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Investigating modularity in the analysis of process algebra models of biochemical systems

Federica Ciocchetta, Maria Luisa Guerriero, Jane Hillston
<span title="2010-02-26">2010</span> <i title="Open Publishing Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qzezkwolyvf33pglm2jldjklca" style="color: black;">Electronic Proceedings in Theoretical Computer Science</a> </i> &nbsp;
In this paper we consider the extent to which the compositional structure which is inherent in process algebra models of biochemical systems can be exploited during model solution.  ...  In this paper we present our preliminary investigations based on a case study of the pheromone pathway in yeast, modelling in the stochastic process algebra Bio-PEPA.  ...  Here we presented a preliminary study of decomposed model analysis for biochemical systems specified in the Bio-PEPA process algebra.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4204/eptcs.19.4">doi:10.4204/eptcs.19.4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/agnnrbvn3nds7oihhka5dkr2mi">fatcat:agnnrbvn3nds7oihhka5dkr2mi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812164951/http://homepages.inf.ed.ac.uk/jeh/Bio-PEPA/biopepa/ciocchetta-guerriero-hillston10_biopepa_modularity(FBTC10).pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/ba/c6baad49ffd9ce022320dad427c3f728d05df66d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4204/eptcs.19.4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Supporting Information from Two classes of functional connectivity in dynamical processes in networks

Venetia Voutsa, Demian Battaglia, Louise J. Bracken, Andrea Brovelli, Julia Costescu, Mario Díaz Muñoz, Brian D. Fath, Andrea Funk, Mel Guirro, Thomas Hein, Christian Kerschner, Christian Kimmich (+13 others)
<span title="2021-10-14">2021</span> <i title="The Royal Society"> figshare.com </i> &nbsp;
The relationship of network structure and dynamics is one of the most extensively investigated problems in the theory of complex systems of the last years.  ...  We delineate these two classes in different categories of dynamical processes—excitations, regular and chaotic oscillators—and provide examples for SC/FC correlations of both classes in each of these models  ...  Social Network Analysis (SNA) Social network analysis adopts concepts and techniques from graph theory, matrix algebra, and stochastic models to consider how structural patterns (and their interdependencies  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.16738887.v2">doi:10.6084/m9.figshare.16738887.v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q763cn6cenayhebm6giel5zvu4">fatcat:q763cn6cenayhebm6giel5zvu4</a> </span>
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Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments

N. A.W. van Riel
<span title="2006-09-26">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Identification of the network components and rate constants that are most critical to the output behaviour of the system is one of the major problems raised in systems biology.  ...  Mathematical models of biochemical networks can look very different.  ...  Acknowledgements The author wishes to thank Mark Musters for his helpful comments and Ad Damen and Paul van den Bosch for useful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbl040">doi:10.1093/bib/bbl040</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17107967">pmid:17107967</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/seoscbai2bblfd37izrnu2jnb4">fatcat:seoscbai2bblfd37izrnu2jnb4</a> </span>
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Contemporary PBSB: Modular Graduate Education in Cells, Systems, and Quantitative Methods

Daniel Gardner, Alessio Accardi, Emre R.F. Aksay, Olaf S. Andersen, Jason R. Banfelder, Olga Boudker, David J. Christini, Olivier Elemento, Bernice Grafstein, Trine Krogh-Madsen
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
We now report a new year-long modular course to prepare first-year Ph.D. students for twenty-first century research in the function, analysis, modeling, and understanding of living systems: Contemporary  ...  The approach actively engages students in a process of directed scientific discovery.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2012.11.2944">doi:10.1016/j.bpj.2012.11.2944</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sor7pizyzfhjfhz6na6k32qg3m">fatcat:sor7pizyzfhjfhz6na6k32qg3m</a> </span>
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Poetic Science: Enriching the Biophysics and Systems Biology Experience

Sherry-Ann Brown
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
We now report a new year-long modular course to prepare first-year Ph.D. students for twenty-first century research in the function, analysis, modeling, and understanding of living systems: Contemporary  ...  The approach actively engages students in a process of directed scientific discovery.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2012.11.2945">doi:10.1016/j.bpj.2012.11.2945</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tesvrxk3n5hlfh7cdmtdy6or2q">fatcat:tesvrxk3n5hlfh7cdmtdy6or2q</a> </span>
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Instances: Incorporating Computational Scientific Thinking Advances into Education & Science Courses

Sofya Borinskaya, NamHwa Kang, Tobias E. Irish, Gregory Mulder, Cristian C. Bordeianu, Robert M. Panoff, Raquell M. Holmes, Rubin H. Landau
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
We now report a new year-long modular course to prepare first-year Ph.D. students for twenty-first century research in the function, analysis, modeling, and understanding of living systems: Contemporary  ...  The approach actively engages students in a process of directed scientific discovery.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2012.11.2942">doi:10.1016/j.bpj.2012.11.2942</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xanonitq2za6zgbwvj5pdijkju">fatcat:xanonitq2za6zgbwvj5pdijkju</a> </span>
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A Sense of Life: Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes

