Bioinformatics


Platform services

Bioimage analysis
High Through-Put Data Analysis
Structural Bioinformatics
In Silico Modeling and SimulationIn Silico Modeling and Simulation
Data Storage, Computational Infrastructure and Bioinformatics Software Development
Services Provided In Collaboration With European Bioinformatics Infrastructure 

Contacts


Novel, large-scale measurement techniques are used routinely in bio- and medical sciences. To fully harness the power of these techniques, and translate the large data sets generated by these methods to biological information, the data need to be collected, managed, and analysed.                                

To address these needs a wide spectrum of bioinformatics services are provided by the bioinformatics network. Services range from pure big data management and analysis to large scale modelling and simulation tasks and consultation.                        

At each Biocenter, the local bioinformatics team is the primary contact point for the service. In addition, national helpdesk mailing list (Tämä sähköpostiosoite on suojattu spamboteilta. Tarvitset JavaScript-tuen nähdäksesi sen.) is available that reaches all biocenters and the group with most expertise will answer your questions. See Contacts


BIOIMAGE ANALYSIS

Biological imaging related bioinformatics services are provided by FIMM and BMT.

Microscopy image analysis recognition and quantification for static and video images as well as image analysis for high-content image analysis, such as high-content screening – BMT.

Basic data processing pipelines that handle and annotate the data from high throughput RNAi and chemical screens – FIMM.


HIGH THROUGH-PUT DATA ANALYSIS

Genome-wide methods related bioinformatics services are provided by BCH, BCK, BCT, BI, FIMM and BMT.

Human (and other species with reference genome) genomics (identification and annotation of somatic mutations and germline variants, copy number variation, structural rearrangements) – FIMM, BI, BCT, BMT.

Bacterial community genomics, transcriptomics and metaproteomics and analysis of species without reference genome – BI, BCT, FIMM.

mRNA expression analysis (gene and isoform level and pathway analysis) – BCT, FIMM, BCH, BMT, BCK, BI.

Small-RNA expression – BCK, FIMM, BCT, BMT.

Epigenetics applications - BCT.

Single cell measurements:The bioinformaticsnetwork members actively develop methods to analyse single-cell RNA-seq and whole-genome data in collaboration with single-cell data producers and bioinformaticians outside the network – BCH, BCT, BMT, FIMM.

Cell free DNA analysis and liquid biomarkers identification – BMT.

Mass spectrometry based proteomics data analysis – BCT, BMT.

Translational NGS analysis for personalized medicine applications: identification of human genomic variation of clinical relevance at the individual level. Identification and annotation of human genomic variation of clinical relevance from trio- or case-control exome-sequencing datasets, discovery of clinically relevant somatic mutations from tumor and patient-matched normal exome-sequencing datasets, and discovery of clinically relevant fusion-genes from RNA-sequencing data – FIMM.


STRUCTURAL BIOINFORMATICS

Structural biology services are provided by BCO, BCT and BI.

In silico modelling and simulation – BCO, BCT.

Protein homology modelling, structural analysis, ligand interaction analysis, in silico screening for potential ligands – BCT.

Evolutionary analysis – BCT, BI


IN SILICO MODELING AND SIMULATION

Computational tool development for unsolved problems – BCT, BCO.

Computer modeling and simulation techniques are important tools for studying the properties of biomolecules and their interactions with other compounds. Whereas bioinformatics is mostly concerned with the statistical analysis of large biological data sets, computer simulations are applied with the objective of explaining the behavior of a given physical system. For such a purpose, a representative theoretical model is developed that includes the most important degrees of freedom of the system. In the course of a computer simulation, an appropriate algorithm advances the state (i.e. the combined values of the degrees of freedom) of the model, resulting in a set of observations (time series, “trajectory” or an ensemble of states) from which relevant system properties are computed. As these properties are based on a theoretical model, they immediately provide insight into the behavior of the actual physical system. Computer simulations also provide a means to carry out “what if” scenarios for studying the response of the system if one aspect is changed, e.g. protein residue mutation studies, change in protonation states, removal of a compound from a chemical network, binding events, and so forth. Some of the computed properties are also measurable by experiment, so that the theoretical model can be immediately validated.

BCO takes advantage of these methods and provides Collaboration-as-a-Service (CaaS) for the analysis of biological systems using sophisticated and advanced in silico modelling and simulation technologies. BCO also offers software development services.


DATA STORAGE, COMPUTATIONAL INFRASTRUCTURE AND BIOINFORMATICS SOFTWARE DEVELOPMENT  

Environment for data storage and computational analysis: FIMM, BCH, BCT, BI, BCK, and BMT.

Bioinformatics network members will serve the local data storage and computational analysis needs by combining the on-site, truly local, infrastructure with the off-site, virtual infrastructure offered by CSC over the high speed data links.

