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Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082)

Yaakov Benenson, Neil Dalchau, Heinz Koeppl, Oded Maler, Michael Wagner
2018 Dagstuhl Reports  
Synthetic biology aims for the rational bottom-up engineering of new biological functionalities.  ...  This was often achieved with the help of two ingredients, a library of previously well-characterized parts and some computational modeling.  ...  We extend an approach developed for diverse models and systems and adapt it to biological circuits, and specifically to continuous-time Markov Chain models of Chemical Reaction Networks.  ... 
doi:10.4230/dagrep.8.2.88 dblp:journals/dagstuhl-reports/BenensonDKM18 fatcat:gh3poeii3ndmffhuiax3bf2pfu

An Agent-Oriented Conceptual Framework for Systems Biology [chapter]

Nicola Cannata, Flavio Corradini, Emanuela Merelli, Andrea Omicini, Alessandro Ricci
2005 Lecture Notes in Computer Science  
We propose a conceptual framework to engineering an agent society which simulate the behavior of a biological process.  ...  Biological processes are complex systems, i.e. a set of components that interacts with each other and with an external dynamic environment.  ...  Acknowledgement We would like to thank Fulvio Esposito, Guido Favia, Russ Altman, Roberto Ciccocioppo for valuable speeches on malaria and pharmacogenomics process modelling.  ... 
doi:10.1007/11599128_8 fatcat:ykvzindvnfcujks2un4lnwizda

A Beginner's Guide to Systems Simulation in Immunology [chapter]

Grazziela P. Figueredo, Peer-Olaf Siebers, Uwe Aickelin, Stephanie Foan
2012 Lecture Notes in Computer Science  
The second contribution is the introduction of a quick guide containing the main steps for modelling and simulation in immunology, together with challenges that occur during the model development.  ...  In addition, to our knowledge, there is few research on the processes for the development of simulation models for the immune system. Hence, for this work, we have two contributions to knowledge.  ...  Moreover, as validation occurs throughout the whole process, if any of the stages is not validated (data available, real world understanding and description, conceptual model, computer model, experimental  ... 
doi:10.1007/978-3-642-33757-4_5 fatcat:ruf4uykxbvhttn45scxv3l5ki4

A Beginners Guide to Systems Simulation in Immunology [article]

Grazziela P. Figueredo, Peer-Olaf Siebers, Uwe Aickelin, Stephanie Foan
2013 arXiv   pre-print
The second contribution is the introduction of a quick guide containing the main steps for modelling and simulation in immunology, together with challenges that occur during the model development.  ...  In addition, to our knowledge, there is few research on the processes for the development of simulation models for the immune system. Hence, for this work, we have two contributions to knowledge.  ...  Moreover, as validation occurs throughout the whole process, if any of the stages is not validated (data available, real world understanding and description, conceptual model, computer model, experimental  ... 
arXiv:1307.1597v2 fatcat:vbozavvlmbawzij4etoios3y5m

A Beginners Guide to Systems Simulation in Immunology

Grazziela P. Figueredo, Peer-Olaf Siebers, Uwe Aickelin, Stephanie Foan
2016 Social Science Research Network  
The second contribution is the introduction of a quick guide containing the main steps for modelling and simulation in immunology, together with challenges that occur during the model development.  ...  In addition, to our knowledge, there is few research on the processes for the development of simulation models for the immune system. Hence, for this work, we have two contributions to knowledge.  ...  Moreover, as validation occurs throughout the whole process, if any of the stages is not validated (data available, real world understanding and description, conceptual model, computer model, experimental  ... 
doi:10.2139/ssrn.2828463 fatcat:zthdqympf5et7exr4l3ugi4dvq

Modelling the dynamics of biosystems

C. Priami
2004 Briefings in Bioinformatics  
The need for a more formal handling of biological information processing with stochastic and mobile process algebras is addressed.  ...  Biology can benefit this approach, yielding a better understanding of behavioural properties of cells, and computer science can benefit this approach, obtaining new computational models inspired by nature  ...  Process algebras have been extensively used in the computer science community for the specification and verification of concurrent and mobile systems.  ... 
doi:10.1093/bib/5.3.259 pmid:15383212 fatcat:kooxjwbrnbgghjketwvsywz2pi

Automated requirements analysis for a molecular watchdog timer

Samuel J. Ellis, Eric R. Henderson, Titus H. Klinge, James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Divita Mathur, Andrew S. Miner
2014 Proceedings of the 29th ACM/IEEE international conference on Automated software engineering - ASE '14  
Our process uses incremental design practices with goal-oriented requirements engineering, software verification tools, and custom software to help automate the software engineering process.  ...  Dynamic systems in DNA nanotechnology are often programmed using a chemical reaction network (CRN) model as an intermediate level of abstraction.  ...  Hetherington et al. and Sumner et al. have composed an advanced computational model of a biological system from sub-models describing its di↵erent aspects [22, 48] .  ... 
doi:10.1145/2642937.2643007 dblp:conf/kbse/EllisHKLLLMM14 fatcat:2e7pmnunknh2bpwpvyxtz4w6yi

