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. More specifically, we offer:
- In silico modeling and simulation of biological systems, in particular molecular systems such as enzymes and membranes.
- Method and software development.
- Special calculation services:
Analysis of the similarity between non-sequential protein residue segments
Scientific Computing Facilities
For its operation, the core facility has access to local and national scientific computing facilities, the latter at the Center of Scientific Computing (CSC). The newest addition to the local facilities is 'Carpo' (physically located in Kajaani, and co-funded by the Academy of Finland and Finnish research institutions), with almost 300 nodes. It will be in operation for the period 2016 - 2020. It is part of the new Finnish Grid and Cloud Infrastructure (FGCI). FGCI are is jointly coordinated with Kai Nordlund (University of Helsinki), representatives of the universities and Pekka Lehtovuori and Jura Tarus (the Center of Scientific Computing).
The local scientific computing facilities and those at the CSC are accessible to all trained users to perform in silico modeling of various (bio)molecular systems. Software is available for various types of modeling and simulation, including molecular dynamics, coarse-grained molecular dynamics, quantum mechanics/molecular mechanics, protein modelling, protein–ligand docking, and the like. Additional software can be made available upon request.
An annually recurring course entitled ‘In silico methodologies in biochemistry and molecular medicine’ is available to gain insight in many useful techniques. This course includes both lecture and practical sessions.
A standard non-negotiable €750 flat rate per year will be charged for a service provision irrespective of the actual amount of time or resources required to complete the service request.
André Juffer, Ph.D.
Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine,
University of Oulu
PL 3000, 90014 University of Oulu, Finland
tel. +358-(0)294 481161
e-mail: andre.juffer (at) oulu.fi
Last updated: 14.2.2020