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Toward community standards and software for whole-cell modeling
OBJECTIVE: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. METHODS: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evalua...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
2016
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451320/ https://www.ncbi.nlm.nih.gov/pubmed/27305665 http://dx.doi.org/10.1109/TBME.2016.2560762 |
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| author | Waltemath, Dagmar Karr, Jonathan R. Bergmann, Frank T. Chelliah, Vijayalakshmi Hucka, Michael Krantz, Marcus Liebermeister, Wolfram Mendes, Pedro Myers, Chris J. Pir, Pinar Alaybeyoglu, Begum Aranganathan, Naveen K Baghalian, Kambiz Bittig, Arne T. Pinto Burke, Paulo E. Cantarelli, Matteo Chew, Yin Hoon Costa, Rafael S. Cursons, Joseph Czauderna, Tobias Goldberg, Arthur P. Gómez, Harold F. Hahn, Jens Hameri, Tuure Hernandez Gardiol, Daniel F. Kazakiewicz, Denis Kiselev, Ilya Knight-Schrijver, Vincent Knüpfer, Christian König, Matthias Lee, Daewon Lloret-Villas, Audald Mandrik, Nikita Medley, J. Kyle Moreau, Bertrand Naderi-Meshkin, Hojjat Palaniappan, Sucheendra K. Priego-Espinosa, Daniel Scharm, Martin Sharma, Mahesh Smallbone, Kieran Stanford, Natalie J. Song, Je-Hoon Theile, Tom Tokic, Milenko Tomar, Namrata Touré, Vasundra Uhlendorf, Jannis Varusai, Thawfeek M Watanabe, Leandro H. Wendland, Florian Wolfien, Markus Yurkovich, James T. Zhu, Yan Zardilis, Argyris Zhukova, Anna Schreiber, Falk |
| author_facet | Waltemath, Dagmar Karr, Jonathan R. Bergmann, Frank T. Chelliah, Vijayalakshmi Hucka, Michael Krantz, Marcus Liebermeister, Wolfram Mendes, Pedro Myers, Chris J. Pir, Pinar Alaybeyoglu, Begum Aranganathan, Naveen K Baghalian, Kambiz Bittig, Arne T. Pinto Burke, Paulo E. Cantarelli, Matteo Chew, Yin Hoon Costa, Rafael S. Cursons, Joseph Czauderna, Tobias Goldberg, Arthur P. Gómez, Harold F. Hahn, Jens Hameri, Tuure Hernandez Gardiol, Daniel F. Kazakiewicz, Denis Kiselev, Ilya Knight-Schrijver, Vincent Knüpfer, Christian König, Matthias Lee, Daewon Lloret-Villas, Audald Mandrik, Nikita Medley, J. Kyle Moreau, Bertrand Naderi-Meshkin, Hojjat Palaniappan, Sucheendra K. Priego-Espinosa, Daniel Scharm, Martin Sharma, Mahesh Smallbone, Kieran Stanford, Natalie J. Song, Je-Hoon Theile, Tom Tokic, Milenko Tomar, Namrata Touré, Vasundra Uhlendorf, Jannis Varusai, Thawfeek M Watanabe, Leandro H. Wendland, Florian Wolfien, Markus Yurkovich, James T. Zhu, Yan Zardilis, Argyris Zhukova, Anna Schreiber, Falk |
| author_sort | Waltemath, Dagmar |
| collection | PubMed |
| description | OBJECTIVE: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. METHODS: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. RESULTS: Our analysis revealed several challenges to representing WC models using the current standards. CONCLUSION: We, therefore, propose several new WC modeling standards, software, and databases. SIGNIFICANCE: We anticipate that these new standards and software will enable more comprehensive models. |
| format | Online Article Text |
