Contact | University of Hawai'i | John A. Burns School of Medicine

 

Services/Service Fees

The Bioinformatics Core Facility provides the following services in hopes of building and maintaining an infrastructure that enables the applications of strong informatics solutions:

  1. Consultation
  2. Data Analysis
  3. Grant Support
  4. Data Management Service
  5. Collaborative Research
  6. Service Fees

Consultation

Experimental Design and Power Calculations – We highly encourage you to consult our bioinformatician prior to experiments to find a solution that fits your needs and budget. We will help design your experiments to obtain maximum leverage and perform data quality control checks for high-throughput data projects.

Liaison with vendors: We will help identify the right product to ensure the quality of your research.

Data Analysis
    • AI and Machine Learning
    • Next Generation Sequence Analysis
      • Assembly and gene annotation
      • DNA-Seq
      • RNA-Seq including fusion gene and LncRNA
      • Small RNA-Seq
      • Chip-Seq
      • Target-Seq
      • Meth-Seq
      • Metagenomics
    • Microarray data analysis
      • Gene expression
      • Exon array for alternative splicing
      • SNP array, GWIS
      • miRNA array
      • DNA methylation array
      • CNV
    • Proteomics data and Protein array
      • Protein mass-spec data for protein expression and interaction
      • Phosphor-screen
      • Glycol-screen
      • PTM (post translation modicication) Profilling
    • Metobolomics data analysis
        • Lipidomics
        • Sugar profiling
        • Entire metabolomics data analysis
  • Multivariate biomarker identification and classification
    • Feature selection algorithms
    • Classification algorithms
  • Gene pattern, function analysis, systems biology
    • Gene and sample correlation and clustering analysis
    • Gene enrichment analysis
    • Gene ontology and pathway analysis
    • Gene network analysis
    • Integrative “omics” data analysis
  • Image data analysis
  • Single Cell Sequencing
  • Nanostring Data Analysis

Grant Support 

We will provide hardware and software support for UH researchers who plan to conduct preliminary data analysis for hypothesis development and testing as part of grant proposal writing. We will provide necessary guidance to include computational biological methods to analyze data in your research analysis plan. Letters of support for your grant proposal can be prepared upon request.

Data Management Service

We will provide data management services and develop a web-based database for collection, storage, integration, and management of clinical data and scientific research data.

Collaborative Research

We are involved in collaborative research of several principal investigators from different UH departments and campuses. We perform bioinformatics data analysis by running routine bioinformatics applications and custom programs developed specifically to fulfill our research objectives.

Hourly Charges:

Type of Service UH Rate
Examples:

  • General exploratory analysis
  • Additional statistical analysis
  • Data visualization for publication
  • NIH GEO/SRA sequence submission
  • Custom-designed pipeline or workflow
  • Machine learning strategy
  • Other data types not included in the standardized workflow listed in standardized services, or data with uncommon reference genomes
  • $120/hr

Standardized Services with Estimated Times:

Type of Service Estimated Time Example Output
RNA-seq 8 hours (Up to 10 samples)
Additional samples: 0.6 hrs/sample 		Mapping stats, gene-level expression table, isoform-level expression table, differential analysis results with figures
RNA-seq microbial 15 hours (Up to 10 samples)
Additional samples: 1.2 hrs/sample 		Mapping stats, species-level abundance table, differential analysis results with figures
WGS/DNA-seq 20 hours (Up to 10 samples)
Additional samples: 1.6 hrs/sample 		VCF, MAF
ChIP-Seq 10 hours (Up to 6 samples)
Additional samples: 1.5 hrs/sample 		Peak Calling Results, Annotation
ATAC-seq 15 hours (Up to 6 samples)
Additional samples: 2 hrs/sample 		Peak Calling Results, Visualization Tracks
10x genomics single-cell gene expression 6 hours (Up to 2 samples)
Additional samples: 2 hrs/sample 		General report from 10x genomics, initial clustering, and biomarker identification
Metagenomics – WGS 15 hours (Up to 10 samples)
Additional samples: 1.2 hrs/sample 		OTU table, diversity analysis, functional analysis, differential analysis
Metagenomics – 16S 6 hours (Up to 10 samples)
Additional samples: 0.5 hrs/sample 		OTU table, diversity analysis, differential analysis
DNA methylation sequencing 15 hours (Up to 6 samples)
Additional samples: 2 hrs/sample 		Gene expression table, initial differential analysis
DNA methylation Microarray 6 hours (Up to 10 samples)
Additional samples: 0.5 hrs/sample 		Gene-level expression table, isoform-level expression table, differential analysis results with figures
Note: The time required for your project can be influenced by various factors, including data quality, species and genome complexity, and downstream analysis requirements. Please consult with the core facility for more accurate time and rate estimations. Rates may be subsidized for early investigators and projects supported by infrastructural grants such as INBRE, Ola HAWAII, COBRE, PIKO and UHCC.

 

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