Services

Please click on the following link to place orders for OSUCCC Shared Resources:

 

 

The Biomedical Informatics Shared Resource (BISR) offers OSUCCC investigators expertise and critical services designed to advance cancer research quality by supporting high-throughput, novel experiments that link multi-dimensional phenotypic and bio-molecular data sets to disseminate innovative cancer research conclusions.

Through utilization of state-of-the-art informatics platforms and methods related to science, clinical and translational research, OSUCCC investigators have access to highly specialized services and computing platforms not typically available otherwise.

Computational Biology Consultation

Computational Biology Consultation provides researchers with:

Data Analytic Pipeline Creation

Data Analytic Pipeline Creation assists researchers with:

Custom Research Management & Support Tools

The OSUCCC has developed several novel data management tools designed to integrate with the data sharing service, creating an optimal flow of data. 

The BISR-created program QUEST organizes data, allows the addition of metadata and controls security access. The directory can be made visible to OSUCCC investigators, who can also request access in collaboration with the data owner. 

Additionally, the BISR develops novel data management interfaces for the CALGB consortium and for the OSUCCC Mouse Phenotype Shared Resource. 

Massively Parallel Sequence Analysis
The sequence output from the Illumina Genome Analyzer II consists of 10-40 million sequence tags of 30-50 bp in length.

The sequencer output is useful to biologists when the BISR provides several standard data transformations. The BISR provides two classes of service for the sequence analysis: 1) an automated pipeline from the sequencing machine to map sequence tags on the appropriate genome and to provide results in a file format using the UCSC genome browser; 2) a sequencing application based on the ChIP-seq technique. This analysis includes peak-finding algorithms, normalization of experiments and comparison to find differences. It enables the identification of condition-specific enrichment of genome locations.

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Analysis of Microarray Methods
The Analysis of Microarray Methods includes mRNA (Affymetrix), SNP and micro-RNA.
Microarray methods results are first analyzed by the Biostatistics Shared Resource to identify genes/probes that have significantly changed expression level in the assay. The BISR not only provides downstream analysis of identifying pathways enriched in the results, but it also helps with data presentation and results submission in public databases.

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Publicly Available Datasets Analysis
The Gene Expression Omnibus (GEO) is one of the world’s largest databases in which primary data from nearly all published microarray experiments are stored. The BISR staff analyzes this publicly available data with the biologist.

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Analysis of qRT-PCR Results
qRT-PCR is a major application in the Nucleic Acids Shared Resource. The BISR supports the results of this analysis, which helps choose control genes, normalize results across experiments and determine changes in gene expression for a number of test genes.

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Pathway & Network Analysis of Results from Microarray and Sequencing Results
Microarray results and sequencing results identify genes that have gene expression change or are bound by a specific protein. The BISR is licensed for the Ingenuity Pathway Analysis program, which enables the identification of biological pathways and networks that are enriched in results. The pathway analysis assists the biologist with navigating the large numbers of gene hits, and it can generate new hypotheses for the biologist to test in the laboratory.

Additionally, the BISR can provide advanced network analysis, such as co-expression network analysis, gene regulatory and interaction network analysis, and dense network motif discovery.

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Image Analysis
Image analysis, including 3D reconstruction, deconvolution and de-noising, offers a variety of image analysis tools to facilitate microscopic image presentation or to make interpretations that otherwise would not be apparent on the original image because of technical limitations.

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Additional Bioinformatics Analysis
A variety of other bioinformatics analyses are available to OSUCCC investigators, including mapping of amino acid residues on 3D structures, threading polypeptides onto known structures of homologous proteins, Genbank searches, BLAST and motif searches.

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caGrid
The implementation of caGrid data service wrappers enables secure, bi-directional access to the data sources. 

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Modeling, Annotation and Curation of Core Data Sources

Modeling, semantic annotation and curation of core data sources includes databases and data sources associated with Shared Resources and investigator projects and laboratories, as well as enterprise systems such as Electronic Health Records, Clinical Trial Management Systems, bio-specimen management systems and data warehouses.

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The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James) 300 W. 10th Ave. Columbus, OH 43210 Phone: 1-800-293-5066 | Email: jamesline@osumc.edu