here are some of the projects that the Bioinformatics Program has developed:



The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal, as stated in RFA: HL-99-013, is the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.

RGD's continued and expanding collaborative efforts with other databases and laboratories around the world allows researchers to access the most current, complete set of rat genomic and genetic data available, as well as the most innovative tools for analyzing this data.


Supporting clinical research through medical informatics, the Bioinformatics Program has spent the past several years developing a database and application infrastructure to support clinical research and outcomes analysis throughout MCW, Froedtert Hospital, and Children’s Hospital. The Bioinformatics Program's Clinical Research team works with these institutions to create new studies,  import existing data, and develop meaningful analytical and reporting tools. The Generic Clinical Research Database (GCRD) consists of a common database schema, security infrastructure, web application, and reporting engine.  Individual studies can take advantage of the existing application, as well as customize GCRD for their own study-specific requirements.  Researchers who wish to link their study specific data to patient data will soon be able to take advantage of the Clinical Repository which will contain patient data such as demographics, diagnoses, procedures, and lab results.

In addition to clinical research, GCRD has been adapted for use in performing outcomes analysis. Within Froedtert Hospital, this system is called Quality Control Management or QCM. The QCM database and web application assists physicians in the collection and management of their patient data.  A reporting engine is utilized by Froedtert staff to build quality control reports for internal consumption as well as external reporting needs.

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The Faculty Collaboration Database (FCD) was developed to foster collaboration between faculty members of the Medical College of Wisconsin and to support and enhance the research advances, patient care needs, educational excellence and business requirements of the College. The FCD was initiated by the Faculty Career Development committee, the CTSI (Clinical and Translational Science Institute) and the Office of Research and developed by the staff of the MCW Bioinformatics program.


The Influenza Primer Design Resource (IPDR) is designed to aid researchers in translating the vast amounts of influenza sequence information into highly effective influenza diagnostics. IPDR consists of a database of all influenza nucleotide sequences (updated weekly) and a variety of bioinformatic analyses that aid in the development of primers and probes used in diagnostic assays.


The MCW fMRI (functional magnetic resonance imaging) database was developed to help fMRI investigators manage and more profitably use the large amounts of continually generated information pertaining to study subjects and fMRI sessions.  This database and web application stores and manages imaging data, survey responses, demographics, and session data, providing the neuroscience community with a wealth of information regarding past and current FMRI experiments conducted at MCW.


Physiogenomics of Stressors in Derived Consomic Rats (PGA/PhysGen)

Funded by National Heart, Lung, and Blood Institute (NHLBI), U01 HL66579, the PhysGen program capitalizes on a variety of technological advances, extending data by manipulating specific genes and assessing the results physiologically in different genetic backgrounds.


SNP Repository/Analysis

For those interested in adding a genetic component to their studies, they can take advantage of the Single-Nucleotide Polymorphism (SNP) database, which contains genetic variations that can be linked back to subject records in the Generic Clinical Research Database.  Dr. Ulrich Broeckel, MD,  brings together the clinical and genetic data for disease-specific analysis and works with developers in the Bioinformatics Program to populate the SNP database.


Clinical Repository

The Clinical Repository System is a data warehouse of all patient data collected from various Children’s Hospital of Wisconsin systems.  It is currently in the design phase and will allow researchers to securely access data in a consistent manner.



Past Projects


Contact us for more information on how we can assist you with your project.
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Page Updated 11/21/2013