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Combining State-Based and Scenario-Based Approaches in Modeling Biological Systems [chapter]

Jasmin Fisher, David Harel, E. Jane Albert Hubbard, Nir Piterman, Michael J. Stern, Naamah Swerdlin
2005 Lecture Notes in Computer Science  
Here we suggest to combine the two formal approaches used in our group -the state-based formalism of statecharts and the scenario-based formalism of live sequence charts (LSCs).  ...  The biological observations can be compared to the requirements in an engineered system, and the mechanistic model would be analogous to the implementation.  ...  By using a scenario-based approach to formalize the behaviors of the biological system and a state-based approach to formalize the mechanism underlying these behaviors, one can formally verify that the  ... 
doi:10.1007/978-3-540-25974-9_20 fatcat:ylrk5seqpjfvrpf6qk3wy6gmue

Toward Verified Biological Models

A. Sadot, J. Fisher, D. Barak, Y. Admanit, M.J. Stern, E.J.A. Hubbard, D. Harel
2008 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We combined two formal modeling approaches in computer science that were originally developed for nonbiological system design.  ...  A more complete understanding of a biological system is gained when different types of data (and/or conclusions drawn from the data) are integrated into a larger scale representation or model of the system  ...  Thus, we modeled the behavioral aspect of the biological system in the scenario-based formalism and the mechanism that underlies this behavior in the state-based formalism.  ... 
doi:10.1109/tcbb.2007.1076 pmid:18451431 fatcat:oqezysf7ejdqbnwlybsrm2paom

MCR-ALS on metabolic networks: Obtaining more meaningful pathways

A. Folch-Fortuny, M. Tortajada, J.M. Prats-Montalbán, F. Llaneras, J. Picó, A. Ferrer
2015 Chemometrics and Intelligent Laboratory Systems  
By using this method, different constraints can be included in the model, and the same source of variability can be present in different pathways, which is reasonable from a biological standpoint.  ...  In this paper a different grey modelling approach, which aims to incorporate a priori knowledge through constraints on the modelling algorithms, is applied to the same case of study.  ...  Supplementary data The stoichiometric matrix S of the constraint-based modelling of P. pastoris can be found online.  ... 
doi:10.1016/j.chemolab.2014.10.004 fatcat:qkb7r6ah3javtp4r25naxe7dxu

DiSH Simulator: Capturing Dynamics of Cellular Signaling with Heterogeneous Knowledge [article]

Khaled Sayed, Yu-Hsin Kuo, Anuva Kulkarni, Natasa Miskov-Zivanov
2017 arXiv   pre-print
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner  ...  The DiSH-Sim is publicly available and is being used to validate discrete cancer microenvironment and infectious disease models.  ...  For example, since PI3K has only three states (LOW, MEDIUM and HIGH), the combination (PI3K 1 ,PI3K 0 ) = 11 will never occur in the model in .  ... 
arXiv:1705.02660v1 fatcat:brsf7kauwvfqtnkcvwuyq5o2na

Climate change, cyanobacteria blooms and ecological status of lakes: A Bayesian network approach

S. Jannicke Moe, Sigrid Haande, Raoul-Marie Couture
2016 Ecological Modelling  
The BN was able to model effects of climate change and management on ecological status of a lake, by combining scenarios, process-based model output, monitoring data and the national lake assessment system  ...  The objective was (i) to assess the combined effect of changes in land use and climate on the ecological status of a lake and (ii) to assess the suitability of the BN modelling approach for this purpose  ...  for information on the national classification system and Peter Friis Hansen for technical help with the Hugin software.  ... 
doi:10.1016/j.ecolmodel.2016.07.004 fatcat:esorllqb5rhh7gbwfgxmekmcku

A multistage decision support framework to guide tree species management under climate change via habitat suitability and colonization models, and a knowledge-based scoring system

