Physiomics
Physiomics is a systematic study of
History
Physiomics arose from the imbalance between the amount of data being generated by
Physiome projects
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.[7] 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.[8] 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.
Research applications
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
Modelling and simulation software
Collaborative physiomics research is promoted in part by the open availability of bioinformatics software 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:
- JSim and Systems Biology Workbench – bioinformatics tools offered by The University of Washington.
- BISEN – a simulation environment made available by The Medical College of Wisconsin.
- SimTK – a collection of biological modelling resources made available by The National NIH Center for Biomedical Computing.
- E-Cell System – a simulation and modelling environment for biological systems offered by Keio University in Tokyo, Japan.
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.
See also
References
- PMID 2047876.
- PMID 12529635.
- ^ .
- .
- PMID 19699228.
- PMID 14696046.
- PMID 12612642.
- PMID 11144666.
- ^ 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 (eds), Bioanalysis, 2,29-48(2013)https://people.maths.ox.ac.uk/maini/PKM%20publications/358.pdf
- ^ 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. Maini, eds), Springer-Verlag Tokyo, 59-65 (2003) https://people.maths.ox.ac.uk/maini/PKM%20publications/158.pdf
- PMID 22796062.
- PMID 22877574.
External links
- List of omics – Lists far more than this page, with references/origins. Maintained by the (CHI) Cambridge Health Institute. One of the earliest lists.
- National Centers for Systems Biology – News and information about systems biology research centers. Archived October 19, 2013, at the Wayback Machine