Welcome & What can we offer
Welcome to the Systems Biology Laboratory located at the Faculty of Informatics of Masaryk University in Brno. The laboratory was established in 2009 with the aim of integrating and intensifying reserach and education activities in the emerging area of Digital Systems Biology at the Faculty of Informatics, Masaryk University.
The long-term research goal of Sybila is to develop and apply computational science and technology to enhance the general understanding of the molecular mechanisms underlying the behavior of living systems and develop scalable methods and tools for modeling and computerized analysis of large and complex living systems.
Another goal is to support education in Systems biology by offering a challenging multi-disciplinary working environment for students aspiring to be in the forefront of modern computational biology.
Computer science technologies together with computer tools employing suitable mathematical and computer science methods can help to obtain exact description of the networks, and in consequence, to infer interesting predictions of systems dynamics evolved in arbitrary environment. In order to cope with large-scale biological models describing interaction in the scale of several functional layers of a living cell, the central requirement imposed on analysis tools is the scalability.
We offer web services and software tools for modelling and analysis of biological processes.
Web-services on-line
E-cyanobacterium.org
Comprehensive modelling platform integrating computational models targeting biophysical processes related with cyanobacteria and their environment, biochemical knowledge, and analysis techniques accessible on-line. The platform reflects SBML and MIRIAM formats and annotation standards.
The website is freely accessible from the URL below. Advanced tasks are accessible for registered users only. Registration can be done by clicking on the Register button on the website home page.
URL: http://www.e-cyanobacterium.org
E-photosynthesis.org
Modelling repository serving computational models of biophysical processes related to photosynthesis. Models are accompanied with numerical simulation tasks accessible on-line. The platform reflects SBML and MIRIAM formats and annotation standards.
The website is freely accessible from the URL below. Advanced tasks are accessible for registered users only. Registration can be done by clicking on the Register button on the website home page.
URL: http://www.e-photosynthesis.org
Esther: Qualitative models analysis platform
Esther is an interface to a suite of tools for discrete simulation and reverse-engineering of gene regulatory and signal transduction networks. For modelling it employs the framework of asynchronous boolean or multi-valued (commonly referred to as Thomas or Qualitative) networks.
The website is freely accessible from the URL below. All functionalities are accessible for registered users only. Registration can be done by clicking on the Register button on the website home page.
BioDiVinE model analysis software
BioDiVinE Pithya
Pithya is an open source tool for parameter synthesis of ODE models of biological processes from temporal specification of known dynamical constraints. The tool can be freely downloaded from the URL below.
URL: https://github.com/sybila/pithya-core/
BioDiVinE Parasim
Parasim is an open source tool for robustness analysis of ODE models with respect to given temporal specification. Given a SBML model, a property and a perturbation set, it computes the robustness of model over the perturbation set with respect to the property. Perturbation set consists of intervals over model parameters and initial variable values. The tool can be freely downloaded from the URL below.
URL: https://github.com/sybila/parasim/wiki
How can you access
Website: http://sybila.fi.muni.cz
General questions
David Šafránek, safranek@fi.muni.cz
phone: +420 549 49 4476
Head: Luboš Brim (brim@fi.muni.cz)
Staff: Matej Hajnal, Martin Demko, Samuel Pastva, Matej Troják