Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology
The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal...
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| Format: | Online |
| Language: | English |
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Frontiers Media SA
2021
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| Online Access: | 25551 |
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| author | David A. Rosenblueth |
| author_browse | David A. Rosenblueth |
| author_facet | David A. Rosenblueth |
| author_sort | David A. Rosenblueth |
| collection | Directory of Open Access Books |
| description | The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal methods to new domains. This progress has spurred a conspicuous optimism in computational biology. This optimism, in turn, has promoted a rapid increase in collaboration between specialists of biology with specialists of computer science. Through sheer complexity, however, many important biological problems are at present intractable, and it is not clear whether we will ever be able to solve such problems. We are in the process of learning what kind of model and what kind of analysis and synthesis techniques to use for a particular problem. Some existing formalisms have been readily used in biological problems, others have been adapted to biological needs, and still others have been especially developed for biological systems. This Research Topic has examples of cases (1) employing existing methods, (2) adapting methods to biology, and (3) developing new methods. We can also see discrete and Boolean models, and the use of both simulators and model checkers. Synthesis is exemplified by manual and by machine-learning methods. We hope that the articles collected in this Research Topic will stimulate new research. |
| format | Online |
| id | doab-20.500.12854ir-43706 |
| institution | Directory of Open Access Books |
| language | eng |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media SA |
| publisherStr | Frontiers Media SA |
| record_format | ojs |
| spelling | doab-20.500.12854ir-437062024-04-05T12:34:52Z Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology David A. Rosenblueth QH426-470 TA1-2040 TP248.13-248.65 Q1-390 model checking Logic programing Answer set programing attractors of Boolean networks synthesis of biochemical models Gene Regulatory Networks Boolean networks biochemical networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal methods to new domains. This progress has spurred a conspicuous optimism in computational biology. This optimism, in turn, has promoted a rapid increase in collaboration between specialists of biology with specialists of computer science. Through sheer complexity, however, many important biological problems are at present intractable, and it is not clear whether we will ever be able to solve such problems. We are in the process of learning what kind of model and what kind of analysis and synthesis techniques to use for a particular problem. Some existing formalisms have been readily used in biological problems, others have been adapted to biological needs, and still others have been especially developed for biological systems. This Research Topic has examples of cases (1) employing existing methods, (2) adapting methods to biology, and (3) developing new methods. We can also see discrete and Boolean models, and the use of both simulators and model checkers. Synthesis is exemplified by manual and by machine-learning methods. We hope that the articles collected in this Research Topic will stimulate new research. 2021-02-11T10:19:10Z 2021-02-11T10:19:10Z 2018-02-27 16:16:44 2016 book 25551 16648714 9782889450428 https://directory.doabooks.org/handle/20.500.12854/43706 eng Frontiers Research Topics image/jpeg Attribution 4.0 International http://www.frontiersin.org/books/Computational_Methods_for_Understanding_Complexity_The_Use_of_Formal_Methods_in_Biology/1066#nogo http://journal.frontiersin.org/researchtopic/2177/computational-methods-for-understanding-complexity-the-use-of-formal-methods-in-biology Frontiers Media SA 10.3389/978-2-88945-042-8 10.3389/978-2-88945-042-8 bf5ce210-e72e-4860-ba9b-c305640ff3ae 9782889450428 111 open access |
| spellingShingle | QH426-470 TA1-2040 TP248.13-248.65 Q1-390 model checking Logic programing Answer set programing attractors of Boolean networks synthesis of biochemical models Gene Regulatory Networks Boolean networks biochemical networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) David A. Rosenblueth Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology |
| title | Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology |
| title_full | Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology |
| title_fullStr | Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology |
| title_full_unstemmed | Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology |
| title_short | Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology |
| title_sort | computational methods for understanding complexity the use of formal methods in biology |
| topic | QH426-470 TA1-2040 TP248.13-248.65 Q1-390 model checking Logic programing Answer set programing attractors of Boolean networks synthesis of biochemical models Gene Regulatory Networks Boolean networks biochemical networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) |
| topic_facet | QH426-470 TA1-2040 TP248.13-248.65 Q1-390 model checking Logic programing Answer set programing attractors of Boolean networks synthesis of biochemical models Gene Regulatory Networks Boolean networks biochemical networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) |
| url | 25551 |
| work_keys_str_mv | AT davidarosenblueth computationalmethodsforunderstandingcomplexitytheuseofformalmethodsinbiology |