TY - GEN A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1674 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 53 EP - 80 ER - TY - GEN A1 - Gambin, Anna A1 - Heiner, Monika T1 - Advances in Biological processes and Petri nets (BioPPN) T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1671 SN - 0169-2968 SN - 1875-8681 VL - 160 IS - 1-2 SP - V EP - VII ER - TY - CHAP A1 - Ismail, Amr A1 - Herajy, Mostafa A1 - Heiner, Monika A1 - Atlam, Elsayed T1 - An Efficient Approach for the Hybrid Simulation of Intracellular Calcium Dynamics T2 - 13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt Y1 - 2018 SN - 978-1-5386-5111-7 U6 - https://doi.org/10.1109/ICCES.2018.8639261 SP - 665 EP - 670 PB - IEEE CY - Piscataway, NJ ER - TY - CHAP A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets T2 - Proceedings of the 2018 Winter Simulation Conference, (WSC 2018) Gothenburg, Sweden Y1 - 2018 SN - 978-1-5386-6572-5 U6 - https://doi.org/10.1109/WSC.2018.8632514 N1 - referierter Beitrag SP - 1346 EP - 1357 PB - IEEE CY - Piscataway, NJ ER - TY - GEN A1 - Blätke, Mary-Ann A1 - Rohr, Christian T1 - BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1682 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 221 EP - 254 ER - TY - GEN A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian A1 - Heiner, Monika T1 - Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks T2 - Computational Biology and Chemistry KW - Coloured Petri nets KW - Hybrid Petri Nets KW - Multi-scale modelling KW - Bistable switch KW - Dendritic spines Y1 - 2018 U6 - https://doi.org/10.1016/j.compbiolchem.2018.05.023 SN - 1476-9271 VL - 76 SP - 87 EP - 100 ER - TY - CHAP A1 - Self, Timothy A1 - Gilbert, David A1 - Heiner, Monika ED - Češka, Milan ED - Šafránek, David T1 - Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models T2 - Computational Methods in Systems Biology, 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings Y1 - 2018 SN - 978-3-319-99428-4 U6 - https://doi.org/10.1007/978-3-319-99429-1_3 N1 - referierter Beitrag SP - 39 EP - 58 PB - Springer CY - Cham ER - TY - GEN A1 - Rohr, Christian T1 - Discrete-Time Leap Method For Stochastic Simulation T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1680 SN - 1875-8681 SN - 0169-2968 VL - 160 IS - 1-2 SP - 181 EP - 198 ER - TY - CHAP A1 - Badawy, Asmaa A1 - Herajy, Mostafa A1 - Awad, Wael A1 - Heiner, Monika T1 - Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets T2 - 13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt Y1 - 2018 SN - 978-1-5386-5111-7 U6 - https://doi.org/10.1109/ICCES.2018.8639484 SP - 268 EP - 272 PB - IEEE CY - Piscataway, NJ ER - TY - GEN A1 - Colombo, Riccardo A1 - Damiani, Chiara A1 - Gilbert, David A1 - Heiner, Monika A1 - Mauri, Giancarlo A1 - Pescini, Dario T1 - Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes T2 - BMC bioinformatics KW - Ensembles KW - Fluxes KW - Kinetic parameters KW - Mechanistic simulations KW - Metabolism KW - ODEs KW - Steady state KW - Systems biology Y1 - 2018 UR - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2181-7 U6 - https://doi.org/10.1186/s12859-018-2181-7 SN - 1471-2105 VL - 19 IS - Suppl. 7 SP - 46 EP - 59 ER - TY - GEN A1 - Liu, Fei A1 - Heiner, Monika A1 - Gilbert, David T1 - Fuzzy Petri nets for modelling of uncertain biological systems T2 - Briefings in Bioinformatics Y1 - 2018 U6 - https://doi.org/10.1093/bib/bby118 SN - 1477-4054 SN - 1467-5463 VL - 2018 ER - TY - GEN A1 - Xu, Hongwei A1 - Curtis, Tanya Y. A1 - Powers, Stephen J. A1 - Raffan, Sarah A1 - Gao, Runhong A1 - Huang, Jianhua A1 - Heiner, Monika A1 - Gilbert, David A1 - Halford, Nigel G. T1 - Genomic, biochemical and modelling analyses of asparagine synthetases from wheat T2 - Frontiers in Plant Science Y1 - 2018 U6 - https://doi.org/10.3389/fpls.2017.02237 SN - 1664-462X VL - 8 ER - TY - GEN A1 - Liu, Fei A1 - Chen, Siyuan A1 - Heiner, Monika A1 - Song, Hengjie T1 - Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets T2 - BMC Systems Biology Y1 - 2018 U6 - https://doi.org/10.1186/s12918-018-0568-8 SN - 1752-0509 VL - 12 IS - Supplement 4 SP - 64 EP - 74 ER - TY - GEN A1 - Baldan, Paolo A1 - Bocci, Martina A1 - Brigolin, Daniele A1 - Cocco, Nicoletta A1 - Heiner, Monika A1 - Simeoni, Marta T1 - Petri Nets for modelling and analysing Trophic Networks T2 - Fundamenta Informaticae Y1 - 2018 U6 - https://doi.org/10.3233/FI-2018-1673 SN - 0169-2968 SN - 1875-8681 VL - 160 IS - 1-2 SP - 27 EP - 52 ER - TY - GEN A1 - Gilbert, David A1 - Heiner, Monika A1 - Rohr, Christian T1 - Petri-net-based 2D Design of DNA Walker Circuits T2 - Natural Computing Y1 - 2018 U6 - https://doi.org/10.1007/s11047-018-9671-4 SN - 1572-9796 SN - 1567-7818 VL - 17 IS - 1 SP - 161 EP - 182 ER - TY - CHAP A1 - Chodak, Jacek A1 - Heiner, Monika ED - Lorenz, Robert ED - Metzger, Johannes T1 - Spike - a command line tool for continuous, stochastic & hybrid simulation of (coloured) Petri nets T2 - Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018 Y1 - 2018 UR - https://opus.bibliothek.uni-augsburg.de/opus4/frontdoor/deliver/index/docId/41861/file/awpn18-lorenz-metzger-OPUS.pdf#page=9 SP - 1 EP - 6 PB - Universität, Institut für Informatik CY - Augsburg ER -