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Published in:

2014 | OriginalPaper | Chapter

1. Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology

Authors : Jonathan Blakes, Jamie Twycross, Savas Konur, Francisco Jose Romero-Campero, Natalio Krasnogor, Marian Gheorghe

Published in: Applications of Membrane Computing in Systems and Synthetic Biology

Publisher: Springer International Publishing

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Abstract

This chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework. The Workbench incorporates three important features, simulation, model checking and optimisation. Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and synthetic biology research.

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next chapter Statistical Model Checking of Membrane Systems with Peripheral Proteins: Quantifying the Role of Estrogen in Cellular Mitosis and DNA Damage
Footnotes
2
The \(\mathbf{P}_{\sim r}\) operator is the probabilistic counter-part of path-quantifiers \(\forall \) and \(\exists \) of CTL.
 
3
At the moment, the NLQ tool is not integrated into the Infobiotics Workbench. But, the properties it generates can be directly used in IBW’s model checking component.
 
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Metadata
Title
Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology
Authors
Jonathan Blakes
Jamie Twycross
Savas Konur
Francisco Jose Romero-Campero
Natalio Krasnogor
Marian Gheorghe
Copyright Year
2014
Book
Applications of Membrane Computing in Systems and Synthetic Biology

Print ISBN: 978-3-319-03190-3

Electronic ISBN: 978-3-319-03191-0

Copyright Year: 2014

DOI
https://doi.org/10.1007/978-3-319-03191-0_1

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