OpenWorm: an open-science approach to modelling Caenorhabditis elegans
OpenWorm is an international collaboration with the aim of understanding how the behaviour of Caenorhabditis elegans (C. elegans) emerges through the underlying biophysical processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2014-11-01
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| Series: | Frontiers in Computational Neuroscience |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fncom.2014.00137/full |
| _version_ | 1818478287079342080 |
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| author | Balazs eSzigeti Balazs eSzigeti Padraig eGleeson Padraig eGleeson Michael eVella Michael eVella Sergey eKhayrulin Sergey eKhayrulin Andrey ePalyanov Andrey ePalyanov Jim eHokanson Jim eHokanson Michael eCurrie Matteo eCantarelli Giovanni eIdili Stephen eLarson |
| author_facet | Balazs eSzigeti Balazs eSzigeti Padraig eGleeson Padraig eGleeson Michael eVella Michael eVella Sergey eKhayrulin Sergey eKhayrulin Andrey ePalyanov Andrey ePalyanov Jim eHokanson Jim eHokanson Michael eCurrie Matteo eCantarelli Giovanni eIdili Stephen eLarson |
| author_sort | Balazs eSzigeti |
| collection | DOAJ |
| description | OpenWorm is an international collaboration with the aim of understanding how the behaviour of Caenorhabditis elegans (C. elegans) emerges through the underlying biophysical processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modelling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modelling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed. |
| first_indexed | 2024-12-10T09:46:01Z |
| format | Article |
| id | doaj.art-5686d8ed437c4c91ac2bb8fe81b6079a |
| institution | Directory Open Access Journal |
| issn | 1662-5188 |
| language | English |
| last_indexed | 2024-12-10T09:46:01Z |
| publishDate | 2014-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Computational Neuroscience |
| spelling | doaj.art-5686d8ed437c4c91ac2bb8fe81b6079a2022-12-22T01:53:49ZengFrontiers Media S.A.Frontiers in Computational Neuroscience1662-51882014-11-01810.3389/fncom.2014.0013799282OpenWorm: an open-science approach to modelling Caenorhabditis elegansBalazs eSzigeti0Balazs eSzigeti1Padraig eGleeson2Padraig eGleeson3Michael eVella4Michael eVella5Sergey eKhayrulin6Sergey eKhayrulin7Andrey ePalyanov8Andrey ePalyanov9Jim eHokanson10Jim eHokanson11Michael eCurrie12Matteo eCantarelli13Giovanni eIdili14Stephen eLarson15University of EdinburghOpenWormUniversity College LondonOpenWormUniversity of CambridgeOpenWormA.P. Ershov Institute of Informatics SystemsOpenWormA.P. Ershov Institute of Informatics SystemsOpenWormDuke UniversityOpenWormOpenWormOpenWormOpenWormOpenWormOpenWorm is an international collaboration with the aim of understanding how the behaviour of Caenorhabditis elegans (C. elegans) emerges through the underlying biophysical processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modelling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modelling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.http://journal.frontiersin.org/Journal/10.3389/fncom.2014.00137/fullC. elegansOpen ScienceEmergent behaviourcomplex systems simulationintegrative modelling |
| spellingShingle | Balazs eSzigeti Balazs eSzigeti Padraig eGleeson Padraig eGleeson Michael eVella Michael eVella Sergey eKhayrulin Sergey eKhayrulin Andrey ePalyanov Andrey ePalyanov Jim eHokanson Jim eHokanson Michael eCurrie Matteo eCantarelli Giovanni eIdili Stephen eLarson OpenWorm: an open-science approach to modelling Caenorhabditis elegans Frontiers in Computational Neuroscience C. elegans Open Science Emergent behaviour complex systems simulation integrative modelling |
| title | OpenWorm: an open-science approach to modelling Caenorhabditis elegans |
| title_full | OpenWorm: an open-science approach to modelling Caenorhabditis elegans |
| title_fullStr | OpenWorm: an open-science approach to modelling Caenorhabditis elegans |
| title_full_unstemmed | OpenWorm: an open-science approach to modelling Caenorhabditis elegans |
| title_short | OpenWorm: an open-science approach to modelling Caenorhabditis elegans |
| title_sort | openworm an open science approach to modelling caenorhabditis elegans |
| topic | C. elegans Open Science Emergent behaviour complex systems simulation integrative modelling |
| url | http://journal.frontiersin.org/Journal/10.3389/fncom.2014.00137/full |
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