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National Bioinformatics Infrastructure Sweden - NBIS

NBIS (National Bioinformatics Infrastructure Sweden) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities and the Knut and Alice Wallenberg Foundation, providing state-of-the-art bioinformatics to the Swedish researchers in Life Sciences. NBIS is also the Swedish contact point to the European infrastructure for biological information ELIXIR.

The Challenge

NBIS is predominantly offering bioinformatics support in various projects, depending on the user needs. In the projects, the NBIS persons are working close to the research group, and they spend part of their time teaching the users in order to propagate the bioinformatics knowledge. Present NBIS staff has expertise in protein bioinformatics, mass spectrometry (MS), next-generation sequencing (NGS), large-scale data handling and integration, metagenomics, systems biology, biostatistics and RNAseq. 

More specifically, NBIS offers:

  • High-quality training programs aimed at the Swedish Life Science research community provide a standard to follow when handling and analysing bioinformatics data. The training follows up-to-date best practices for effective teaching, using Open and FAIR training materials. Moreover, our training is inclusive and meets the needs of the research community in terms of accessibility.
  • Infrastructure and tools for bioinformatics analyses in order to facilitate these analyses for the users.

The solution

The NBIS compute and storage facility hosted at Uppsala Multidisciplinary Center for Advanced Computational Science (SNIC-UPPMAX) provides high-performance computing and storage resources, maintain relevant bioinformatics software and data, and offer associated user support.  Starting from December 2015, EGI is contributing with additional pledged resources to allow the bioinformatics community to use Cloud Computing and Online Storage services needed to develop portals for Life Science researchers worldwide.

The NBIS toolkits are based on:

  • A web page front end to the services exposed to the users.
  • A backend consisting of a variety of software and scripts.
  • The EGI computing and storage resources such as the EGI Cloud Compute and the EGI Online Storage to host some of the NBIS portals.

Services from EGI

EGI Cloud Compute

Run virtual machines on-demand with complete control over computing resources.

EGI Online Storage

Store, share and access your files and their metadata on a global scale.

EGI Check-in

Login with your own credentials

Training and consultancy

Dedicated computing and storage for training and education and consultancy activities

Impact

Pconsc3.net

239 active users over the last 6 years

ProQ3

1,677 active users over the last 6 years

BOCTOPUS

2,464 active users over the last 6 years

subcons

427 active users over the last 6 years

topcons2

28,634 active users over the last 6 years

scampi2

1,056 active users over the last 6 years

>1,513,594 millions of (Cloud) CPU hours

over the last 6 years

260 VMs

instantiated in the EGI Federated Cloud infrastructure over the last 6 years

2M (Cloud) CPU hours

over the last two years

Highlights

NBIS Toolkits

TOPCONS: Consensus prediction of membrane protein topology and signal peptide.

SubCons: An ensemble method for human subcellular localization predictions.

PconsC3: A method for accurate contact prediction for all family sizes.

SCAMPI: Prediction of membrane protein topology from first principles.

BOCTOPUS: Topology prediction of transmembrane beta-barrel proteins.

ProQ3: Model Quality Assessment using Rosetta energy, and deep learning.

NBIS Training

NBIS offers a spectrum of training events, ranging from introductory classes to advanced workshops, e.g. on R and Python programming, general high-throughput sequencing data analysis, RNA-seq and single-cell RNA-seq.

NBIS also provides a 2-year advisory program for PhD students interested in having a bioinformatics expert as an additional mentor.

Nanjiang Shu, Deputy Head of System Development at NBIS, says: 

“We appreciate the robust service provided by EGI during the past few years of collaboration. I believe more and more researchers will benefit from the work powered by the services provided by EGI.”

Participating Partners