Infobiotics Workbench

The Infobiotics Workbench is a executable biology framework implementing multi-compartmental stochastic and deterministic simulation, formal model analysis and structural/parameter model optimisation for computational systems and synthetic biology.

The Infobiotics Workbench is comprised of the following components:

• a modelling language based on P systems which allows modular and parsimonious multi-cellular model development where the outermost compartments can be positioned in 2-dimensional space to facilitate modelling at either extra-, inter- or intracellular levels of detail

• deterministic and stochastic simulator using algorithms optimised for large multi-compartmental systems (the simulator also accept a subset of SBML, allowing for visual model specification using tools such as CellDesigner)

• formal model analysis for the study of temporal and spatial model properties supported the model checkers PRISM and MC2

• model structure and parameter optimisation using a variety of evolutionary and population-based algorithms to automatically generate models whose dynamics match specified target timeseries

• a user-friendly front-end for performing in-silico experiments, plotting and visualisation of simulations with many runs and compartments

Documentation

To learn more about model specification and available experiments visit the documentation page where you will find text and video tutorials and a repository of example models.

For a brief overview see our latest publication in Bioinformatics (Blakes2011).

Download

Infobiotics Workbench is a free software released under the terms of the GNU General Public License and its source code is available for download together with binaries for Linux, Mac OS and Windows.

Project team

The following people have been involved in the development and testing of the Infobiotics Workbench.

• Prof. Natalio Krasnogor - principal investigator and team leader
• Dr. Jamie Twycross - multi-compartmental stochastic simulator
• Dr. Francisco Romero-Campero - model checking and modelling language
• Jonathan Blakes - user interface, data analysis and testing
• Daven Sanassy - stochastic simulations algorithms test suite
• Dr. James Smaldon - testing and validation with DPD
• Dr. Karima Righetti - wet-lab implementation of models
• Dr. Claudio Lima - optimisation algorithms
• Dr. Hongqing Cao - P-systems optimiser

Funding

This work was funded by EPSRC grant EP/E017215/1.

Publications

• DOI BibTeX
  J. Blakes, J. Twycross, F.J. Romero-Campero, N. Krasnogor
  The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
  in Bioinformatics, 27(23):3323-3324, December 2011

  @ARTICLE{Blakes2011,
    title = {The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology},
    author = {Blakes, J. and Twycross, J. and Romero-Campero, F. J. and Krasnogor, N.},
    year = 2011,
    doi = {10.1093/bioinformatics/btr571},
    month = dec,
    journal = {Bioinformatics},
    volume = {27},
    number = {23},
    pages = {3323--3324}
  }
  

• DOI eprint BibTeX
  J. Smaldon, F.J. Romero-Campero, F. Fernández Trillo, M. Gheorghe, C. Alexander, N. Krasnogor
  A computational study of liposome logic: towards cellular computing from the bottom up
  in Systems and Synthetic Biology, 4(3):157-179, September 2010

  @ARTICLE{Smaldon2010,
    title = {A computational study of liposome logic: towards cellular computing from the bottom up},
    author = {Smaldon, James and Romero-Campero, Francisco J. and Fernández Trillo, Francisco and Gheorghe, Marian and Alexander, Cameron and Krasnogor, Natalio},
    year = 2010,
    doi = {10.1007/s11693-010-9060-5},
    month = sep,
    journal = {Systems and Synthetic Biology},
    volume = {4},
    number = {3},
    pages = {157--179}
  }
  

• DOI BibTeX
  H. Cao, F.J. Romero-Campero, S. Heeb, M. Cámara, N. Krasnogor
  Evolving cell models for systems and synthetic biology
  in Systems and Synthetic Biology, 4(1):55-84, March 2010

  @ARTICLE{Cao2010,
    title = {Evolving cell models for systems and synthetic biology},
    author = {Cao, Hongqing and Romero-Campero, Francisco J. and Heeb, Stephan and Cámara, Miguel and Krasnogor, Natalio},
    year = 2010,
    doi = {10.1007/s11693-009-9050-7},
    month = mar,
    journal = {Systems and Synthetic Biology},
    volume = {4},
    number = {1},
    pages = {55--84}
  }
  

