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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

M. Sc. Mostafa Herajy

Contact

locationBuilding 1c - 2nd floor, Room 202
 Walther-Pauer-Str. 2
 D-03046 Cottbus
phone+49-(0)355-69-3825
fax+49-(0)355-69-3587
e-mailM.Herajy@tu-cottbus.de

Short Biography

1980Born in Aswan, Egypt
1998-2002B.Sc. In Computers and Informatics- Faculty of Computers and Informatics - Ismalia, Egypt.
2003-2007Instructor, Mathematics Dept., Faculty of Education, Port Said, Egypt.
2004-2007M.Sc. In Computers and Information Sciences, Faculty of Computers and Information Sciences, Ainshams, Cairo, Egypt
Since 2008Assistant Lecturer, Mathematics and Computer Dept., Faculty of Science, Port Said, Egypt
since 2009DAAD Scholarship Holder
2010-2013DSSZ Group at BTU - Cottbus, Germany

Research Interests

Computational Steering, Hybrid Petri Nets, and Hybrid Simulation of Biochemical Networks

Publications

28 entries


  • [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 ]
  • [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 for publication: May, 18 2017). [ 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 ] [ BibTeX ]
  • [IHH18]
    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, 2018 (peer-reviewed, accepted for publication: September 2018). [ 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 ]
  • [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 ]
  • [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 for publication: 13 July 2015). [ url ] [ doi ] [ 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 ]
  • [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 ]
  • [HH14.sld]
    M Herajy andM Heiner:
    A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
    Talk, PETRI NETS 2014, Tunis, June 2014. [ pdf ] [ 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 ]
  • [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 ]
  • [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.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 ]
  • [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 ]
  • [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+.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 ]
  • [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]
    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 ]
  • [HH11.sld]
    M. Herajy and M. Heiner:
    Generalized Hybrid Petri Nets;
    Talk, Formal Methods in Molecular Biology, Dagstuhl seminar, April 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 ]

… the end …

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