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The
National Simulation Resource Physiome Project is a North American project at The University of Washington. The key elements of the NSR Project are the databasing of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Other North American projects include the Biological Network Modeling Center at the California Institute of Technology, the National Center for Cell Analysis and Modeling at The University of Connecticut, and the NIH Center for Integrative Biomedical Computing at The University of Utah.
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In 1993, the
International Union of Physiological Sciences (IUPS) in Australia presented a physiome project with the purpose of providing a quantitative description of physiological dynamics and functional behavior of the intact organism. The Physiome Project became a major focus of the IUPS in 2001.
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were being used to generate large amounts of genomic data, effective methods needed to be designed to experimentally interpret and computationally organize this data. Science can be illustrated as a cycle linking knowledge to observations. In the post-genomic era, the ability of computational methods
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A. Madzvamuse, R.D.K. Thomas, T. Sekimura, A.J. Wathen P.K. Maini, The moving grid finite element method applied to biological problems, In
Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, Proceedings of Chubu 2002 Conference (T. Sekimura, S. Noji, N. Ueno and P.K.
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H. Perfahl, H.M. Byrne, T. Chen, V. Estrella, T. Alarcon, A. Lapin, R.A. Gatenby, R.J. Gillies, M.C. Lloyd, P.K. Maini, M. Reuss, M.R. Owen, 3D multiscale modelling of angiogenesis and vascular tumour growth, in, Micro and Nano Flow
Systems Flow Systems for Bioanalysis, M.W. Collins and C.S. Konig
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There are many different possible applications of physiomics, each requiring different computational models or the combined use of several different models. Examples of such applications include a three dimensional model for
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Tools such as these are developed using markup languages specific to bioinformatics research. Many of these markup languages are freely available for use in software development, such as CellML, NeuroML, and SBML.
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Kamath, Ravi S.; Fraser, Andrew G.; Dong, Yan; Poulin, Gino; Durbin, Richard; Gotta, Monica; Kanapin, Alexander (2003). "Systematic functional analysis of the
Caenorhabditis elegans genome using RNAi".
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such as simulation programs and modelling environments. There are many institutions and research groups that make their software available to the public. Examples of openly available software include:
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Kell, D.B.; Oliver, S.G. (2004). "Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-drive science in the post-genomic era".
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and their networks. A few of the methods for determining individual relationships between the DNA sequence and physiological function include
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588:– Lists far more than this page, with references/origins. Maintained by the (CHI) Cambridge Health Institute. One of the earliest lists.
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Sanford, Karl; Soucaille, Phillipe; Whited, Gregg; Chotani, Gopal (2002). "Genomics to fluxomics and physiomics — pathway engineering".
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to aid in this observation became evident. This cycle, aided by computer models, is the basis for bioinformatics and, thus, physiomics.
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analysis. The relationships derived from methods such as these are organized and processed computationally to form distinct networks.
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SimTK – a collection of biological modelling resources made available by The
National NIH Center for Biomedical Computing.
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E-Cell System – a simulation and modelling environment for biological systems offered by Keio
University in Tokyo, Japan.
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JSim and
Systems Biology Workbench – bioinformatics tools offered by The University of Washington.
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use these experimentally determined networks to develop further predictions of gene function.
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in humans, and predictive algorithms for the growth of viral infections within insect hosts.
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and the technological ability to analyze the data on a large scale. As technologies such as
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Hunter, P.; Borg, T. (2003). "Integration from proteins to organs: the
Physiome Project".
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BISEN – a simulation environment made available by The
Medical College of Wisconsin.
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Collaborative physiomics research is promoted in part by the open availability of
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Physiomics arose from the imbalance between the amount of data being generated by
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Varner, J. D. (2000). "Large-scale prediction of phenotype: Concept".
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542:"Modelling the within-host growth of viral infections in insects"
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Bailey, J.E (1991). "Toward a science of metabolic engineering".
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Gilmore, S.J.; Vaughan, Jr; Madzvamuse, A.; Maini, P.K. (2012).
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594:– News and information about systems biology research centers.
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https://people.maths.ox.ac.uk/maini/PKM%20publications/158.pdf
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https://people.maths.ox.ac.uk/maini/PKM%20publications/358.pdf
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White, S.M.; Burden, J.P.; Maini, P.K.; Hails, R.S. (2012).
314:"Physiology, physiomics, and biophysics: A matter of words"
485:Maini, eds), Springer-Verlag Tokyo, 59-65 (2003)
500:"A mechanochemical model of striae distensae"
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318:Progress in Biophysics and Molecular Biology
98:, a mathematical model for the formation of
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425:"Strategies for the Physiome Project"
390:Nature Reviews Molecular Cell Biology
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592:National Centers for Systems Biology
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35:features that are associated with
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472:(eds), Bioanalysis, 2,29-48(2013)
106:Modelling and simulation software
429:Annals of Biomedical Engineering
331:10.1016/j.pbiomolbio.2009.08.001
287:Current Opinion in Microbiology
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423:Bassingthwaighte, JB (2000).
299:10.1016/S1369-5274(02)00318-1
45:metabolic pathway engineering
96:biological pattern formation
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561:10.1016/j.jtbi.2012.07.022
69:high-throughput sequencing
598:October 19, 2013, at the
519:10.1016/j.mbs.2012.06.007
312:Welch, G. Rickey (2009).
94:growth, the modelling of
31:to construct networks of
19:is a systematic study of
190:10.1126/science.2047876
112:bioinformatics software
85:Research applications
27:. Physiomics employs
226:10.1038/nature01278
184:(5013): 1668–1675.
367:10.1002/bies.10385
260:Biotechnol. Bioeng
441:10.1114/1.1313771
220:(6920): 231–237.
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163:References
157:Proteomics
17:Physiomics
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355:BioEssays
152:Phenomics
609:Category
596:Archived
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527:22796062
459:11144666
410:12612642
375:14696046
340:19699228
242:12529635
142:Genomics
136:See also
41:proteins
21:physiome
450:3425440
198:2047876
178:Science
59:History
25:biology
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545:(PDF)
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92:tumor
37:genes
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455:PMID
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238:PMID
194:PMID
49:RNAi
47:and
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515:doi
511:240
445:PMC
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398:doi
363:doi
326:doi
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230:hdl
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