Difference between revisions of "CSB modelling principles"
Jump to navigation
Jump to search
(2 intermediate revisions by the same user not shown) | |||
Line 45: | Line 45: | ||
==Further reading and resources== | ==Further reading and resources== | ||
; Concepts | ; Concepts | ||
− | {{#pmid: | + | {{#pmid: 23578462}} |
− | {{#pmid: | + | {{#pmid: 21762717}} |
− | {{#pmid:18937364}} | + | {{#pmid: 21704063}} |
− | {{#pmid: | + | {{#pmid: 20824468}} |
− | {{#pmid: | + | {{#pmid: 19381532}} |
− | {{#pmid: | + | {{#pmid: 18937364}} |
+ | {{#pmid: 16962764}} | ||
+ | {{#pmid: 16849185}} | ||
+ | {{#pmid: 15763552}} | ||
;Applications | ;Applications | ||
− | {{#pmid: | + | {{#pmid: 21863502}} |
− | {{#pmid:21197651}} | + | {{#pmid: 21197651}} |
− | {{#pmid: | + | {{#pmid: 20836044}} |
<!-- {{WWW|WWW_UniProt}} --> | <!-- {{WWW|WWW_UniProt}} --> |
Latest revision as of 21:21, 17 February 2014
Quantitative Systems Models: Principles
This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.
Developing predictive, quantitative systems models can be considered the holy grail of the field, yet it is a formidable challenge. Not only do we require that models are quantitatively correct, which is a difficult task given that our knowledge of kinetic parameters and time-varying concentrations is incomplete, we also need to integrate models over several spatial and temporal orders of magnitude - from molecular-scale reactions to organ- and organism-scale phenotypes.
Introductory reading
Blinov & Moraru (2012) Logic modeling and the ridiculome under the rug. BMC Biol 10:92. (pmid: 23171629) |
Tenazinha & Vinga (2011) A survey on methods for modeling and analyzing integrated biological networks. IEEE/ACM Trans Comput Biol Bioinform 8:943-58. (pmid: 21116043) |
Santos et al. (2011) A practical guide to genome-scale metabolic models and their analysis. Meth Enzymol 500:509-32. (pmid: 21943912) |
Contents
- Principles
- Applications
Further reading and resources
- Concepts
Kirk et al. (2013) Model selection in systems and synthetic biology. Curr Opin Biotechnol 24:767-74. (pmid: 23578462) |
Bradley et al. (2011) OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project. Prog Biophys Mol Biol 107:32-47. (pmid: 21762717) |
Qu et al. (2011) Multi-scale modeling in biology: how to bridge the gaps between scales?. Prog Biophys Mol Biol 107:21-31. (pmid: 21704063) |
Vallabhajosyula & Raval (2010) Computational modeling in systems biology. Methods Mol Biol 662:97-120. (pmid: 20824468) |
Frazier et al. (2009) Computational representation of biological systems. Methods Mol Biol 541:535-49. (pmid: 19381532) |
Kestler et al. (2008) Network modeling of signal transduction: establishing the global view. Bioessays 30:1110-25. (pmid: 18937364) |
Ridgway et al. (2006) Accommodating space, time and randomness in network simulation. Curr Opin Biotechnol 17:493-8. (pmid: 16962764) |
Coveney & Fowler (2005) Modelling biological complexity: a physical scientist's perspective. J R Soc Interface 2:267-80. (pmid: 16849185) |
Takahashi et al. (2005) Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico. FEBS Lett 579:1783-8. (pmid: 15763552) |
- Applications
Nookaew et al. (2011) Genome-scale metabolic models of Saccharomyces cerevisiae. Methods Mol Biol 759:445-63. (pmid: 21863502) |
Kriete et al. (2011) Computational systems biology of aging. Wiley Interdiscip Rev Syst Biol Med 3:414-28. (pmid: 21197651) |
Bhattacharya et al. (2010) Toward failure analyses in systems biology. Wiley Interdiscip Rev Syst Biol Med 2:507-517. (pmid: 20836044) |