Scalable bioinformatics web-servers powered by cloud computing
Wednesday, September 28, 2016 - 14:00
NBIS (National Bioinformatics Infrastructure Sweden, http://nbis.se, https://bils.se) is a distributed national research infrastructure supported by the Swedish Research Council, Science for Life Laboratory and all major Swedish universities, providing state-of-the-art bioinformatics to the Swedish life science researchers community. NBIS is also the Swedish contact point to the European infrastructure for biological information ELIXIR.
The NBIS team has expertise in protein bioinformatics, mass spectrometry (MS), next generation sequencing (NGS), large-scale data handling, metagenomics, systems biology, biostatistics and RNA sequencing. NBIS is predominantly offering support in various projects, depending on the user needs, as well as infrastructure and tools for bioinformatics analyses.
BILS works together with SNIC (Swedish National Infrastructure for Computing, who represents Sweden in the EGI Council) developing systems and strategies for long-term large-scale storage of bioinformatics data (MS proteomics data, NGS sequence data).
One important task of NBIS is to develop a scalable, robust and easy-to-use platform for hosting web-servers of bioinformatics tools, and cloud computing is the most feasible solution for a such platform. Thanks to the collaboration with EGI through an SLA signed in December 2015, NBIS is now having access to cloud resources from three EGI Federated Cloud sites for a total amount of resources consisting of 324 CPU Cores, 648 GB of RAM and around 7 TB of temporary and permanent storage.
With the generous amount of cloud resources provided by EGI (through the VO vo.nbis.se), NBIS has deployed a number of high profile bioinformatics tools, including
Pcons.net: a Meta server for 3D proteins structure prediction;
PconsC2/PconsC3: A method for accurate contact prediction for all family sizes;
SCAMPI: Prediction of membrane protein topology from first principles;
BOCTOPUS: Topology prediction of transmemrane beta-barrel proteins;
ProQ3: Model Quality Assessment using Rosetta energy; and
TOPCONS: Consensus prediction of membrane protein topology and signal peptide.
Among those services, TOPCONS has completed more than 4 million queries from 6700 unique users distributed in 73 countries since Feb. 2015.
We believe that our platform will benefit the whole research community even more in the future with continuous collaboration with the EGI cloud.
Bioscientists, bioinformatics service providers, cloud service providers.
Benefits for Audience
Best practices of operating a scientific service in a cloud environment. Overview of EGI Service/Operation Level Agreement negotiation.