Development of a framework for whole-cell model creation
Resumo
The use of whole-cell models in research has the potential to be a powerful tool for scientific discovery, allowing researchers to test hypotheses faster than using in-vitro or in vivo methods. Such models can be considered the equivalent of Computer Aided Design for Biology. However, given their complexity, it is still difficult to employ them as an instrument in investigations. In order to solve this problem, we are developing a framework with the purpose to guide and help scientists through the process of creating whole-cell models faster, enabling them to use these tools as part of their research. This paper brings details of the early stages of the framework’s development process.
Palavras-chave:
Computational Systems Biology
Referências
CARRERA, J.; COVERT, M. W. (2015) “Why Build Whole-Cell Models?” In: Trends in Cell Biology, v. 25, n. 12, p. 719–722, 2015.
COVERT, M. W. (2014) “Simulating a living cell”. Scientific American, v. 310, n. 1, p. 44–51.
FALL, C.P.; MARLAND, E.S.; WAGNER, J.M.; TYSON, J.J. (2002) “Computational cell biology”. Springer.
FREDDOLINO, P. L.; TAVAZOIE, S. (2012) “The dawn of virtual cell biology”. Cell, v. 150, n. 2, p. 248–250.
GOLDBERG, A. P.; CHEW, Y. H.; KARR, J. R. (2016) “Toward Scalable Whole-Cell Modeling of Human Cells”. Proceedings of the 2016 annual ACM Conference on SIGSIM Principles of Advanced Discrete Simulation - SIGSIM-PADS ’16, p. 259–262.
KARR, J. R. et al. (2012) “A whole-cell computational model predicts phenotype from genotype”. Cell, v. 150, n. 2, p. 389–401.
KARR, J. R.; TAKAHASHI, K.; FUNAHASHI, A. (2015) “The principles of wholecell modeling”, In: Current Opinion in Microbiology, v. 27, p. 18–24.
MACKLIN, D. N.; RUGGERO, N. A.; COVERT, M. W. (2014) “The future of wholecell modeling”, In: Current Opinion in Biotechnology, v. 28, p. 111–115.
PURCELL, O. et al. (2013) “Towards a whole-cell modeling approach for synthetic biology”. Chaos, v. 23, n. 2, p. 1–8.
SANGHVI, J. C. et al. (2013) “Accelerated discovery via a whole-cell model”. Nature Methods, v. 10, n. 12, p. 1192–1195.
TOMITA, M. (2001) “Whole-cell simulation: A grand challenge of the 21st century, In: Trends in Biotechnology, v. 19, n. 6, p. 205–210.
TOMITA, M. et al. (1999) “E-CELL: Software environment for whole-cell simulation”, In: Bioinformatics, v. 15, n. 1, p. 72–84.
COVERT, M. W. (2014) “Simulating a living cell”. Scientific American, v. 310, n. 1, p. 44–51.
FALL, C.P.; MARLAND, E.S.; WAGNER, J.M.; TYSON, J.J. (2002) “Computational cell biology”. Springer.
FREDDOLINO, P. L.; TAVAZOIE, S. (2012) “The dawn of virtual cell biology”. Cell, v. 150, n. 2, p. 248–250.
GOLDBERG, A. P.; CHEW, Y. H.; KARR, J. R. (2016) “Toward Scalable Whole-Cell Modeling of Human Cells”. Proceedings of the 2016 annual ACM Conference on SIGSIM Principles of Advanced Discrete Simulation - SIGSIM-PADS ’16, p. 259–262.
KARR, J. R. et al. (2012) “A whole-cell computational model predicts phenotype from genotype”. Cell, v. 150, n. 2, p. 389–401.
KARR, J. R.; TAKAHASHI, K.; FUNAHASHI, A. (2015) “The principles of wholecell modeling”, In: Current Opinion in Microbiology, v. 27, p. 18–24.
MACKLIN, D. N.; RUGGERO, N. A.; COVERT, M. W. (2014) “The future of wholecell modeling”, In: Current Opinion in Biotechnology, v. 28, p. 111–115.
PURCELL, O. et al. (2013) “Towards a whole-cell modeling approach for synthetic biology”. Chaos, v. 23, n. 2, p. 1–8.
SANGHVI, J. C. et al. (2013) “Accelerated discovery via a whole-cell model”. Nature Methods, v. 10, n. 12, p. 1192–1195.
TOMITA, M. (2001) “Whole-cell simulation: A grand challenge of the 21st century, In: Trends in Biotechnology, v. 19, n. 6, p. 205–210.
TOMITA, M. et al. (1999) “E-CELL: Software environment for whole-cell simulation”, In: Bioinformatics, v. 15, n. 1, p. 72–84.
Publicado
30/10/2018
Como Citar
CARVALHO, Frederico Chaves; AMBRÓSIO, Paulo Eduardo.
Development of a framework for whole-cell model creation. In: ARTIGOS CURTOS - SIMPÓSIO BRASILEIRO DE BIOINFORMÁTICA (BSB) , 2018, Niterói.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2018
.
p. 1-6.
DOI: https://doi.org/10.5753/bsb_estendido.2018.8796.
