Services via Biocenter Finland
SBL is a member of the Biocenter Finland Bioinformatics infrastructural network and closely collaborates with Structural Biology and Translational technologies infrastructure networks.
Bioinformatics
Bioinformatics covers a very broad set of research disciplines where computational approaches are being developed and applied in order to exploit better existing and new experimental data. Due to the broad nature of the general field, and the levels of funding and personnel it is impossible to cover all aspects. Our current focus is on supporting and developing, in particular, Translational activities, Structural bioinformatics, as well as IT support for high volume data producers such as from Bioimaging. Our core obligations are related to:
Protein structure analysis
Protein structure analysis services:
- Prediction of protein 3D structure from sequence
- Identification of structurally similar proteins
- Prediction of sequence-structure-function relationships
- Modeling and visualization platform for users, analysis of domains in primary sequences, homology and annotation
- Small molecule databases for high-throughput screening
- Software and databases via consortia coordinated by CSC
IT Services
Data storage and archiving, hardware and software support: We are aiming to provide secure data storage and archiving to the BioCity community, for large data sets and small ones. We are currently in discussion with CSC IT Center for Science on how to exploit the ELIXIR EU program in order to help support the infrastructure in Turku.
We are currently building the storage node. It will be based on Hitachi AMS2100 technology, and offer at first stage 8 TB of storage to share. Access to storage will employ iRODS integrated Rule-Oriented Data System.
The node includes two RX300 S6 servers, each with two Xeon E5620 processors and 72 GB of RAM. Therefore, we can host memory-demanding computations, unlike regular desktop machines.
We are also managing Hitachi AMS Extension Tray purchased by Biocenter Finland Biological infrastructure network, which starts with 24 TB of storage capacity. The management service is available for all groups on the campus, who would like to build storage for themselves.
SBL participates on software consortia arranged by CSC. We do have local installations of Accelrys DiscoveryStudio, Tripos Sybyl, Schrödinger Maestro, Cambridge Structural Database, CCP4 suite, Coot, Phenix, Modeller and Bodil.