Bud Mishra, Raoul-Sam Daruwala, Yi Zhou, Nadia Ugel, Alberto Policriti, Marco Antoniotti, Salvatore Paxia, Marc Rejali, Archisman Rudra, Vera Cherepinsky, Naomi Silver, William Casey (+24 others)
<span title="2003-09-26">2003</span> <i title="Mary Ann Liebert Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zlgxgb5uazdqdfh5i5hk25cjge" style="color: black;">Omics</a> </i> &nbsp;
, organs, and organisms by drawing upon mathematical and computational approaches developed in the fields of dynamical systems, kinetic analysis, computational theory, and logic.  ...  effort (www.biospice.org), and participating in design of the systems, languages, and experiments involved in this effort.  ...  impose on biological systems, as well as the deciphering of the modular structure of large-scale biochemical processes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/153623103322452387">doi:10.1089/153623103322452387</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14583115">pmid:14583115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dwlspzwk2ng6lk57y2mvlcgaoi">fatcat:dwlspzwk2ng6lk57y2mvlcgaoi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922091337/http://repository.ias.ac.in/5472/1/318.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/45/1f/451f09a9d95ed460da64a3fff96acf2f9d74d5ac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/153623103322452387"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle

Ilya R. Akberdin, Ilya N. Kiselev, Sergey S. Pintus, Ruslan N. Sharipov, Alexander Yu Vertyshev, Olga L. Vinogradova, Daniil V. Popov, Fedor A. Kolpakov
<span title="2021-09-26">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
The integrated modular model validated on diverse including original experimental data and different exercise modes provides a comprehensive in silico platform in order to decipher and track cause–effect  ...  of many genes in working muscle fibres, the systematic understanding of signaling–metabolic pathway interrelations with downstream genetic regulation in the skeletal muscle is still elusive.  ...  developed model and its modules in visual form and provides possibilities for editing and simulation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms221910353">doi:10.3390/ijms221910353</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34638694">pmid:34638694</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8508736/">pmcid:PMC8508736</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/guhb4i6er5f3tcmo73dpljbzoa">fatcat:guhb4i6er5f3tcmo73dpljbzoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210928090508/https://mdpi-res.com/d_attachment/ijms/ijms-22-10353/article_deploy/ijms-22-10353-v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/27/ed/27ede1d3139904a46f7d2a2d99633c0db2fca9bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms221910353"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8508736" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Surviving heat shock: Control strategies for robustness and performance

H. El-Samad, H. Kurata, J. C. Doyle, C. A. Gross, M. Khammash
<span title="2005-01-24">2005</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives.  ...  It also suggests a mathematical and conceptual modular decomposition that defines the functional blocks or submodules of the heat shock system.  ...  We thank Irina Grigorova for critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0403510102">doi:10.1073/pnas.0403510102</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15668395">pmid:15668395</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC549435/">pmcid:PMC549435</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yzkmkpmtyrbizornggx4sd7txa">fatcat:yzkmkpmtyrbizornggx4sd7txa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20081203085640/http://biochemistry.ucsf.edu:80/labs/elsamad/people/Hana_El_Samad/publications/PNAS-HS.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ab/44/ab44d6c0790ea123f1da0a3d67a4dd0f90c9faa7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0403510102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC549435" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ANTS 2012 special issue

Marco Dorigo, Mauro Birattari, Christian Blum, Anders Lyhne Christensen, Andries Engelbrecht, Roderich Groß, Thomas Stützle
<span title="2013-06-26">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pjsg6rax5je33dmgu7rpti4aya" style="color: black;">Swarm Intelligence</a> </i> &nbsp;
Bio-PEPA is a timed process algebra, which integrates a wide range of modelling and analysis techniques, starting from a single microscopic specification.  ...  The approach is based on Ciocchetta and Hillston's Bio-PEPA, which was originally developed in the context of biochemical networks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11721-013-0086-7">doi:10.1007/s11721-013-0086-7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ydemaqigwjf2hetxqxmajppxmi">fatcat:ydemaqigwjf2hetxqxmajppxmi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812042251/http://naturalrobotics.group.shef.ac.uk/publications/2013-si-dorigo.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/41/6b412fa712c55a4ea0d1fb3d29e2f07bb1ea8a04.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11721-013-0086-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Ten top reasons for systems biology to get into model-driven engineering