BI provides general web based analysis pipelines.

BMT provides interactive web based data visualization and analysis services for user datasets.

BCT provides software tools for various data analysis needs; and full scientific IT support – infrastructure and technical – for the biocenter and BF networks.


SERVICES PROVIDED IN COLLABORATION WITH EUROPEAN BIOINFORMATICS INFRASTRUCTURE

ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.

Services from international bioinformatics collaborators

http://www.elixir-europe.org/platforms

See Also http://www.ebi.ac.uk and http://www.sib.swiss/

The Finland ELIXIR Node (ELIXIR-FI) is operated by CSC - IT Center for Science Ltd and is part of the Biocenter Finland Bioinformatics Network. Service specialisation currently focuses on (secure) scientific cloud services, user authentication and data access services to the national and international life science community. ELIXIR-FI Node also co-leads ELIXIR Compute platform.

Node service specialisation

Service name

Description

Host institute

Responsible Contact

Year of establishment

Life Cycle state

Associated ELIXIR Platform

Cloud services

IaaS cloud services accessed via Internet or private network connections https://research.csc.fi/cloud-computing

CSC cloud services and datacenters are ISO27001 compliant (current status).

Access to service is free for national research use.  The pricing information for other kind  usage is available at: https://research.csc.fi/pricing-of-computing-services

CSC

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Product owners: Jussi Heikonen

2014, 2015

Mature

Compute

CSC Chipster

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. http://chipster.csc.fi/

CSC publicly provides Chipster virtual machine images.

http://chipster.github.io/chipster/

Chipster is available as a service for national use, for international use via EGI FedCloud and can be provided for other users and industry using CSC Cloud https://research.csc.fi/pricing-of-computing-services

CSC

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Product owner:

Eija Korpelainen

ELIXIR EGI Competence Center lead:

Kimmo Mattila

2005

Emerging

Compute, Tools

AAI - Identity and Access

Authorization and authentication infrastructure services (AAI) of ELIXIR.

https://www.elixir-europe.org/services/compute/aai

With ELIXIR ID Users – students, researchers and citizens – can employ their academic, corporate or social media identity IDs assigned to them when logging into numerous ELIXIR services.

The Finnish Node provides and develops AAI services in co-operation with the Czech Node.

https://www.elixir-europe.org/services/compute/aai

https://www.csc.fi/identity-and-access-management

CSC

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Manager: Manne Miettinen

Senior expert:

Mikael Linden

2014

HAKA Identity Federation 2005

Mature

Compute

AAI - REMS

CSC develops and hosts an open source tool REMS to assist a DAC to manage Data Access Applications and access rights to sensitive datasets. REMS is a key component in ELIXIR AAI.

http://www.csc.fi/rems

CSC

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Product owner: Tommi Jalkanen

Mikael Linden

2013

Mature

Compute

Training and Events

Courses in bioinformatics and HPC at CSC are open for academics, government and industry participants.

https://www.csc.fi/web/training

CSC

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Product owner: Jussi Enkovaara

Eija Korpelainen

1971

Mature

Training

Collections and registries from the Finnish population: SISU data resource

Finland ELIXIR Node supports national data custodians (biobanks) in building a data resource for Sequence Initiative Suomi and affiliated projects

http://www.sisuproject.fi/

Institute for Molecular Medicine Finland - FIMM

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Ilkka Lappalainen, Timo Miettinen (FIMM)

n/a

Emerging

Data

 See also www.csc.fi


CONTACT PERSONS

Platform coordinator
Matti Nykter / tel. +358 50 318 6869 / matti.nykter (at) uta.fi
Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere
Bioinformatics helpdesk that reaches service provides listed below: Tämä sähköpostiosoite on suojattu spamboteilta. Tarvitset JavaScript-tuen nähdäksesi sen.

Partners
Jussi Paananen (BCK) http://www.uef.fi/web/bioinformaticsAndré Juffer (BCO) http://www.oulu.fi/biocenter/biocomputing-and-bioinformaticsSampsa Hautaniemi (BCH) http://research.med.helsinki.fi/sysbio/Imre Västrik, Matti Kankainen (FIMM) https://www.fimm.fi/en/services/technology-centre/bioinformaticsLiisa Holm (BI) http://ekhidna2.biocenter.helsinki.fi/Matti Nykter (BMT) http://cofa.uta.fi/bioinformatics.htmlMark Johnson (BCT) http://www.abo.fi/fakultet/en/biokemisblLaura Elo (BCT) https://www.btk.fi/bioinformatics/front-page/Tommi Nyrönen (ELIXIR-FI) http://www.elixir-europe.org and www.csc.fi