Publications of Former Research Groups

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Journal Article (3)

  1. Journal Article
    Blätke, M. A.; Dittrich, A.; Rohr, C.; Heiner, M.; Schaper, F.; Marwan, W.: JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology. Molecular BioSystems 9 (6), pp. 1290 - 1307 (2013)
  2. Journal Article
    Rohr, C.; Marwan, W.; Heiner, M.: Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinformatics 26 (7), pp. 974 - 975 (2010)
  3. Journal Article
    Heiner, M.; Richter, R.; Rohr, C.; Schwarick, M.: Snoopy - A Tool to Design and Execute Graph-Based Formalisms. [Extended Version]. Petri Net Newsletter 74 (April), pp. 8 - 22 (2008)

Book Chapter (4)

  1. Book Chapter
    Heiner, M.; Rohr, C.; Schwarick , M.; Tovchigrechko, A. A.: MARCIE’s Secrets of Efficient Model Checking. In: Transactions on petri nets and other models of concurrency XI. Lecture Notes in Computer Science, Vol. 9930, pp. 286 - 296. Springer, Berlin, Heidelberg (2016)
  2. Book Chapter
    Blätke, M. A.; Rohr, C.; Heiner, M.; Marwan, W.: A Petri-Net-Based Framework for Biomodel Engineering. In: Large-Scale Networks in Engineering and Life Sciences, pp. 317 - 366. Springer International Publishing, Cham (2014)
  3. Book Chapter
    Rohr, C.: Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators. In: Transactions on Petri Nets and Other Models of Concurrency VIII. Lecture Notes in Computer Science, Vol. 8100, pp. 142 - 158. Springer, Berlin, Heidelberg (2013)
  4. Book Chapter
    Marwan, W.; Rohr, C.; Heiner, M.: Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks. In: Bacterial Molecular Networks. Methods in Molecular Biology, Vol. 804, pp. 409 - 437. Springer, New York, NY (2012)

Conference Paper (11)

  1. Conference Paper
    Rohr, C.: Discrete-Time Leap Method For Stochastic Simulation. In: Proceedings of the International Workshop on Petri Nets and Software Engineering 2016, including the International Workshop on Biological Processes & Petri Nets 2016. CEUR Workshop Proceedings, Vol. 1591, pp. 362 - 376. 7rd International Workshop on Biological Processes & Petri Nets (BioPPN 2016), Toruń, Poland , June 20, 2016. (2016)
  2. Conference Paper
    Beccuti, M.; Blätke, M. A.; Falk, M.; Hardy, S.; Heiner, M.; Maus, C.; Nähring, C.; Rohr, C.: Dictyostelium discoideum: Aggregation and Synchronisation of Amoebas in Time and Space. Dagstuhl Seminar 14481 "Multiscale Spatial Computational Systems Biology", Wadern, Germany, November 23, 2014 - November 28, 2014. Dagstuhl Reports 4 (11), pp. 195 - 214 (2015)
  3. Conference Paper
    Blätke, M. A.; Rohr, C.: A coloured Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit. In: Proceedings of the 6th International Workshop on Biological Processes & Petri Nets co-located with 36th International Conference on Application and Theory of Petri Nets and Concurreny (PETRI NETS 2015), Vol. 1373, pp. 37 - 54. 6th International Workshop on Biological Processes & Petri Nets co-located with 36th International Conference on Application and Theory of Petri Nets and Concurreny (PETRI NETS 2015), Brussels, Belgium, June 21, 2015 - June 26, 2015. (2015)
  4. Conference Paper
    Cordero, F.; Gambin, A.; Kierzek, A.; Madelaine, G.; Niehren, J.; Rohr, C.; Wronowska, W.: Multiscale modeling of S1P metabolism, secretion and signaling. Dagstuhl Seminar 14481 "Multiscale Spatial Computational Systems Biology", Wadern, Germany, November 23, 2014 - November 28, 2014. Dagstuhl Reports 4 (11), pp. 195 - 214 (2015)
  5. Conference Paper
    Herajy, M.; Liu, F.; Rohr, C.: Coloured hybrid Petri nets for systems biology. In: BioPPN 2014, a satellite event of PETRI NETS 2014. CEUR Workshop Proceedings, Vol. 1159, pp. 60 - 76. 5th International Workshop on Biological Processes & Petri Nets (BioPPN 2014), Tunis, Tunesia, June 23, 2014. (2014)
  6. Conference Paper
    Heiner, M.; Rohr, C.; Schwarick , M.: MARCIE – Model Checking and Reachability Analysis Done Efficiently. In: Application and Theory of Petri Nets and Concurrency. PETRI NETS 2013. Lecture Notes in Computer Science, Vol. 7927, pp. 389 - 399. International Conference on Application and Theory of Petri Nets and Concurrency - PETRI NETS 2013, Milano, Italy, June 24, 2013 - June 28, 2013. Springer, Berlin, Heidelberg (2013)
  7. Conference Paper
    Heiner, M.; Herajy, M.; Liu, F.; Rohr, C.; Schwarick , M.: Snoopy – A Unifying Petri Net Tool. In: Application and Theory of Petri Nets. PETRI NETS 2012. Lecture Notes in Computer Science, Vol. 7347, pp. 398 - 407. International Conference on Application and Theory of Petri Nets and Concurrency - PETRI NETS 2012, Trento, Italy, September 29, 2010 - October 01, 2010. (2012)
  8. Conference Paper
    Rohr, C.: Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators. In: Proceedings of the 3rd International Workshop on Biological Processes & Petri Nets, a satellite event of PETRI NETS 2012. CEUR Workshop Proceedings, Vol. 852, pp. 62 - 75. 3rd International Workshop on Biological Processes & Petri Nets (BioPPN 2012), Hamburg, Germany, June 25, 2012. (2012)
  9. Conference Paper
    Schwarick , M.; Heiner, M.; Rohr, C.: MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly. In: 2011 Eighth International Conference on Quantitative Evaluation of Systems (QEST), pp. 91 - 100. 2011 Eighth International Conference on Quantitative Evaluation of Systems (QEST), Aachen, Germany, September 05, 2011 - September 08, 2011. (2011)
  10. Conference Paper
    Heiner, M.; Rohr, C.; Schwarick , M.; Streif, S.: A comparative study of stochastic analysis techniques. In: CMSB '10 Proceedings of the 8th International Conference on Computational Methods in Systems Biology, pp. 96 - 106. 8th International Conference on Computational Methods in Systems Biology - CMSB '10, Trento, Italy, September 29, 2010 - October 01, 2010. (2010)
  11. Conference Paper
    Rohr, C.: Simulative CSL model checking of Stochastic Petri nets in IDD-MC. In: Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010). CEUR Workshop Proceedings, Vol. 643, pp. 88 - 93. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), Cottbus, Germany, October 07, 2010 - October 08, 2010. (2010)

Talk (8)

  1. Talk
    Rohr, C.: Discrete-time leap method for stochastic simulation. 7th International Workshop on Biological Processes & Petri Nets (BioPPN 2016), Toruń, Poland (2016)
  2. Talk
    Blätke, M. A.; Rohr, C.: A coloured Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit. 6th International Workshop on Biological Processes & Petri Nets (BioPPN 2015), Brussels, Belgium (2015)
 
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