Beta Workbench (BetaWB)

Category Cross-Omics>Pathway Analysis/Tools

Abstract BetaWB is a collection of tools based on the programming language BlenX, explicitly designed to represent biological entities and their interactions.

The BlenX programming language is inspired by ‘process calculus’ Beta-binders and it is intended for modeling any system whose basic steps of computation is an interaction between sub-components.

Beta-binders is a comparatively new modeling formalism introduced for systems biology.

The BetaWB includes the BetaWB simulator, a stochastic simulator based on an efficient variant of the Gillespie Stochastic Simulation Algorithm (SSA), the BetaWB designer, a graphical editor for developing models and the BetaWB plotter, a tool to analyze the results of a stochastic simulation run.

1) BetaWB simulator --

The core of BetaWB is a command-line application (core BetaWB) that hosts three (3) tools: a) the BetaWB simulator, b) the BetaWB CTMC generator and c) the BetaWB reactions generator.

These three tools share the BlenX compiler and the BlenX runtime environment.

The core BetaWB takes as input the text files that represent a BlenX program passes them to the compiler that translates these files into a runtime representation that is then stored in the runtime environment.

a) The BetaWB simulator is a 'stochastic simulation engine'. The runtime environment provides the stochastic simulation engine with primitives for checking the current state of the system and for modifying it.

The stochastic simulation engine drives the simulation, handling the time evolution of the environment in a stochastic way and preserves the semantics of the language.

The stochastic simulation engine implements an efficient variant of the Gillespie’s algorithms.

When rates are drawn from an exponential distribution and models are in a finite-state, a BlenX program gives rise to a continuous-time Markov process (CTMC).

b) The BetaWB CTMC generator adds to the core blocks a set of iterators to exhaustively traverse the whole state space of a BlenX program.

The CTMC generator also labels all the transitions between states with their exponential rate.

c) The BetaWB reactions generator identifies state changes that can be performed by entities and complexes generated by the execution of a BlenX program and produce a description of the system as a list of species and a list of chemical reactions in which species are involved.

These lists are abstracted as a directed graph (digraph) in which nodes represent species and edges represent reactions.

This graph can be reduced to avoid presence of reactions with infinite rate.

The final result is an SBML description of the original BlenX program.

The core BetaWB is enriched by two (2) additional tools for input/output operations: the BetaWB designer and the BetaWB plotter.

2) BetaWB designer --

The BetaWB designer is a tool that allows you to write BlenX programs both in a textual and graphical way.

The two representations are interchangeable: the tool can parse and generate the graphical representation from any valid BlenX program, and generate the textual representation from the graphical form.

In particular, it is possible to draw boxes, pi-processes, interactions, events and to form complexes using graphs.

The textual representation can then be used as input to the core BetaWB.

3) BetaWB plotter --

The BetaWB plotter is a graphical tool that parses and display simulation outputs as changes in concentrations, graphs of the reactions executed by the simulator and other views of the relations between entities and reactions.

The BetaWB plotter provides you with a picture of the dynamic behavior of a simulated model and the topology of the network that originated that behavior.

The current version of BetaWB is beta 2.0. Notable improvements and additions since the last main release include:

1) New language primitives.

2) Parametric processes and boxes definitions.

3) User-defined rate functions, variables and constants.

4) Transition system and CTMC generation.

5) Systems Biology Markup Language (SBML) models export.

System Requirements

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Manufacturer

Manufacturer Web Site Beta Workbench (BetaWB)

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G6G Abstract Number 20383

G6G Manufacturer Number 104021