Bioinformatics Shared Resource (BSR)
BSR offers services related to genomic sequence and expression. 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 the following:
* Design and analysis next generation sequencing experiments: long and short read and hybrid.
* Support for analysis of genomic sequencing analysis, exome sequencing, ChIP-Seq, RNA-Seq and metagenomics.
* Data mining and custom analysis of bioinformatics data
* 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 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).
Deliverables
We provide support for a comprehensive process that includes experiment design, data acquisition, primary analysis, secondary analysis, and publication. "Primary
analysis" refers to next generation sequencing services through to sequence alignments: de-multiplexing, adaptor clipping/trimming, sequence alignment, counts matrix, and quality assessment. "Secondary analysis" refers to calculation of response
variables for next-gen 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.
The deliverables for other types of analyses will be decided on a case-by-case basis.
Rates
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:
- Primary analysis
- Secondary analysis
- Custom analysis
- Training
- Grant support
- Publication support
Education
Bioinformatics & Data Analysis is a 3 credit course that provides a broad overview of bioinformatics as applied to biomedical research and human health. This course includes a total of three units which are broadly categorized as: data mining and accessing data from genomic databases, DNA sequencing, and introduction to transcriptomics. This course emphasizes a direct, hands-on experience. As such, most classes are 75% lecture and 25% hands-on.
Advanced Bioinformatics is a 3 credit course that provides advanced training in bioinformatic tools and techniques. This course includes a total of four units which are broadly categorized as: advanced genomic data processing and analysis, metagenomics, variant calling, and advanced transcriptomics. Other topics such as data integration, biological data interpretation, R and UNIX-based scripting, and systems biology will be covered. This course emphasizes a direct, hands-on experience. As such, most classes are 50% lecture and 50% in-class application with data analysis tools applying the concepts covered in the previous lectures.