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Services

The UEF Bioinformatics Center provides infrastructure, data analysis and consultancy services and training. The UEF Bioinformatic Center has expertise especially in processing data from different omics methodologies and service coverage includes i.a. experimental design, data analysis, data visualization, workflow development and training. The BIC offers services particularly for the UEF research community but services are also available for other Finnish research institutions and non-academic customers. The project requests are evaluated together with customer based on available expertise, feasibility and available resources. A detailed report describing the analysis tools and methods used together with analysis results is provided at the end of each project. The data are analyzed using widely used freely available tools and published or in-house developed workflows. The infrastructure services and training are provided free of charge, but the data analysis and consultancy services are charged based on project fees and actual working hours. The data analysis services are available in two different categories: Basic and Advanced.

Contribution of The UEF Binformatics Center to scientific publication is to be acknowledged in the each article. See more detailed information regarding citing and acknowledgement from Acknowledge or cite.

Basic analysis service

Basic analysis service covers standardized but configurable analysis of genomics or transcriptomics sequencing data generated by using Illumina sequencing technology, either single-end or paired-end. Also array based genotype data analyses are supported.

  • Genomics
    • Quality control and preprocessing
    • Alignment and alignment postprocessing
    • Germline or somatic variant calling (SNVs and InDels)
    • Variant annotation and filtering
  • Transcriptomics
    • Quality control and preprocessing
    • Alignment and alignment postprocessing
    • Gene expression quantification and quality control
    • Data exploration (e.g. visualization, clustering)
    • Differential gene expression analysis (RNA-seq)
    • Chromatin and gene regulation analysis (ChIP-seq, ATAC-seq)
  • Genotypes
    • Quality control and preprocessing
    • Association testing between variants and few phenotypes (GWAS)

Advanced analysis service

Advanced analysis service includes the same standard analysis as basic service, but provides also additional and customized analyses that will be adjusted for each individual project's needs. Also singe-cell sequencing data analyses are supported.

  • Genomics
    • Advanced variant calling (CNVs and SVs)
    • Customized annotation and filtering
    • Advanced genome-wide result browser (Bravo)
  • Transcriptomics
    • Customized gene expression analysis and visualization
    • Enrichment and pathway analysis
  • Genotypes
    • Genotype imputation and quality control
    • Phenome-wide association testing (PheWAS)
    • Customized statistical analysis
    • Advanced genome-wide result browser (PheWeb)
  • Single-cell sequencing (10x Genomics platform)
    • Gene expression and regulation data analysis
  • Method development
    • New or customized analysis workflow design and development

Project and user fees

Prices (VAT 0%) for all different service options for both internal UEF and external customers are given below. In principal billing is based on project fees and actual working hours. The final price of the service may vary based on the size and complexity of the project. The costs will be estimated separately for each project and agreed with customer before initialization of the project. To request a quote, please contact the UEF Bioinformatcs Center (Contact information).

Infrastructure service Price UEF
(VAT 0%)
Price Other
(VAT 0%)
solu.uef.fi: interactive computing server free na
sampo.uef.fi: High-Performance Computing cluster free na
Basic analysis service Price UEF
(VAT 0%)
Price Other
(VAT 0%)
Project initialization and standard data analysis
- includes 10 hours of work
480€ 860€
- additional work 48€/h 86€/h
Advanced analysis service Price UEF
(VAT 0%)
Price Other
(VAT 0%)
Project initialization, customized data analysis
- includes 20 hours of work
960€ 1720€
- additional work 48€/h 86€/h
Consulting and Training Price UEF
(VAT 0%)
Price Other
(VAT 0%)
Bioinformatics consultation
- data analysis and management, experiment design etc.
48€/h 86€/h
Pre-configured server or container installation
- includes 2 hours of work
96€/pcs 172€/pcs
Customized, bespoken server or container installation with project special requirements
- includes 10 hours of work
480€/pcs 860€/pcs
Textual description of required data analysis and data management plan for grant applications 150€/page 300€/page
Workshop or face-to-face training on topics upon request 48€/h 86€/h
Mentoring within Faculty of Health Sciences
- mentoring session biannually for PhD students who performs significant amount of data analysis applying bioinformatics methods (1 hour/session)
- other researchers or additional mentoring

free

48€/h

na

na

Request service

Please use the service request form to suggest or request paid or free service from UEF Bioinformatics Center: Service Request Form.

home/services.txt · Last modified: 09.09.2020 16:30 by Juha Kekäläinen