SIGNAL -Stochastic process algebra for biochemical signaling pathway analysis

Research output

Research output per year 2008 2009 2010 2011 2013

• 9 Article
• 8 Conference contribution
• 2 Chapter
• 2 Chapter (peer-reviewed)

Research output per year

Research output per year

Search results

• 2013

  HYPE: Hybrid modelling by composition of flows

  Galpin, V., Bortolussi, L. & Hillston, J., Jul 2013, In: Formal Aspects of Computing. 25, 4, p. 503-541 39 p.

  Research output: Contribution to journal › Article › peer-review

  • Process Algebra 100%
  • Hybrid Modeling 100%
  • Syntactics 33%
  • Continuous Evolution 33%
  • Equivalence Relation 33%
• 2012

  Bio-PEPAd: A non-Markovian extension of Bio-PEPA

  Caravagna, G. & Hillston, J., 2012, In: Theoretical Computer Science. 419, p. 26-49 24 p.

  Research output: Contribution to journal › Article › peer-review

  • Biological System 100%
  • Process Algebra 50%
  • Stochastic Simulation 50%
  • And-States 25%
  • Markov Process 25%

• Formal methods for checking the consistency of biological models

  Clark, A., Galpin, V., Gilmore, S., Guerriero, M. L. & Hillston, J., 2012, Advances in Systems Biology. Goryanin, I. I. & Goryachev, A. B. (eds.). Springer, Vol. 736. p. 461-475 15 p. (Advances in Experimental Medicine and Biology).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • formal modeling 100%
  • Process Algebra 50%
  • Logical Reasoning 50%
  • Petri Net 50%
  • Mathematical Method 50%
• 2011

  Equivalences for a biological process algebra

  Galpin, V., Oct 2011, In: Theoretical Computer Science. 412, 43, p. 6058-6082 25 p.

  Research output: Contribution to journal › Article › peer-review

  • Signalling Cascade 100%

• A semantic equivalence for Bio-PEPA based on discretisation of continuous values

  Galpin, V. & Hillston, J., 6 May 2011, In: Theoretical Computer Science. 412, 21, p. 2142-2161 20 p.

  Research output: Contribution to journal › Article › peer-review

  • Discretization 100%
  • Step Size 50%
  • Process Algebra 50%
  • Step Size α 50%
  • Discrete Level 25%

• A semi-quantitative equivalence for abstracting from fast reactions

  Galpin, V., Hillston, J. & Ciocchetta, F., 2011, Proceedings Third International Workshop on Computational Models for Cell Processes. Petre, I. & Vink, E. P. D. (eds.). Vol. 67. p. 34-49 16 p. (EPTCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Process Algebra 100%
  • Stochastic Process 50%
  • In-Process 50%

• Stochastic properties of the plant circadian clock

  Guerriero, M. L., Pokhilko, A., Fernández, A. P., Halliday, K. J., Millar, A. J. & Hillston, J., 2011, In: Journal of the Royal Society. Interface.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Stochasticity 100%
  • Computational Modeling 50%
  • Light Dark Cycle 33%
• 2010

  Query-based verification of qualitative trends and oscillations in biochemical systems

  Ballarini, P. & Guerriero, M. L., 28 Apr 2010, In: Theoretical Computer Science. 411, 20, p. 2019-2036 18 p.

  Research output: Contribution to journal › Article › peer-review

  • Deadlock State 100%

• Formal Methods for Biochemical Signalling Pathways

  Calder, M., Gilmore, S., Hillston, J. & Vyshemirsky, V., 2010, Formal Methods: State of the Art and New Directions. Boca, P., Bowen, J. P. & Siddiqi, J. (eds.). Springer, p. 185-215 31 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • Formal Method 100%
  • Biochemical Reaction 100%
  • Analysis Technique 50%
  • Stochastics 50%
  • Continuous Time 50%

• Investigating modularity in the analysis of process algebra models of biochemical systems

  Ciocchetta, F., Guerriero, M. L. & Hillston, J., 2010, Proceedings Third Workshop From Biology To Concurrency and Back. Merelli, E. & Quaglia, P. (eds.). Vol. 19. p. 55-69 15 p. (EPTCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Process Algebra 100%
  • Stochastic Process 20%