Integrative metabolic engineering

George H McArthur IV, Pooja P Nanjannavar, Emily H Miller, Stephen S Fong
2015 AIMS Bioengineering  
Recent advances in experimental and computational synthetic biology are extremely useful for achieving metabolic engineering objectives.  ...  Computational tools that aid in the design and in silico simulation of metabolic pathways are especially useful.  ...  Fisher and other members of the Fong Lab for helpful discussions and for comments on the manuscript.  ... 
doi:10.3934/bioeng.2015.3.93 fatcat:2s26fw57nzauphsmyz2iledite

Available Instruments for Analyzing Molecular Dynamics Trajectories

I. V. Likhachev, N. K. Balabaev, O. V. Galzitskaya
2016 Open Biochemistry Journal  
Molecular dynamics trajectories are the result of molecular dynamics simulations.  ...  In this review, we describe different programs for processing molecular dynamics trajectories.  ...  This work was funded in part by the Russian Science Foundation (grant number 14-14-0536) for OVG, the programs "Molecular and Cellular Biology" (01201353567) for IVL, and grant MES RK Grant 2835/GF3 of  ... 
doi:10.2174/1874091x01610010001 pmid:27053964 pmcid:PMC4797681 fatcat:qogx6q4upjdqrgfd4nvq7vssim

Monte Carlo Methods to Model Radiation Interactions and Induced Damage [chapter]

Antonio Muñoz, Martina C. Fuss, M. A. Cortés-Giraldo, Sébastien Incerti, Vladimir Ivanchenko, Anton Ivanchenko, J. M. Quesada, Francesc Salvat, Christophe Champion, Gustavo García Gómez-Tejedor
2011 Radiation Damage in Biomolecular Systems  
Mean features of each model, as the type of radiation to consider, the energy range covered by primary and secondary particles, the type of interactions included in the simulation and the considered target  ...  This review is devoted to the analysis of some Monte Carlo (MC) simulation programmes which have been developed to describe radiation interaction with biologically relevant materials.  ...  (COST Action MP1002) and the Australian Research Council through its Centres of Excellence program.  ... 
doi:10.1007/978-94-007-2564-5_13 fatcat:savrrrbd55hz5axfl52ox4yeda

The Spectrum of Mechanism-oriented Models for Explanations of Biological Phenomena [article]

C. Anthony Hunt, Ahmet Erdemir, Feilim Mac Gabhann, William W. Lytton, Edward A. Sander, Mark K. Transtrum, Lealem Mulugeta
2018 arXiv   pre-print
To encourage improved semantic and methodological clarity, we describe the spectrum of Mechanism-oriented Models being used to develop explanations of biological phenomena.  ...  These model types are intended to contribute to the foundation of an ontology of mechanism-based simulation research in the life sciences.  ...  [32] developed and validated the first Simulation of an Analogous-mechanism Model for how DNA recombination might occur.  ... 
arXiv:1801.04909v1 fatcat:kuiful7fnjdqdl5dy22z2stmgm

A model of TLR4 signaling and tolerance using a qualitative, particle–event-based method: Introduction of spatially configured stochastic reaction chambers (SCSRC)

Gary An
2009 Mathematical Biosciences  
The component detail of the SCSRC may allow for sequential parsing of various preconditioning effects, something not possible without computational modeling and simulation, and may give insight into the  ...  spatial chamber configuration and molecular event rules, and experimentally define biochemical reaction rate constants.  ...  Acknowledgments This work was supported in part by the National Institute of Disability Rehabilitation Research (NIDRR) Grant H133E070024.  ... 
doi:10.1016/j.mbs.2008.10.001 pmid:18950646 fatcat:c6chmxvc3jfoxghzjlpaxmm57y

Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology [chapter]

Jonathan Blakes, Jamie Twycross, Savas Konur, Francisco Jose Romero-Campero, Natalio Krasnogor, Marian Gheorghe
2013 Emergence, Complexity and Computation  
Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and  ...  This chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework.  ...  Some parts of this paper are based on the first authors PhD thesis [13] .  ... 
doi:10.1007/978-3-319-03191-0_1 fatcat:vz4edynpzbglxiyg23evljxeqi

Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack

David Henderson, Lesley A. Ogilvie, Nicholas Hoyle, Ulrich Keilholz, Bodo Lange, Hans Lehrach, OncoTrack Consortium
2014 Biotechnology Journal  
To be able to develop, manipulate, and execute computer models of biological processes, we have developed PyBioS (pybios.molgen.mpg.de), an object oriented modeling platform [84, 85] .  ...  DNA and RNA are, however, not the only players in the complex biological processes we have to control and model.  ... 
doi:10.1002/biot.201400109 pmid:25074435 pmcid:PMC4314672 fatcat:e6hoxnv4x5dgvf6xb4aqp6wohm

Building large knowledge bases in molecular biology

O Schmeltzer, C Médigue, P Uvietta, F Rechenmann, F Dorkeld, G Perrière, C Gautier
1993 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
As a joint effort between our computer science and molecular biology research projects, the knowledge bases we have developed in molecular genetics have shown however that the basic object-oriented model  ...  The increasing complexity and size of the objects to be described and managed have led biologists to rely on advanced data models such as the object-oriented model.  ...  Such an approach allows simulation at an intermediate level of precision, and it makes it possible without requiring experimental data as for differential equations.  ... 
pmid:7584356 fatcat:3nlmy3xkpjaihmhazn7p2ajc6u
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