Anantha M. Prasad, Louis R. Iverson, Stephen N. Matthews, Matthew P. Peters
2016 Landscape Ecology  
We combine a tree species habitat model-DISTRIB II, a species colonization model-SHIFT, and knowledgebased scoring system-MODFACs, to illustrate a decision support framework.  ...  Conclusion The combination of these multiple components using diverse approaches leads to tools and products that may help managers make management decisions in the face of a changing climate.  ...  Acknowledgments Thanks to the Northern Research Station, USDA Forest Service, for funding, and external reviewers Maria Janowiak and Laura Leites for their help in improving the manuscript.  ... 
doi:10.1007/s10980-016-0369-7 fatcat:jw2mtgapcrf27ljpnwyotvia64

Crafting game-models using reactive system design

David Harel, Itai Segall, Hillel Kugler, Yaki Setty
2008 Proceedings of the 2008 Conference on Future Play Research, Play, Share - Future Play '08  
Finally, we suggest integrating future games and game design methods into the emerging field of biological modeling, to which reactive system design has recently been successfully applied.  ...  The approach makes it possible to describe behaviors of different parts of the system using different reactive system design languages and tools.  ...  The user interacts with the model through front-end, while the state-based and the scenario-based programs run in the background.  ... 
doi:10.1145/1496984.1497005 dblp:conf/fplay/HarelSKS08 fatcat:bhyaidvw5vbohhbuqowzuabncm

Formal Modelling of C. elegans Development. A Scenario-Based Approach [chapter]

Na'aman Kam, David Harel, Hillel Kugler, Rami Marelly, Amir Pnueli, Jane Albert Hubbard, Michael J. Stern
2004 Natural Computing Series  
The approach stems from the conceptual compatibility of the methods and logic of data collection and analysis in the field of developmental genetics with the languages, methods and tools of scenario-based  ...  We present preliminary results of a new approach to the formal modeling of biological phenomena.  ...  To accomplish this, we also depart in a significant way from the intra-object, state-based, statechart approach used in the previous work, and instead use a more recently-developed interobject, scenario-based  ... 
doi:10.1007/978-3-642-18734-6_8 fatcat:pdeiomti5fhzndkj4ilj2twp5y

Formal Modeling of C. elegans Development: A Scenario-Based Approach [chapter]

Na'aman Kam, David Harel, Hillel Kugler, Rami Marelly, Amir Pnueli, E. Jane Albert Hubbard, Michael J. Stern
2003 Lecture Notes in Computer Science  
The approach stems from the conceptual compatibility of the methods and logic of data collection and analysis in the field of developmental genetics with the languages, methods and tools of scenario-based  ...  We present preliminary results of a new approach to the formal modeling of biological phenomena.  ...  To accomplish this, we also depart in a significant way from the intra-object, state-based, statechart approach used in the previous work, and instead use a more recently-developed interobject, scenario-based  ... 
doi:10.1007/3-540-36481-1_2 fatcat:mlthslm35nalrn7p3b2s3yih2y

Predicting Lake Quality for the Next Generation: Impacts of Catchment Management and Climatic Factors in a Probabilistic Model Framework

S. Jannicke Moe, Raoul-Marie Couture, Sigrid Haande, Anne Lyche Solheim, Leah Jackson-Blake
2019 Water  
Here, we applied a Bayesian network as a meta-model for linking future climate and land-use scenarios for the time horizon 2050–2070, via process-based catchment and lake models, to cyanobacteria abundance  ...  Explorative scenarios showed that the combination of low wind and high temperature gave the most synergistic effects on cyanobacteria under high levels of eutrophication (Chl-a concentration).  ...  Acknowledgments: We thank the participants of the MARS workshop on Bayesian network modelling of catchment case studies for useful discussions, especially Samu Mäntyniemi and David N. Barton.  ... 
doi:10.3390/w11091767 fatcat:n4iovm6365b7vggsl3g6dydsnu

