Process calculi for biological processes
Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in si...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Bernini, Andrea [verfasserIn] Brodo, Linda [verfasserIn] Degano, Pierpaolo [verfasserIn] Falaschi, Moreno [verfasserIn] Hermith, Diana [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2018 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
Enthalten in: Natural computing - Dordrecht : Springer Science + Business Media B.V., 2002, 17(2018), 2 vom: 06. März, Seite 345-373 |
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| Übergeordnetes Werk: |
volume:17 ; year:2018 ; number:2 ; day:06 ; month:03 ; pages:345-373 |
| Links: |
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| DOI / URN: |
10.1007/s11047-018-9673-2 |
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| Katalog-ID: |
SPR016352246 |
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| 520 | |a Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. | ||
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| 650 | 4 | |a Quantitative biology |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a Brodo, Linda |e verfasserin |4 aut | |
| 700 | 1 | |a Degano, Pierpaolo |e verfasserin |4 aut | |
| 700 | 1 | |a Falaschi, Moreno |e verfasserin |4 aut | |
| 700 | 1 | |a Hermith, Diana |e verfasserin |4 aut | |
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10.1007/s11047-018-9673-2 doi (DE-627)SPR016352246 (SPR)s11047-018-9673-2-e DE-627 ger DE-627 rakwb eng 004 ASE 54.28 bkl 54.72 bkl Bernini, Andrea verfasserin aut Process calculi for biological processes 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. Algorithmic Systems Biology (dpeaa)DE-He213 In-silico simulation (dpeaa)DE-He213 Functional and dynamic modeling (dpeaa)DE-He213 Quantitative biology (dpeaa)DE-He213 Brodo, Linda verfasserin aut Degano, Pierpaolo verfasserin aut Falaschi, Moreno verfasserin aut Hermith, Diana verfasserin aut Enthalten in Natural computing Dordrecht : Springer Science + Business Media B.V., 2002 17(2018), 2 vom: 06. März, Seite 345-373 (DE-627)340872314 (DE-600)2065639-7 1572-9796 nnns volume:17 year:2018 number:2 day:06 month:03 pages:345-373 https://dx.doi.org/10.1007/s11047-018-9673-2 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 54.28 ASE 54.72 ASE AR 17 2018 2 06 03 345-373 |
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10.1007/s11047-018-9673-2 doi (DE-627)SPR016352246 (SPR)s11047-018-9673-2-e DE-627 ger DE-627 rakwb eng 004 ASE 54.28 bkl 54.72 bkl Bernini, Andrea verfasserin aut Process calculi for biological processes 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. Algorithmic Systems Biology (dpeaa)DE-He213 In-silico simulation (dpeaa)DE-He213 Functional and dynamic modeling (dpeaa)DE-He213 Quantitative biology (dpeaa)DE-He213 Brodo, Linda verfasserin aut Degano, Pierpaolo verfasserin aut Falaschi, Moreno verfasserin aut Hermith, Diana verfasserin aut Enthalten in Natural computing Dordrecht : Springer Science + Business Media B.V., 2002 17(2018), 2 vom: 06. März, Seite 345-373 (DE-627)340872314 (DE-600)2065639-7 1572-9796 nnns volume:17 year:2018 number:2 day:06 month:03 pages:345-373 https://dx.doi.org/10.1007/s11047-018-9673-2 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 54.28 ASE 54.72 ASE AR 17 2018 2 06 03 345-373 |
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10.1007/s11047-018-9673-2 doi (DE-627)SPR016352246 (SPR)s11047-018-9673-2-e DE-627 ger DE-627 rakwb eng 004 ASE 54.28 bkl 54.72 bkl Bernini, Andrea verfasserin aut Process calculi for biological processes 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. Algorithmic Systems Biology (dpeaa)DE-He213 In-silico simulation (dpeaa)DE-He213 Functional and dynamic modeling (dpeaa)DE-He213 Quantitative biology (dpeaa)DE-He213 Brodo, Linda verfasserin aut Degano, Pierpaolo verfasserin aut Falaschi, Moreno verfasserin aut Hermith, Diana verfasserin aut Enthalten in Natural computing Dordrecht : Springer Science + Business Media B.V., 2002 17(2018), 2 vom: 06. März, Seite 345-373 (DE-627)340872314 (DE-600)2065639-7 1572-9796 nnns volume:17 year:2018 number:2 day:06 month:03 pages:345-373 https://dx.doi.org/10.1007/s11047-018-9673-2 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 54.28 ASE 54.72 ASE AR 17 2018 2 06 03 345-373 |
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Bernini, Andrea @@aut@@ Brodo, Linda @@aut@@ Degano, Pierpaolo @@aut@@ Falaschi, Moreno @@aut@@ Hermith, Diana @@aut@@ |
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Bernini, Andrea |
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Bernini, Andrea ddc 004 bkl 54.28 bkl 54.72 misc Algorithmic Systems Biology misc In-silico simulation misc Functional and dynamic modeling misc Quantitative biology Process calculi for biological processes |
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004 ASE 54.28 bkl 54.72 bkl Process calculi for biological processes Algorithmic Systems Biology (dpeaa)DE-He213 In-silico simulation (dpeaa)DE-He213 Functional and dynamic modeling (dpeaa)DE-He213 Quantitative biology (dpeaa)DE-He213 |
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ddc 004 bkl 54.28 bkl 54.72 misc Algorithmic Systems Biology misc In-silico simulation misc Functional and dynamic modeling misc Quantitative biology |
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process calculi for biological processes |
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Process calculi for biological processes |
| abstract |
Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. |
| abstractGer |
Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. |
| abstract_unstemmed |
Abstract Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies. |
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Process calculi for biological processes |
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https://dx.doi.org/10.1007/s11047-018-9673-2 |
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Brodo, Linda Degano, Pierpaolo Falaschi, Moreno Hermith, Diana |
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Brodo, Linda Degano, Pierpaolo Falaschi, Moreno Hermith, Diana |
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| doi_str |
10.1007/s11047-018-9673-2 |
| up_date |
2024-07-03T22:34:19.506Z |
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| score |
7.4012833 |