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M. Sc. Mostafa Herajy

Contact

Short Biography

Research Interests

• project GE-SEED

Publications

32 entries

• [HLH24]
  M Herajy, F Liu and M Heiner:
  Design Patterns for the Construction of Computational Biological Models;
  Briefings in Bioinformatics, 25, 2024 (accepted: 10 June 2024). [ doi ] [ BibTeX ]
• [IHAH20]
  A Ismail, M Herajy, ES Atlam and M Heiner:
  A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-models via Coloured Hybrid Petri Nets;
  Modelling and Simulation in Engineering, 2020, 2020 (Article ID 4715172, 14 pages). [ doi ] [ BibTeX ]
• [IHH19]
  A Ismail, M Herajy and M Heiner:
  A Graphical Approach for the Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets;
  In Automated Reasoning for Systems Biology and Medicine, (P Zuliani and P Liς, Eds.), Springer, Cham, pages 349–367, 2019 (first online: 12. June 2019). [ url ] [ doi ] [ BibTeX ]
• [IHHA18]
  A Ismail, M Herajy, M Heiner and E Atlam:
  An Efficient Approach for the Hybrid Simulation of Intracellular Calcium Dynamics;
  In 13th International Conference on Computer Engineering and Systems (ICCES), IEEE, pages 665–670, 2018. [ doi ] [ BibTeX ]
• [HH18]
  M Herajy and M Heiner:
  An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets;
  In Proceedings of the 2018 Winter Simulation Conference (WSC 2018), Gothenburg, Sweden, IEEE, 978-1-5386-6572-5/18, pages 1346-1357, December 2018. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [BHAH18]
  A Badawy, M Herajy, W Awad and M Heiner:
  Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets;
  In 13th International Conference on Computer Engineering and Systems (ICCES), IEEE, pages 268–272, 2018. [ doi ] [ BibTeX ]
• [HH17]
  Herajy, M and Heiner, M:
  Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation;
  Fundamenta Informaticae, 160(1-2):53-80, 2018 (accepted: May 18, 2017). [ doi ] [ BibTeX ]
• [HLH17]
  M Herajy, F Liu and M Heiner:
  Efficient Modelling of Yeast Cell Cycles Based on Multisite Phosphorylation Using Coloured Hybrid Petri Nets with Marking-dependent Arc Weights;
  J. Nonlinear Analysis: Hybrid Systems, 27(February):191-212, 2018 (online: October 10, 2017). [ doi ] [ BibTeX ]
• [HLRH18]
  M Herajy, F Liu, C Rohr and M Heiner:
  Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks;
  Computational Biology and Chemistry, 76:87-100, 2018. [ doi ] [ BibTeX ]
• [HH18.sld]
  M Herajy and M Heiner:
  An improved simulation of hybrid biological models with many stochastic events and quasi-disjoint subnets;
  Talk, WSC 2018, Gothenburg, December 2018. [ pdf ] [ BibTeX ]
• [HLRH17.manual]
  M Herajy, F Liu, C Rohr and M Heiner:
  (Coloured Hybrid Petri Nets in Snoopy - User Manual;
  Technical report 01-17, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2017. [ url ] [ BibTeX ]
• [HLRH17]
  M Herajy, F Liu, C Rohr and M Heiner:
  Snoopy's Hybrid Simulator: a Tool to Construct and Simulate Hybrid Biological Models;
  BMC Systems Biology, 2017 (published: July 28, 2017). [ url ] [ doi ] [ BibTeX ]
• [HH16]
  M Herajy and M Heiner:
  Accelerated Simulation of Hybrid Biological Models with Quasi-disjoint Deterministic and Stochastic Subnets;
  In Proc. 5th Int. Workshop on Hybrid Systems Biology (HSB 2016), Springer, LNBI, volume 9957, pages 20-38, October 2016. [ url ] [ doi ] [ BibTeX ]
• [HH16.sld]
  M Herajy and M Heiner:
  Accelerated Simulation of Hybrid Biological Models with Quasi-disjoint Deterministic and Stochastic Subnets;
  Talk, 5th Int. Workshop on Hybrid Systems Biology (HSB 2016), October 2016. [ url ] [ pdf ] [ BibTeX ]
