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Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082)
2018
Dagstuhl Reports
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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]
2005
Lecture Notes in Computer Science
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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]
2012
Lecture Notes in Computer Science
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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]
2013
arXiv
pre-print
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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
2016
Social Science Research Network
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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
2004
Briefings in Bioinformatics
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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
2014
Proceedings of the 29th ACM/IEEE international conference on Automated software engineering - ASE '14
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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
2015
AIMS Bioengineering
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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
2016
Open Biochemistry Journal
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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]
2011
Radiation Damage in Biomolecular Systems
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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]
2018
arXiv
pre-print
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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)
2009
Mathematical Biosciences
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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]
2013
Emergence, Complexity and Computation
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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
2014
Biotechnology Journal
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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
1993
Proceedings. International Conference on Intelligent Systems for Molecular Biology
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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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