dc.contributor.author |
Shahidi, Niloofar |
|
dc.contributor.author |
Pan, Michael |
|
dc.contributor.author |
Safaei, Soroush |
|
dc.contributor.author |
Tran, Kenneth |
|
dc.contributor.author |
Crampin, Edmund J |
|
dc.contributor.author |
Nickerson, David P |
|
dc.coverage.spatial |
United States |
|
dc.date.accessioned |
2022-06-19T23:19:47Z |
|
dc.date.available |
2022-06-19T23:19:47Z |
|
dc.date.issued |
2021-05-13 |
|
dc.identifier.citation |
(2021). PLoS Computational Biology, 17(5), e1008859-. |
|
dc.identifier.issn |
1553-734X |
|
dc.identifier.uri |
https://hdl.handle.net/2292/60000 |
|
dc.description.abstract |
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in biology and physiology are often not modular and therefore difficult to assemble into larger models. Even when this is possible, the resulting model may not be useful due to inconsistencies either with the laws of physics or the physiological behaviour of the system. Here, we propose a general methodology for composing models, combining the energy-based bond graph approach with semantics-based annotations. This approach improves model composition and ensures that a composite model is physically plausible. As an example, we demonstrate this approach to automated model composition using a model of human arterial circulation. The major benefit is that modellers can spend more time on understanding the behaviour of complex biological and physiological systems and less time wrangling with model composition. |
|
dc.format.medium |
Electronic-eCollection |
|
dc.language |
eng |
|
dc.publisher |
Public Library of Science (PLoS) |
|
dc.relation.ispartofseries |
PLoS computational biology |
|
dc.rights |
Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. |
|
dc.rights.uri |
https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm |
|
dc.rights.uri |
https://creativecommons.org/licenses/by/4.0/ |
|
dc.subject |
Arteries |
|
dc.subject |
Humans |
|
dc.subject |
Computational Biology |
|
dc.subject |
Blood Circulation |
|
dc.subject |
Models, Biological |
|
dc.subject |
Models, Cardiovascular |
|
dc.subject |
Semantics |
|
dc.subject |
Computer Graphics |
|
dc.subject |
Computer Simulation |
|
dc.subject |
Software |
|
dc.subject |
Networking and Information Technology R&D |
|
dc.subject |
Science & Technology |
|
dc.subject |
Life Sciences & Biomedicine |
|
dc.subject |
Biochemical Research Methods |
|
dc.subject |
Mathematical & Computational Biology |
|
dc.subject |
Biochemistry & Molecular Biology |
|
dc.subject |
MATHEMATICAL-MODEL |
|
dc.subject |
SYSTEMS BIOLOGY |
|
dc.subject |
BLOOD-FLOW |
|
dc.subject |
MULTISCALE |
|
dc.subject |
NETWORK |
|
dc.subject |
CIRCULATION |
|
dc.subject |
01 Mathematical Sciences |
|
dc.subject |
06 Biological Sciences |
|
dc.subject |
08 Information and Computing Sciences |
|
dc.title |
Hierarchical semantic composition of biosimulation models using bond graphs. |
|
dc.type |
Journal Article |
|
dc.identifier.doi |
10.1371/journal.pcbi.1008859 |
|
pubs.issue |
5 |
|
pubs.begin-page |
e1008859 |
|
pubs.volume |
17 |
|
dc.date.updated |
2022-05-17T00:12:22Z |
|
dc.rights.holder |
Copyright: The author |
en |
dc.identifier.pmid |
33983945 (pubmed) |
|
pubs.author-url |
https://www.ncbi.nlm.nih.gov/pubmed/33983945 |
|
pubs.publication-status |
Published |
|
dc.rights.accessrights |
http://purl.org/eprint/accessRights/OpenAccess |
en |
pubs.subtype |
Research Support, Non-U.S. Gov't |
|
pubs.subtype |
research-article |
|
pubs.subtype |
Journal Article |
|
pubs.subtype |
Research Support, N.I.H., Extramural |
|
pubs.elements-id |
852842 |
|
pubs.org-id |
Bioengineering Institute |
|
pubs.org-id |
ABI Associates |
|
dc.identifier.eissn |
1553-7358 |
|
dc.identifier.pii |
PCOMPBIOL-D-21-00472 |
|
pubs.number |
ARTN e1008859 |
|
pubs.record-created-at-source-date |
2022-05-17 |
|
pubs.online-publication-date |
2021-05-13 |
|