Bioinformatics Shared Resource (BSR)
BSR offers services related to genomic sequence and expression. The BSR is located in the Hills Building and staffed by Julie Dragon, Ramiro Barrantes and Marni Slavik. More than 50 clients gain access to our services through their association
with the University of Vermont or outside institutions. Our services can be funded through grants or fee-for-service mechanisms.
Services
Services of the BSR include design and analysis of oligonucleotide microarray (Affymetrix GeneChip) and massively parallel sequencing
(
Illumina HiSeq), or MPS, experiments. Services associated with MPS support genomic sequencing, exome sequencing, ChIP-Seq, and RNA-Seq. Downstream services
include exploratory multivariate analysis, linear modeling, system biological analyses, data analysis workshops, text describing methodology/figures for manuscripts, and deposition of data in a public database.
Computing Services
Computing and secure long-term storage resources are provided by the University of Vermont Enterprise Technology Services (ETS) and University of Vermont's Advanced Computing Core (VACC).
Rates
We collaborate with other arms of the Vermont Integrative Genomics Resource (VIGR) to provide support for a comprehensive process that includes experiment design, data acquisition, primary analysis, secondary analysis, and publication. "Primary
analysis" refers to massively parallel sequencing (MPS) services through to sequence alignments: de-multiplexing, adaptor clipping/trimming, sequence alignment, and quality assessment. "Secondary analysis" refers to calculation of response
variables for both microarray and MPS experiments (expression statistics, sequence variants and peak intensities), univariate/multivariate statistical analysis, and interpretation of response variables in the context of information about human
genetic variation, the functional consequences of variation, and biological systems.
Hourly Rate-Based Services
Hourly rate-based analytical services are $130/hour for internal investigators, and $190/hour for external investigators. The following services are included in this rate:
- (1 hour minimum is required for BSR analysis services; no charge for first hour)
- Primary analysis
- Secondary analysis
- Grant support
- Publication support
Education
Methods in Bioinformatics is a 3 credit course that provides a methodological survey of bioinformatics techniques. Particular emphasis is given to popular bioinformatics applications. Topics include genome sequencing, gene expression, protein
structure, metagenomics, and phylogenetics, as well as activities utilizing relevant software to analyze bioinformatics data.