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

  • Jonathan BlakesEmail author
  • Jamie Twycross
  • Savas Konur
  • Francisco Jose Romero-Campero
  • Natalio Krasnogor
  • Marian Gheorghe
Part of the Emergence, Complexity and Computation book series (ECC, volume 7)


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.


Model Check Synthetic Biology Boolean Network Linear Temporal Logic System Biology Markup Language 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



JB, JT, SK, NK and MG acknowledge the support provided for synthetic biology research by EPSRC ROADBLOCK project (EP/I031642/1 & EP/I031812/1), EPSRC AUDACIOUS project (EP/J004111/1) and FP7 STREP CADMAD project. JR-C acknowledges support from Cellular Computing Applications into Systems and Synthetic Biology, TIN2009-13192, and Computational Modelling and Simulation in Systems Biology, P08-TIC-04200. MG was also partially supported by the MuVet project, (CNCS–UEFISCDI), grant number PN-II-ID-PCE-2011-3-0688. Some parts of this paper are based on the first author’s Ph.D. thesis [13].


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Jonathan Blakes
    • 1
    Email author
  • Jamie Twycross
    • 1
  • Savas Konur
    • 2
  • Francisco Jose Romero-Campero
    • 3
  • Natalio Krasnogor
    • 1
  • Marian Gheorghe
    • 2
  1. 1.ICOS Research Group, School of Computer ScienceUniversity of NottinghamNottinghamUK
  2. 2.Department of Computer ScienceUniversity of SheffieldSheffieldUK
  3. 3.Department of Computer Science and Artificial IntelligenceUniversity of SevilleSevilleSpain

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