@inproceedings{BlaetkeRohr, author = {Bl{\"a}tke, Mary-Ann and Rohr, Christian}, title = {A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit}, series = {Proceedings of the 6th International Workshop on Biological Processes \& Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015}, booktitle = {Proceedings of the 6th International Workshop on Biological Processes \& Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015}, editor = {Heiner, Monika and Wagler, Annegret K.}, pages = {37 -- 54}, language = {en} } @misc{BarbotHaddadHeineretal., author = {Barbot, Benoit and Haddad, Serge and Heiner, Monika and Picaronny, Claudine}, title = {A Rare Event Method Applied to Signalling Cascades}, series = {International Journal on Advances in Systems and Measurements}, volume = {8}, journal = {International Journal on Advances in Systems and Measurements}, number = {1-2}, issn = {1942-261x}, pages = {69 -- 79}, language = {en} } @inproceedings{OPUS4-15077, title = {Biological Processes \& Petri Nets, 6th International Workshop BioPPN 2015, Brussels, 22 June 2015, Proceedings}, editor = {Heiner, Monika and Wagler, Annegret K.}, url = {http://nbn-resolving.de/urn:nbn:de:0074-1373-4}, language = {en} } @incollection{BlaetkeHeinerMarwan, author = {Bl{\"a}tke, Mary-Ann and Heiner, Monika and Marwan, Wolfgang}, title = {BioModel Engineering with Petri Nets}, series = {Algebraic and Discrete Mathematical Methods for Modern Biology}, booktitle = {Algebraic and Discrete Mathematical Methods for Modern Biology}, editor = {Robeva, Raina S.}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, isbn = {978-0-12-801213-0}, pages = {141 -- 193}, language = {en} } @inproceedings{HeinerSchwarickWegener, author = {Heiner, Monika and Schwarick, Martin and Wegener, Jan-Thierry}, title = {Charlie - an extensible Petri net analysis tool}, series = {Application and Theory of Petri Nets and Concurrency, 36th International Conference, PETRI NETS 2015, Brussels, Belgium, June 21-26, 2015, Proceedings}, booktitle = {Application and Theory of Petri Nets and Concurrency, 36th International Conference, PETRI NETS 2015, Brussels, Belgium, June 21-26, 2015, Proceedings}, publisher = {Springer International Publishing}, address = {Cham}, isbn = {978-3-319-19487-5}, doi = {10.1007/978-3-319-19488-2_10}, pages = {200 -- 211}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets}, series = {Frontiers in Environmental Science}, volume = {3}, journal = {Frontiers in Environmental Science}, issn = {2296-665X}, doi = {10.3389/fenvs.2015.00053}, pages = {53}, language = {en} } @misc{OPUS4-15078, title = {Multiscale Spatial Computational Systems Biology}, editor = {Gilbert, David and Heiner, Monika and Takahashi, Koichi and Uhrmacher, Adelinde M.}, address = {Dagstuhl}, doi = {10.4230/DagRep.4.11.138}, url = {http://nbn-resolving.de/nbn:de:0030-drops-49723}, pages = {88}, abstract = {This report documents the program and the outcomes of Dagstuhl Seminar 14481 "Multiscale Spatial Computational Systems Biology". This seminar explored challenges arising from the need to model and analyse complex biological systems at multiple scales (spatial and temporal), which falls within the general remit of Computational Systems Biology. A distinguishing factor of the seminar was the modelling exercise -- where teams explored different modelling paradigms, in order to better understand the details of the approaches, their challenges, potential applications, and their pros and cons. This activity was carried out in a collaborative and self-directed manner using the Open Space Technology approach as evidenced by a high degree of communication both within and between the teams. Eight teams were formed, and reports from five of them are included in this document.}, language = {en} } @misc{GilbertHeiner, author = {Gilbert, David and Heiner, Monika}, title = {Preface Advances in Computational Methods in Systems Biology}, series = {Theoretical Computer Science}, volume = {599}, journal = {Theoretical Computer Science}, issn = {0304-3975}, doi = {doi:10.1016/j.tcs.2015.08.013}, pages = {2 -- 3}, language = {en} } @misc{ParvuGilbertHeineretal., author = {P{\^a}rvu, Ovidiu and Gilbert, David and Heiner, Monika and Liu, Fei and Saunders, Nigel and Shaw, Simon}, title = {Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes}, series = {ACM Transactions on Modeling and Computer Simulation (TOMACS)}, volume = {25}, journal = {ACM Transactions on Modeling and Computer Simulation (TOMACS)}, number = {2}, issn = {1558-1195}, doi = {10.1145/2742546}, pages = {13}, language = {en} }