Physiomics is a systematic study of

physiome The physiome of an individual's or species' physiological state is the description of its functional behavior. The physiome describes the physiological dynamics of the normal intact organism and is built upon information and structure (genome, prote ...

biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary ...

. Physiomics employs

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

to construct networks of

physiological Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemica ...

features that are associated with

genes In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

and their networks. A few of the methods for determining individual relationships between the DNA sequence and physiological function include metabolic pathway engineering and RNAi analysis. The relationships derived from methods such as these are organized and processed computationally to form distinct networks.

Computer models Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be deter ...

use these experimentally determined networks to develop further predictions of gene function.

History

Physiomics arose from the imbalance between the amount of data being generated by

genome projects Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and ot ...

and the technological ability to analyze the data on a large scale. As technologies such as

high-throughput sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...

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 to aid in this observation became evident. This cycle, aided by computer models, is the basis for bioinformatics and, thus, physiomics.

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. 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.

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

tumor A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...

growth, the modelling of

biological pattern formation The science of pattern formation deals with the visible, (statistically) orderly outcomes of self-organization and the common principles behind similar patterns in nature. In developmental biology, pattern formation refers to the generation of c ...

, a mathematical model for the formation of

stretch marks Stretch marks, also known as striae () or striae distensae, are a form of scarring on the skin with an off-color hue. Over time they may diminish, but will not disappear completely. Striae are caused by tearing of the dermis during periods of r ...

in humans, and predictive algorithms for the growth of viral infections within insect hosts.

Modelling and simulation software

Collaborative physiomics research is promoted in part by the open availability of

bioinformatics software The list of bioinformatics software tools can be split up according to the license used: * List of proprietary bioinformatics software * List of open-source bioinformatics software Alternatively, here is a categorization according to the respective ...

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.

References

External links