Magali Roux-Rouquié, Debora Schuch da Rosa
<span title="">2006</span> <i title="ACM Press"> Proceedings of the 2006 international workshop on Global integrated model management - GaMMa &#39;06 </i> &nbsp;
Recent progresses in post-genomic biology allow addressing issues at the system level through the coupling of experimental and modeling approaches that constitute the core of Systems Biology (SB).  ...  Current models in SB are reviewed and the main requirements to conduct models integration are identified.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge Corrado Priami for many useful discussions. Work was supported by grants from CNRS (STIC-SANTE) and UNITN.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1138304.1138316">doi:10.1145/1138304.1138316</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bixas24amvexjovuapuw5z6swu">fatcat:bixas24amvexjovuapuw5z6swu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160809172413/http://biodataconsulting.com/pages/resources/magali/GaMMa06.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e4/d7/e4d724e1fba124601a723e15c806760ef4dd607f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1138304.1138316"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Design and development of software tools for Bio-PEPA

Adam Duguid, Stephen Gilmore, Maria Luisa Guerriero, Jane Hillston, Laurence Loewe
<span title="">2009</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7n2gtrr2tzevzonkaymviwxhsa" style="color: black;">Proceedings of the 2009 Winter Simulation Conference (WSC)</a> </i> &nbsp;
This paper surveys the design of software tools for the Bio-PEPA process algebra.  ...  Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks.  ...  Stephen Gilmore and Maria Luisa Guerriero are supported by the EPSRC grant EP/E031439/1 "Stochastic Process Algebra for Biochemical Signalling Pathway Analysis".  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/wsc.2009.5429725">doi:10.1109/wsc.2009.5429725</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/wsc/DuguidGGHL09.html">dblp:conf/wsc/DuguidGGHL09</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vpmsziaa5zb4bkcswi42edkw5a">fatcat:vpmsziaa5zb4bkcswi42edkw5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171117090613/https://core.ac.uk/download/pdf/28975627.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2a/c0/2ac09cdcc9b628f1574912bc8468447a20be5d9c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/wsc.2009.5429725"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Energy-based analysis of biochemical cycles using bond graphs

P. J. Gawthrop, E. J. Crampin
<span title="2014-09-24">2014</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pgnawoixszagldk2tfhndhrgzu" style="color: black;">Proceedings of the Royal Society A</a> </i> &nbsp;
However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible.  ...  In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function.  ...  This construction allows a modular approach to modelling in which cellular processes and reactions can be broken down into components, which are then connected to form a model of the system under study  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspa.2014.0459">doi:10.1098/rspa.2014.0459</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25383030">pmid:25383030</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4197480/">pmcid:PMC4197480</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pdac3brmsncmtdceld6gdztrii">fatcat:pdac3brmsncmtdceld6gdztrii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302010717/http://pdfs.semanticscholar.org/9b62/be5141df32ac689d900b428858f4f284c736.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9b/62/9b62be5141df32ac689d900b428858f4f284c736.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspa.2014.0459"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197480" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior [chapter]

Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud Mishra
<span title="">2002</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In this paper we describe XS-systems: computational models whose aim is to provide the users of S-systems with the extra tool of an automaton modeling the temporal evolution of complex biochemical reactions  ...  Several biological and biochemical mechanisms can be modeled with relatively simple sets of differential algebraic equations (DAE).  ...  First, the use of XS-systems automata as semantics of S-systems in connection with the modular design of large maps simulating biochemical systems is still not completely resolved.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-36265-7_41">doi:10.1007/3-540-36265-7_41</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g4u7rh5rtvb2vjr7ruuvawfhwe">fatcat:g4u7rh5rtvb2vjr7ruuvawfhwe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060927024914/http://www.dimi.uniud.it/~policrit/Papers/HiPC-2002-final.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/bd/f0bd53558f7f88363929f0b8ab6eeeae3eeddffb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-36265-7_41"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Computational Approaches for Translational Clinical Research in Disease Progression

Mary F. McGuire, Madurai Sriram Iyengar, David W. Mercer
<span title="2011-08-01">2011</span> <i title="BMJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xwb6ks7gznawzcx6edh5he5htm" style="color: black;">Journal of Investigative Medicine</a> </i> &nbsp;
Trauma is the leading cause of mortality in Americans under 45 years of age, and its rapid progression offers both opportunities and challenges for computational analysis of trends in molecular patterns  ...  In this paper we review a selection of published research regarding computational methodologies, primarily from systems biology, that support translational research from the molecular level to the bedside  ...  modular control elements or related biological processes 18-21 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2310/jim.0b013e318224d8cc">doi:10.2310/jim.0b013e318224d8cc</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21712727">pmid:21712727</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3196807/">pmcid:PMC3196807</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bxnxrhooefb4lgdpf6n6ezpppi">fatcat:bxnxrhooefb4lgdpf6n6ezpppi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206100449/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3196807&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/a9/dca9394355cc57ccb4907691dcb178c0087f1616.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2310/jim.0b013e318224d8cc"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196807" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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