• DOI BibTeX
  J. Twycross, L.R. Band, M.J. Bennett, J.R. King, N. Krasnogor
  Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study
  in BMC Systems Biology, 4(1):34, 2010

  @ARTICLE{Twycross2010,
    title = {Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study},
    author = {Twycross, Jamie and Band, Leah R and Bennett, Malcolm J and King, John R and Krasnogor, Natalio},
    year = 2010,
    doi = {10.1186/1752-0509-4-34},
    journal = {BMC Systems Biology},
    volume = {4},
    number = {1},
    pages = {34}
  }
  

• DOI BibTeX
  M. Gheorghe, V. Manca, F.J. Romero-Campero
  Deterministic and stochastic P systems for modelling cellular processes
  in Natural Computing, 9(2):457-473, June 2010

  @ARTICLE{Gheorghe2010,
    title = {Deterministic and stochastic P systems for modelling cellular processes},
    author = {Gheorghe, Marian and Manca, Vincenzo and Romero-Campero, Francisco J.},
    year = 2010,
    doi = {10.1007/s11047-009-9158-4},
    month = jun,
    journal = {Natural Computing},
    volume = {9},
    number = {2},
    pages = {457--473}
  }
  

• DOI BibTeX
  C. García-Martínez, C. Lima, J. Twycross, N. Krasnogor, M. Lozano
  P system model optimisation by means of evolutionary based search algorithms
  in Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10, p.187, Portland, Oregon, USA, 2010

  @INPROCEEDINGS{Garcia-Martinez2010,
    title = {P system model optimisation by means of evolutionary based search algorithms},
    author = {García-Martínez, Carlos and Lima, Claudio and Twycross, Jamie and Krasnogor, Natalio and Lozano, Manuel},
    year = 2010,
    doi = {10.1145/1830483.1830517},
    booktitle = {Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10},
    pages = {187},
    address = {Portland, Oregon, USA}
  }
  

• DOI BibTeX
  F.J. Romero-Campero, J. Twycross, M. Cámara, M. Bennett, M. Gheorghe, N. Krasnogor
  Modular Assembly Of Cell Systems Biology Models Using P Systems
  in International Journal of Foundations of Computer Science, 20(03):427-442, June 2009

  @ARTICLE{Romero-Campero2009,
    title = {Modular Assembly Of Cell Systems Biology Models Using P Systems},
    author = {Romero-Campero, Francisco J. and Twycross, Jamie and Cámara, Miguel and Bennett, Malcolm and Gheorghe, Marian and Krasnogor, Natalio},
    year = 2009,
    doi = {10.1142/S0129054109006668},
    month = jun,
    journal = {International Journal of Foundations of Computer Science},
    volume = {20},
    number = {03},
    pages = {427--442}
  }
  

• DOI BibTeX
  F.J. Romero-Campero, J. Twycross, H. Cao, J. Blakes, N. Krasnogor
  A Multiscale Modeling Framework Based on P Systems
  in Membrane Computing, Lecture Notes in Computer Science 5391, p.63-77, 2009

  @INCOLLECTION{Romero-Campero2009a,
    title = {A Multiscale Modeling Framework Based on P Systems},
    author = {Romero-Campero, Francisco José and Twycross, Jamie and Cao, Hongqing and Blakes, Jonathan and Krasnogor, Natalio},
    year = 2009,
    doi = {10.1007/978-3-540-95885-7_5},
    booktitle = {Membrane Computing},
    publisher = {Springer Berlin Heidelberg},
    volume = {5391},
    series = {Lecture Notes in Computer Science},
    pages = {63--77}
  }
  

• DOI BibTeX
  F.J. Romero-Campero, N. Krasnogor
  An Approach to the Engineering of Cellular Models Based on P Systems
  in Mathematical Theory and Computational Practice, Lecture Notes in Computer Science 5635, p.430-436, 2009

