NBIS infrastructure activities are based on requests from the community, and on needs identified by our staff. The infrastructure include services such as:
NBIS work on developing and maintaining easy-to-use bioinformatics tools. We offer software development as a support service, but also develop tools in European and Nordic collaborations. For a non-exhaustive list of tools developed/maintained by NBIS staff, see our tools page.
NBIS can assist Swedish scientists in various data management issues, such as writing data management plans, publishing of datasets in repositories, guidance on how to work with sensitive human data, etc. For more information please see our Data management page.
NBIS provides a data handling pipeline for proteomics laboratories that converts raw mass spectrometry data into standard formats and provides secure storage at the national storage. Data can be further shared between different users and processed through the Proteios Software Environment interface, which also provides protein identification and quantification workflows. Open access to published research data is an important aim of the national infrastructure, and the platform provides users with facilitated publication of raw and processed data at ProteomeXchange through the PRIDE partner repository. See also the technical description.
NBIS also drives a project that aims to serve users with high-throughput mass spectrometry shotgun proteomics data processing. The framework for this is currently Galaxy, and it is our intention to deliver the platform to individual groups or core facilities. Technically the platform will be running on a cloud instance owned by the respective user, but it will also be possible to install on one’s own hardware. The platform is highly flexible and can access files at the national file storage or local files provided by the users.
NBIS maintains a number of protein structure prediction web servers, including one of the most popular membrane protein prediction methods, TOPCONS.
Since 2015 NBIS collaborates with EGI, and receives computing and storage resources for the operation of these protein prediction web servers. A total of 204 vCPU cores, 648GB of RAM and 32TB of block storage are provisioned with a dedicated Service Level Agreement (SLA) between EGI and NBIS. This capacity allocation is officially supported by the following EGI resource providers: IN2P3-IRES (FR), INFN-CLOUD-BARI (IT) and TR-FC1-ULAKBIM (TR).