Modelling the Structure and Dynamics of Biological Pathways.
There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN...
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| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-08-01
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| Series: | PLoS Biology |
| Online Access: | https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1002530&type=printable |
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| _version_ | 1850232231212089344 |
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| author | Laura O'Hara Alessandra Livigni Thanos Theo Benjamin Boyer Tim Angus Derek Wright Sz-Hau Chen Sobia Raza Mark W Barnett Paul Digard Lee B Smith Tom C Freeman |
| author_facet | Laura O'Hara Alessandra Livigni Thanos Theo Benjamin Boyer Tim Angus Derek Wright Sz-Hau Chen Sobia Raza Mark W Barnett Paul Digard Lee B Smith Tom C Freeman |
| author_sort | Laura O'Hara |
| collection | DOAJ |
| description | There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system's dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems. |
| format | Article |
| id | doaj-art-c3c71f4edf7e47079a0cdaf49db9d4fb |
| institution | OA Journals |
| issn | 1544-9173 1545-7885 |
| language | English |
| publishDate | 2016-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj-art-c3c71f4edf7e47079a0cdaf49db9d4fb2025-08-20T02:03:15ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852016-08-01148e100253010.1371/journal.pbio.1002530Modelling the Structure and Dynamics of Biological Pathways.Laura O'HaraAlessandra LivigniThanos TheoBenjamin BoyerTim AngusDerek WrightSz-Hau ChenSobia RazaMark W BarnettPaul DigardLee B SmithTom C FreemanThere is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system's dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems.https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1002530&type=printable |
| spellingShingle | Laura O'Hara Alessandra Livigni Thanos Theo Benjamin Boyer Tim Angus Derek Wright Sz-Hau Chen Sobia Raza Mark W Barnett Paul Digard Lee B Smith Tom C Freeman Modelling the Structure and Dynamics of Biological Pathways. PLoS Biology |
| title | Modelling the Structure and Dynamics of Biological Pathways. |
| title_full | Modelling the Structure and Dynamics of Biological Pathways. |
| title_fullStr | Modelling the Structure and Dynamics of Biological Pathways. |
| title_full_unstemmed | Modelling the Structure and Dynamics of Biological Pathways. |
| title_short | Modelling the Structure and Dynamics of Biological Pathways. |
| title_sort | modelling the structure and dynamics of biological pathways |
| url | https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1002530&type=printable |
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