Embedded Files
DESCRIPTION
BlenX is a language based on the process calculi and rule-based paradigms and it is specifically designed to account for the complexity of signalling networks. The Beta Workbench (BetaWB) is a collection of tools built on top of the BlenX language. The BetaWB includes the BlenX simulator, a network-free stochastic simulator based on an efficient variant of the Gillespie's stochastic algorithm, the BetaWB designer, a tool for writing models using a nice graphical editor, and the BetaWB plotter, a tool to analyse simulation results. BlenX and BetaWB have been designed and implemented in collaboration with Lorenzo Dematté. A module to convert BlenX models into SBML descriptions has been implemented by Roberto Larcher.
At COSBI you can find the BetaWB designer, the BetaWB plotter and the version 3.0 of the BlenX simulator. Here you can find version 4.1 of the BlenX simulator. The BlenX simulator is released under the COSBI-SSLA license and by downloading the binaries below you agree to that license.
BINARIES
version 4.1 - 21/10/2011
Besides bug fixing, version 4.1 offers a new set of functionalities to better manage the creation of complexes.
DOCUMENTATION
OTHER TOOLS SUPPORTING BLENX
MAIN REFERENCES
The Beta Workbench: a computational tool to study the dynamics of biological systems. [pdf]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
Briefings in Bioinformatics 9(5):437-449, © Oxford Journals, 2008.
(here you find a presentation of the BetaWB)
Programming Biology in BlenX. [pdf]
Lorenzo Dematté, Roberto Larcher, Alida Palmisano, Corrado Priami, Alessandro Romanel.
In Systems Biology for Signaling Networks 1:777-820, Ed. Sangdun Choi, © Springer, 2010.
(here you find an informal presentation of the BlenX language and two case studies)
Dynamic Biological Modelling: a language-based approach. [pdf]
Alessandro Romanel.
PhD thesis , University of Trento, 2010.
(here you find a formal presentation of the BlenX language and its abstract machine, details on its implementation and some case studies)
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