The Center for Biomedical Informatics (CBMI) offers software tools to facilitate biomedical research. These tools allow investigators to store, integrate, query, analyze, and visualize complex clinical and molecular data sets. The CBMI provides comprehensive training resources and facilitates collaborative studies for the identification of diagnostic and prognostic biomarkers and the subsequent development of personalized therapies.
The CBMI focuses on Biomedical Informatics (BMI) as an academic discipline and as a facilitator of a broad range of research projects and their application to evidence-based changes in the treatment and management of patients.
Services & Resources
Consultation
Initial consultations, training sessions, and basic use of applications are fully subsidized for ICTS members.
General Tools
- Genome annotation tools allow researchers to find annotation for genes or microarray probes.
- The Clinical Investigation Data Exploration Repository (CIDER) contains routine patient care (inpatient and outpatient) data to help investigators rapidly convert novel advances in basic science to patient care, and it provides quick feedback on customized diagnostics and therapeutics for further refinements in the laboratory.
- Through the Promoter Analysis Pipeline (PAP) investigators can determine significant transcription factor binding sites in the non-coding region of genes (the PAP has been developed to allow for the analysis of a set of co-expressed genes and the prediction of their transcriptional regulatory mechanisms). Log in or sign up.
Microarray Data Management and Analysis
- The Molecular Informatics Portal (MIP) for microarray data retrieval and analysis allows registered users to download raw data files and annotated microarray chip data sets (providing access to the latest genomic annotation from Gene Ontology, Entrez Gene, UniGene, and others). The MIP offers centralized storage, management, and access of Affymetrix microarray expression and SNP genotyping (chips that are processed at the Genome technology Access Center are uploaded onto CBMI servers, and researchers can then download their chips via a web interface). Log in or sign up.
- Function Express and SpotFire offer access to microarray analysis applications; these software tools are available to facilitate microarray analysis.
- Consultation on microarray expression and SNP analyses (copy number and LOH) are provided on a fee for service basis.
Sequence Analysis
- Centralized storage and management of medical re-sequencing or mutation profiling data.
- The Mutation Profiling Pipeline provides automated analysis of medical re-sequencing or mutation profiling data.
Biospecimen Inventory Management
- Consultation on use of the biospecimen management system Tissue Suite (caTissue) can aid with migration of legacy biospecimen inventory and tracking data as well as to utilize Tissue Suite for prospective biospecimen collection purposes.
Consultation for Clinical Study Data Management
- Consultation on clinical study or trial data capture and modeling through ClinPortal, and its companion application for electronic form creation, Clinical Study Designer (CSD).
For a complete listing please go to the Center For Biomedical Informatics website.
Facilities & Other Resources
Access the standard description of CBMI facilities and other resources for grant application purposes.