#Services

The UEF Bioinformatics Center provides infrastructure, data analysis, consultancy and training services. The Bioinformatic Center has expertise especially in processing data from different omics methodologies and service coverage includes e.g. experimental design, data analysis, data visualization and workflow development. The Bioinformatics Center primarily 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. Reports describing the analysis tools and methods used together with analysis results are 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.

Contribution of the Bioinformatics Center to scientific publications is to be acknowledged in the each article. See more detailed information regarding citing and acknowledgement from [[guides:cite|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.

UEF Bioinformatics Center collaborates with THL Biobank to offer genetic imputation service using a Finnish haplotype reference panel [[https://thl.fi/en/web/thl-biobank/for-researchers/sample-collections/thl-biobank-imputation-reference-panel|SISu v3 of the THL Biobank]]. Interested parties should [[https://link.webropolsurveys.com/Participation/Public/41725caf-746e-4d66-8982-f60ee2f9f689?displayId=Fin2069414|request the service]] from BIC and apply for a usage permission from the THL Biobank [[https://thl.fi/en/research-and-development/thl-biobank/contact-information|admin.biobank (at) thl.fi]]

* **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
  - Customized genome-wide result browser (PheWeb), example [[http://r4.finngen.fi/pheno/G6_ALZHEIMER|FinnGen Release 4, Alzheimer disease]].
* **Single-cell sequencing (10x Genomics platform)**
  - Gene expression and regulation data analysis
  - Customized single-cell gene expression browser (UCSC Cell Browser), example [[https://cells.ucsc.edu/?ds=covid19-immuno%2Fall|COVID-19 Immunological Response]].
* **Method development**
  - New or customized analysis workflow design and development

##Project and user fees

Prices (VAT 0%) for 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 ([[home:contact|Contact information]]). 


^Infrastructure service                                 ^   Price UEF\\ (VAT 0%)^  Price Other\\ (VAT 0%)^
|tuma.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     |  510€|  890€|
| - additional work|  51€/h|  89€/h|


^Advanced analysis service                                                 ^  Price UEF\\ (VAT 0%)^  Price Other\\ (VAT 0%)^		
|Project initialization, customized data analysis\\  - includes 20 hours of work     |  1020€|  1780€|
| - additional work|  51€/h|  89€/h|

^Consulting and Training                                             ^   Price UEF\\ (VAT 0%)^  Price Other\\ (VAT 0%)^		
|Bioinformatics consultation\\  - data analysis and management, experiment design etc. |  51€/h|  89€/h|
|Genomic study consultation and coordination\\  - study design, budgeting, choice of genotyping/sequencing provider, bioinformatics etc. |  51€/h|  89€/h|
|Pre-configured server or container installation\\  - includes 2 hours of work     |  102€/pcs|  178€/pcs|
|Customized, bespoken server or container installation with project special requirements\\  - includes 10 hours of work |     51€/pcs|         890€/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  |  51€/h|  89€/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\\ \\ 51€/h|  \\ na\\ \\ na|

## Request service

Please use the service request form to suggest or request paid or free service from UEF Bioinformatics Center: [[https://link.webropolsurveys.com/S/EDDEDAD2661BC306|Service Request Form]].