• [HH15]
  Herajy, M and Heiner, M:
  Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets;
  Frontiers in Environmental Science, 3(53), 2015 (accepted: July 13, 2015). [ url ] [ doi ] [ BibTeX ]
• [HH14a]
  M Herajy and M Heiner:
  Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks;
  Fundamenta Informaticae, 129(1-2):49-67, 2014. [ url ] [ doi ] [ BibTeX ]
• [HLR14]
  M Herajy, F Liu and C Rohr:
  Coloured hybrid Petri nets for systems biology;
  In Proc. of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 60-76, June 2014. [ url ] [ pdf ] [ BibTeX ]
• [HH14b]
  M Herajy and M Heiner:
  A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
  In Proc. PETRI NETS 2014, Tunis, Springer, LNCS, volume 8489, pages 374–384, June 2014. [ url ] [ doi ] [ BibTeX ]
• [HH14.sld]
  M Herajy and M Heiner:
  A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
  Talk, PETRI NETS 2014, Tunis, June 2014. [ pdf ] [ BibTeX ]
• [HSH13]
  M Herajy, M Schwarick and M Heiner:
  Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle;
  ToPNoC VIII, LNCS 8100, 2013. [ pdf ] [ doi ] [ BibTeX ]
• [Herajy13]
  Mostafa Herajy:
  Computational Steering of Multi-Scale Biochemical Networks;
  PhD thesis, BTU Cottbus, Dep. of CS, January 2013. [ pdf ] [ BibTeX ]
• [HH13.manual]
  M Herajy and M Heiner:
  Snoopy Computational Steering Framework – User Manual Version 1.0;
  Technical report 02-13, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2013. [ pdf ] [ BibTeX ]
• [HH+12]
  M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
  Snoopy – a unifying Petri net tool;
  In Proc. PETRI NETS 2012, Hamburg, Springer, LNCS, volume 7347, 398–407, June 2012. [ url ] [ doi ] [ BibTeX ]
• [HH12]
  M Herajy and M Heiner:
  Hybrid Representation and Simulation of Stiff Biochemical Networks;
  J. Nonlinear Analysis: Hybrid Systems, 6(4):942–959, November 2012. [ url ] [ doi ] [ BibTeX ]
• [HH12+.sld]
  M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
  Snoopy – a unifying Petri net tool;
  Talk, PETRI NETS 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
• [HS12.sld1]
  M Herajy and M Schwarick:
  A Hybrid Petri Net Model of the Eukaryotic Cell Cycle;
  Talk, 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2012, Hamburg, June 2012. [ pdf ] [ BibTeX ]
• [HH12.csp]
  M Herajy and M Heiner:
  Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks;
  In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2012), CEUR-WS.org, CEUR Workshop Proceedings, volume 928, pages 147–159, September 2012. [ url ] [ pdf ] [ BibTeX ]
• [HH12.poster]
  M Herajy and M Heiner:
  Distributed Collaborative and Interactive Simulationof Large Scale Biochemical Networks; BioPPN 12, June 2012;
  Poster, 2012. [ pdf ] [ BibTeX ]
• [HS12]
  M Herajy and M Schwarick:
  A Hybrid Petri Net Model of the Eukaryotic Cell Cycle;
  In Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2012, CEUR-WS.org, CEUR Workshop Proceedings, volume 852, pages 29-43, June 2012. [ url ] [ pdf ] [ BibTeX ]
• [HH11.sld]
  M. Herajy and M. Heiner:
  Generalized Hybrid Petri Nets;
  Talk, Formal Methods in Molecular Biology, Dagstuhl seminar, April 2011. [ pdf ] [ BibTeX ]
• [HH11]
  M Herajy and M Heiner:
  Hybrid Representation and Simulation of Stiff Biochemical Networks through Generalised Hybrid Petri Nets;
  Technical report 02-11, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2011. [ pdf ] [ BibTeX ]
• [HH10]
  M Herajy and M Heiner:
  Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions;
  In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 66–79, October 2010. [ pdf ] [ BibTeX ]