TY - CHAP A1 - Blätke, Mary-Ann A1 - Rohr, Christian ED - Heiner, Monika ED - Wagler, Annegret K. T1 - A Colored Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit T2 - Proceedings of the 6th International Workshop on Biological Processes & Petri Nets (BioPPN 2015), Brussels, Belgium, June 22, 2015 Y1 - 2015 UR - http://ceur-ws.org/Vol-1373/ N1 - peer reviewed SP - 37 EP - 54 ER - TY - GEN A1 - Barbot, Benoit A1 - Haddad, Serge A1 - Heiner, Monika A1 - Picaronny, Claudine T1 - A Rare Event Method Applied to Signalling Cascades T2 - International Journal on Advances in Systems and Measurements Y1 - 2015 UR - http://www.iariajournals.org/systems_and_measurements/sysmea_v8_n12_2015_paged.pdf SN - 1942-261x VL - 8 IS - 1-2 SP - 69 EP - 79 ER - TY - CHAP ED - Heiner, Monika ED - Wagler, Annegret K. T1 - Biological Processes & Petri Nets, 6th International Workshop BioPPN 2015, Brussels, 22 June 2015, Proceedings Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1373-4 ER - TY - CHAP A1 - Blätke, Mary-Ann A1 - Heiner, Monika A1 - Marwan, Wolfgang ED - Robeva, Raina S. T1 - BioModel Engineering with Petri Nets T2 - Algebraic and Discrete Mathematical Methods for Modern Biology Y1 - 2015 UR - http://store.elsevier.com/product.jsp?isbn=9780128012130 SN - 978-0-12-801213-0 SP - 141 EP - 193 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - CHAP A1 - Heiner, Monika A1 - Schwarick, Martin A1 - Wegener, Jan-Thierry T1 - Charlie – an extensible Petri net analysis tool T2 - Application and Theory of Petri Nets and Concurrency, 36th International Conference, PETRI NETS 2015, Brussels, Belgium, June 21-26, 2015, Proceedings Y1 - 2015 UR - http://link.springer.com/chapter/10.1007/978-3-319-19488-2_10 SN - 978-3-319-19487-5 U6 - https://doi.org/10.1007/978-3-319-19488-2_10 N1 - peer reviewed SP - 200 EP - 211 PB - Springer International Publishing CY - Cham ER - TY - GEN A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets T2 - Frontiers in Environmental Science Y1 - 2015 UR - http://www.frontiersin.org/environmental_informatics/10.3389/fenvs.2015.00053/abstract U6 - https://doi.org/10.3389/fenvs.2015.00053 SN - 2296-665X VL - 3 SP - 53 ER - TY - GEN ED - Gilbert, David ED - Heiner, Monika ED - Takahashi, Koichi ED - Uhrmacher, Adelinde M. T1 - Multiscale Spatial Computational Systems Biology N2 - 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. KW - Multiscale, multidimensional, computational modelling, space, time, systems biology, synthetic biology Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?nbn:de:0030-drops-49723 UR - http://drops.dagstuhl.de/opus/volltexte/2015/4972/ CY - Dagstuhl ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika T1 - Preface Advances in Computational Methods in Systems Biology T2 - Theoretical Computer Science Y1 - 2015 U6 - https://doi.org/doi:10.1016/j.tcs.2015.08.013 SN - 0304-3975 VL - 599 SP - 2 EP - 3 ER - TY - GEN A1 - Pârvu, Ovidiu A1 - Gilbert, David A1 - Heiner, Monika A1 - Liu, Fei A1 - Saunders, Nigel A1 - Shaw, Simon T1 - Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes T2 - ACM Transactions on Modeling and Computer Simulation (TOMACS) Y1 - 2015 UR - http://dl.acm.org/citation.cfm?id=2742546 U6 - https://doi.org/10.1145/2742546 SN - 1558-1195 SN - 1049-3301 VL - 25 IS - 2 SP - 13 ER -