  @INCOLLECTION{Romero-Campero2009b,
    title = {An Approach to the Engineering of Cellular Models Based on P Systems},
    author = {Romero-Campero, Francisco J. and Krasnogor, Natalio},
    year = 2009,
    doi = {10.1007/978-3-642-03073-4_44},
    booktitle = {Mathematical Theory and Computational Practice},
    publisher = {Springer Berlin Heidelberg},
    volume = {5635},
    series = {Lecture Notes in Computer Science},
    pages = {430--436}
  }
  

• DOI BibTeX
  J. Smaldon, N. Krasnogor, C. Alexander, M. Gheorghe
  Liposome logic
  in Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09, p.161, Montreal, Québec, Canada, 2009

  @INPROCEEDINGS{Smaldon2009,
    title = {Liposome logic},
    author = {Smaldon, James and Krasnogor, Natalio and Alexander, Cameron and Gheorghe, Marian},
    year = 2009,
    doi = {10.1145/1569901.1569924},
    booktitle = {Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09},
    pages = {161},
    address = {Montreal, Québec, Canada}
  }
  

• DOI BibTeX
  J. Smaldon, J. Blakes, N. Krasnogor, D. Lancet
  A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics
  in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.249, Atlanta, GA, USA, 2008

  @INPROCEEDINGS{Smaldon2008,
    title = {A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics},
    author = {Smaldon, James and Blakes, Jonathan and Krasnogor, Natalio and Lancet, Doron},
    year = 2008,
    doi = {10.1145/1389095.1389134},
    booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
    pages = {249},
    address = {Atlanta, GA, USA}
  }
  

• DOI eprint BibTeX
  F.J. Romero-Campero, H. Cao, M. Camara, N. Krasnogor
  Structure and parameter estimation for cell systems biology models
  in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.331, Atlanta, GA, USA, 2008

  @INPROCEEDINGS{Romero-Campero2008,
    title = {Structure and parameter estimation for cell systems biology models},
    author = {Romero-Campero, Francisco J. and Cao, Hongqing and Camara, Miguel and Krasnogor, Natalio},
    year = 2008,
    doi = {10.1145/1389095.1389153},
    booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
    pages = {331},
    address = {Atlanta, GA, USA}
  }
  

• DOI BibTeX
  L. Bianco, D. Pescini, P. Siepmann, N. Krasnogor, F.J. Romero-Campero, M. Gheorghe
  Towards a P Systems Pseudomonas Quorum Sensing Model
  in Membrane Computing, Lecture Notes in Computer Science 4361, p.197-214, 2006

  @INCOLLECTION{Bianco2006,
    title = {Towards a P Systems Pseudomonas Quorum Sensing Model},
    author = {Bianco, Luca and Pescini, Dario and Siepmann, Peter and Krasnogor, Natalio and Romero-Campero, Francisco J. and Gheorghe, Marian},
    year = 2006,
    doi = {10.1007/11963516_13},
    booktitle = {Membrane Computing},
    publisher = {Springer Berlin Heidelberg},
    volume = {4361},
    series = {Lecture Notes in Computer Science},
    pages = {197--214}
  }
  

• DOI BibTeX
  F. Bernardini, M. Gheorghe, N. Krasnogor, R.C. Muniyandi, M.J. Pérez-Jímenez, F.J. Romero-Campero
  On P Systems as a Modelling Tool for Biological Systems
  in Membrane Computing, Lecture Notes in Computer Science 3850, p.114-133, 2006

  @INCOLLECTION{Bernardini2006,
    title = {On P Systems as a Modelling Tool for Biological Systems},
    author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio and Muniyandi, Ravie C. and Pérez-Jímenez, Mario J. and Romero-Campero, Francisco José},
    year = 2006,
    doi = {10.1007/11603047_8},
    booktitle = {Membrane Computing},
    publisher = {Springer Berlin Heidelberg},
    volume = {3850},
    series = {Lecture Notes in Computer Science},
    pages = {114--133}
  }