Tools

We make weekly builds of the sb.os dvd. You can find it here.
We build 32bit and 64bit versions.
The software list is here.



(Systems Biology Operational Software) is a Linux live DVD designed to fit the needs of systems biologists. It features a collection of up-to-date free software tools and kinetic models installed in a Linux environment. SB.OS is based on the popular Linux distribution Ubuntu 11.04 and ready to use for all non-commercial purposes.
is a biological network layout and visualization tool which has been developed as part of the Google Summer of Code 2011. It consists of a layout algorithm C/C++ library (biographer-layout) which creates an graph layout optimized for biological networks, especially for bi-partite reaction graphs and a Javascript web component (biographer-visualization) for interactive in-browser visulalization of those networks. A server component (biographer-server) puts all sub projects together and provides network import from various sources and subsequent visualization.
can be used to predict the network behavior for metabolic, signaling and gene regulatory networks. The library can calculate biochemical scopes based on give biochemical reaction networks and predefined initial conditions. It supports a static mode, which calculates the set of in principle producible compounds and a dynamic mode which allows to follow the activity of compounds with time considering catalytic and inhibitory events.
The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models. The development has been driven in collaboration with the Systems Biology Institute in Tokyo and partners at Linköping University and the University of Gothenburg. The current version of the software tool is available at rxncon.org. ...more
In Systems Biology models are created in various formats. So far only few formats (like SBML) allow the annotation of the biological context of a model. This service will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.
is set of open-source tools used to perform spatio-temporal simulations in discrete structures. The framework contains modules to digitize, represent, analyze, and model spatial distributions of species in static and dynamic structures (e.g. growing).
SBML based identification of optimal inhibition targets in Python.
The semanticSBML project: Create, check, annotate, merge SBML (System Biology Markup Lanugage) models. The program includes a graphical user interface as well as a console interface that can process batch jobs. For tool developers a programming interface is provided.
is a computational tool for automatic model management and generation. It can help you to create and manage different versions of a model you are working on. One of the main advantages is that the user only has to specify one single model structure and a set of directives that detail the family of candidate models.
A web-based tool for assessing the metabolic function of reaction networks.
The project: Search Medline abstracts for key words related to enzyme kinetic parameters. One has to specify a constant that have to appear in the abstract. In addition, one can specify other entities such as an enzyme, a compound, or a species.
SBML based model reduction in Python.
A Systems Biology Markup Language (SBML) based Sensitivity Analysis Tool.
A Systems Biology Markup Language (SBML) based Parameter Estimation Tool.