| id | pubmed-5451320 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2016 |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-54513202017-05-31 Toward community standards and software for whole-cell modeling Waltemath, Dagmar Karr, Jonathan R. Bergmann, Frank T. Chelliah, Vijayalakshmi Hucka, Michael Krantz, Marcus Liebermeister, Wolfram Mendes, Pedro Myers, Chris J. Pir, Pinar Alaybeyoglu, Begum Aranganathan, Naveen K Baghalian, Kambiz Bittig, Arne T. Pinto Burke, Paulo E. Cantarelli, Matteo Chew, Yin Hoon Costa, Rafael S. Cursons, Joseph Czauderna, Tobias Goldberg, Arthur P. Gómez, Harold F. Hahn, Jens Hameri, Tuure Hernandez Gardiol, Daniel F. Kazakiewicz, Denis Kiselev, Ilya Knight-Schrijver, Vincent Knüpfer, Christian König, Matthias Lee, Daewon Lloret-Villas, Audald Mandrik, Nikita Medley, J. Kyle Moreau, Bertrand Naderi-Meshkin, Hojjat Palaniappan, Sucheendra K. Priego-Espinosa, Daniel Scharm, Martin Sharma, Mahesh Smallbone, Kieran Stanford, Natalie J. Song, Je-Hoon Theile, Tom Tokic, Milenko Tomar, Namrata Touré, Vasundra Uhlendorf, Jannis Varusai, Thawfeek M Watanabe, Leandro H. Wendland, Florian Wolfien, Markus Yurkovich, James T. Zhu, Yan Zardilis, Argyris Zhukova, Anna Schreiber, Falk IEEE Trans Biomed Eng Article OBJECTIVE: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. METHODS: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. RESULTS: Our analysis revealed several challenges to representing WC models using the current standards. CONCLUSION: We, therefore, propose several new WC modeling standards, software, and databases. SIGNIFICANCE: We anticipate that these new standards and software will enable more comprehensive models. 2016-06-10 2016-10 /pmc/articles/PMC5451320/ /pubmed/27305665 http://dx.doi.org/10.1109/TBME.2016.2560762 Text en http://creativecommons.org/licenses/by/3.0/ This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/licenses/by/3.0/. Personal use of this material is permitted. However, permission to use this material for any other purposes must be obtained from the IEEE by sending an email to pubs-permissions@ieee.org. |
| spellingShingle | Article Waltemath, Dagmar Karr, Jonathan R. Bergmann, Frank T. Chelliah, Vijayalakshmi Hucka, Michael Krantz, Marcus Liebermeister, Wolfram Mendes, Pedro Myers, Chris J. Pir, Pinar Alaybeyoglu, Begum Aranganathan, Naveen K Baghalian, Kambiz Bittig, Arne T. Pinto Burke, Paulo E. Cantarelli, Matteo Chew, Yin Hoon Costa, Rafael S. Cursons, Joseph Czauderna, Tobias Goldberg, Arthur P. Gómez, Harold F. Hahn, Jens Hameri, Tuure Hernandez Gardiol, Daniel F. Kazakiewicz, Denis Kiselev, Ilya Knight-Schrijver, Vincent Knüpfer, Christian König, Matthias Lee, Daewon Lloret-Villas, Audald Mandrik, Nikita Medley, J. Kyle Moreau, Bertrand Naderi-Meshkin, Hojjat Palaniappan, Sucheendra K. Priego-Espinosa, Daniel Scharm, Martin Sharma, Mahesh Smallbone, Kieran Stanford, Natalie J. Song, Je-Hoon Theile, Tom Tokic, Milenko Tomar, Namrata Touré, Vasundra Uhlendorf, Jannis Varusai, Thawfeek M Watanabe, Leandro H. Wendland, Florian Wolfien, Markus Yurkovich, James T. Zhu, Yan Zardilis, Argyris Zhukova, Anna Schreiber, Falk Toward community standards and software for whole-cell modeling |
| title | Toward community standards and software for whole-cell modeling |
| title_full | Toward community standards and software for whole-cell modeling |
| title_fullStr | Toward community standards and software for whole-cell modeling |
| title_full_unstemmed | Toward community standards and software for whole-cell modeling |
| title_short | Toward community standards and software for whole-cell modeling |
| title_sort | toward community standards and software for whole-cell modeling |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451320/ https://www.ncbi.nlm.nih.gov/pubmed/27305665 http://dx.doi.org/10.1109/TBME.2016.2560762 |
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