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Services:Bioinformatics

Services

Experiment design

  • The Bioinformatics Core is available to help you design microarray and sequencing experiments, including appropriate number of replicates, choice of arrays, and choice of controls.

Data analysis

  • We can analyze your data, assist you with analysis, or teach you how to analyze your data yourself using academic or commercial analysis software. We can help you choose appropriate analysis methods and tools, and can provide access to popular analysis programs.
  • See also Sequencing Analysis Services for specifics

Grant applications and publications

  • We are happy to review or contribute to the microarray or sequencing portion of grant applications and manuscripts, including the analysis of preliminary data and preparation of figures.

Array annotation

  • In some cases the Core can provide additional annotation (e.g. pathways, Gene Ontology, or homolgy to other organisms) for microarray data sets.

Custom array design

  • The Agilent oligonucleotide microarray platform supports custom microarray designs. The Bioinformatics Core can assist with probe selection and annotation for custom arrays.

Custom algorithm/ software design

  • As part of our analysis services, the core develops many software tools for custom analysis. These are released as part of several open source projects. See USeq, TiMAT2, GNomEx, and GenoViz.

Public database submissions

  • Publication in top-tier journals frequently requires submission of microarray or sequencing data to a public database such as GEO or ArrayExpress. We can assist you with the submission of array descriptions, experiment descriptions, and data.

Computing Resources

  • The Bioinformatics Core has access to 6 large Linux server class machines which we use for general analysis (3 8-processor machine with 32G RAM, and 2 4-processor machines with 16G RAM each). The Core purchased and makes use of a 13 node / 156 processor cluster at the Center for High Performance Computing for more compute-intensive sequence analysis. The core also purchased a high-performance Macintosh kiosk workstation for genomic visualizations that is available for external use. Contact the core for details.

Contacting Us

  • If you have an analysis request, you may submit a request using an online submission form.
  • You may also view a current list of open requests and their assigned owners.
  • if you have a general question, you can contact the core directly at BioInformaticsCore.