An integrative modeling framework reveals plasticity of TGF-β signaling

Geoffroy Andrieux, Michel Le Borgne, Nathalie Théret
2014 BMC Systems Biology  
Results: Using a new formalism, CADBIOM, which is based on guarded transitions and includes temporal parameters, we have built the first discrete model of TGF-β signaling networks by automatically integrating  ...  We identify 31 different combinations of TGF-β with other extracellular stimuli involved in non-canonical TGF-β pathways that regulate specific gene networks.  ...  Emmanuel Käs (CNRS UMR 5099, Toulouse, France) for help in writing this manuscript and the GenOuest Bioinformatics Platform for hosting the CADBIOM website.  ... 
doi:10.1186/1752-0509-8-30 pmid:24618419 pmcid:PMC4007780 fatcat:q55ydcqoendevkhdfrnzle5mpq

Article Commentary: Dealing with Diversity in Computational Cancer Modeling

David Johnson, Steve McKeever, Georgios Stamatakos, Dimitra Dionysiou, Norbert Graf, Vangelis Sakkalis, Konstantinos Marias, Zhihui Wang, Thomas S. Deisboeck
2013 Cancer Informatics  
General approaches to enabling interoperability using XML-based markup languages for biological modeling are reviewed, concluding with a discussion on efforts towards developing cancer-specific XML markup  ...  This paper discusses the need for interconnecting computational cancer models from different sources and scales within clinically relevant scenarios to increase the accuracy of the models and speed up  ...  Acknowledgements The authors would like to thank the participating institutions of the project consortium and its members.  ... 
doi:10.4137/cin.s11583 pmid:23700360 pmcid:PMC3653811 fatcat:gr2li3oeynarxpgc422bd5p6iu

Machine Perception in Automation: A Call to Arms

Dietmar Bruckner, Rosemarie Velik, Yoseba Penya
2011 EURASIP Journal on Embedded Systems  
This paper is intended for giving a retrospection on perception systems in automation, followed by reviewing state-of-the-art approaches for handling diverse and complex sensor information as well as highlighting  ...  future requirements for more human-like systems that have the ability of performing their actions in complex and unpredictable environments.  ...  Sensor fusion based on models derived from biology is called biological sensor fusion. Approaches to biological sensor fusion made so far can be found in [12] [13] [14] [15] [16] [17] [18] .  ... 
doi:10.1155/2011/608423 fatcat:jurty2iwanfh5fwmtfcmc7vggq

Article Commentary: Predictive Modeling of Drug Treatment in the Area of Personalized Medicine

Lesley A. Ogilvie, Christoph Wierling, Thomas Kessler, Hans Lehrach, Bodo M. H. Lange
2015 Cancer Informatics  
Using fundamental knowledge on the interactions occurring between the components of a complex biological system, large-scale in silico models with predictive capabilities can be generated.  ...  Here, we describe how mechanistic virtual patient models, based on systematic molecular characterization of patients and their diseases, have the potential to shift the theranostic paradigm for oncology  ...  Acknowledgments The authors would like to thank their colleagues at Alacris Theranostics GmbH and the Dahlem Centre for Genome Research and Medical Systems Biology (DCGMS) for fruitful discussions and  ... 
doi:10.4137/cin.s19330 fatcat:lhv4nv5wdzfddbjqn243kq3wqi

Introducing AlienScenarios: a project to develop scenarios and models of biological invasions for the 21 st century

Franz Essl, Bernd Lenzner, Franck Courchamp, Stefan Dullinger, Jonathan M. Jeschke, Ingolf Kühn, Brian Leung, Dietmar Moser, Núria Roura-Pascual, Hanno Seebens
2019 NeoBiota  
The ASNs further serve as overarching concept to parameterize quantitative models of global, continental and regional futures of biological invasions.  ...  We will also establish the first global mechanistic invasion model considering major processes of biological invasions such as source pools, driver dynamics and establishment rates.  ...  Acknowledgements We acknowledge funding by the BiodivERsA and Belmont-Forum call 218 on biodiversity scenarios (  ... 
doi:10.3897/neobiota.45.33366 fatcat:txqxmild7zb3fmh2hzs5qemugq
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