• Modelling and analysis of the NF-κB pathway in Bio-PEPA

  Ciocchetta, F., Degasperi, A., Hillston, J. & Heath, J., 2010, Transactions on Computational Systems Biology XII: Special Issue on Modeling Methodologies. Springer, Vol. XII. p. 229-262 34 p. (Lecture Notes in Computer Science; vol. 5945).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed)

  • External Stimulus 100%
  • Alternative Complement Pathway C3 C5 Convertase 100%
  • Nuclear Factor 100%
  • Complement Factor B 100%
  • Stochastic Simulation 100%

• Modelling biological systems with delays in Bio-PEPA

  Caravagna, G. & Hillston, J., 2010, Proceedings of MeCBIC 2010. p. 85-101 17 p. (Electronic Proceedings in Theoretical Computer Science; vol. 40).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Biological System 100%
  • Stochastics 40%
  • Process Algebra 40%
  • Stochastic Simulation 40%
  • Delay-Differential Equation 20%

• On verifying Bio-PEPA models

  Clark, A., Gilmore, S., Guerriero, M. L. & Kemper, P., 2010, Proceedings of the 8th International Conference on Computational Methods in Systems Biology. New York, NY, USA: ACM, p. 23-32 10 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  File

  • Computational Modeling 100%
  • Process Algebra 100%
  • Static Program Analysis 100%
  • Signaling Pathway 100%
  • Step Verification 100%

• Verification and Testing of Biological Models

  Clark, A., Gilmore, S., Hillston, J. & Kemper, P., 2010, Simulation Conference (WSC), Proceedings of the 2010 Winter . Institute of Electrical and Electronics Engineers, p. 620-630 11 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Discrete Event Simulation 100%
  • Developing Model 100%
  • Continuous Simulation 100%
  • Simulation Modeling 100%
  • Cardinality 100%
• 2009

  Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway

  Guerriero, M. L., Dudka, A., Underhill-day, N., Heath, J. K. & Priami, C., 1 Jan 2009, In: BMC Systems Biology. 3, 1, 12 p., 40.

  Research output: Contribution to journal › Article › peer-review

  • JAK-STAT Signaling 100%
  • Glycoprotein Gp 130 100%
  • Narrative 100%
  • Case Study 100%
  • Signal Attenuation 33%

• Design and Development of Software Tools for Bio-PEPA

  Duguid, A., Gilmore, S., Guerriero, M., Hillston, J. & Loewe, L., 2009, Proceedings of the Winter Simulation Conference 2009. ACM, p. 956-967 12 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  File

  • Modelers 100%
  • Software Development Tool 100%
  • Biological System 100%
  • Biochemicals 100%
  • Reaction Network 100%

• Equivalence and discretisation in Bio-PEPA

  Galpin, V. & Hillston, J., 2009, Computational Methods in Systems Biology: 7th International Conference, CMSB 2009, Bologna, Italy, August 31-September 1, 2009. Proceedings. Degano, P. & Gorriero, R. (eds.). Springer, p. 189-204 16 p. (Lecture Notes in Computer Science; vol. 5688).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Discretization 100%
  • Step Size 50%
  • Process Algebra 50%
  • Step Size α 50%
  • Discrete Level 25%

• Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems

  Ciocchetta, F., Gilmore, S., Guerriero, M. L. & Hillston, J., 2009, In: Electronic Notes in Theoretical Computer Science. 232, p. 17-38 22 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Model Checking 100%
  • Stochastic Simulation 75%
  • State Space 25%
  • model checker 25%

• Process Algebra Modelling Styles for Biomolecular Processes

  Calder, M. & Hillston, J., 2009, Transactions on Computational Systems Biology XI. Springer, p. 1-25 25 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed)

  • Process Algebra 100%
  • Modelers 33%
  • In-Process 33%

• The Bio-PEPA Tool Suite

  Ciocchetta, F., Duguid, A., Gilmore, S., Guerriero, M. L. & Hillston, J., 2009, Quantitative Evaluation of Systems, 2009. QEST '09. Sixth International Conference on the. Institute of Electrical and Electronics Engineers, p. 309-310 2 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  File

  • End-Users 100%
  • Single Source 100%
  • Rapid Prototyping 100%
  • Modeling Environment 100%
• 2008

  HYPE applied to the modelling of hybrid biological systems

  Galpin, V., Hillston, J. & Bortolussi, L., 2008, In: Electronic Notes in Theoretical Computer Science. 218, p. 33-51 19 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Biological System 100%
  • Modelers 50%
  • Process Algebra 50%
  • Hybrid System Model 50%