Systems biology:

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• Systems biology
• a new term for an old science

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• A Brief History of Systems Biology
• Basic Concepts in Systems Biology
• Basic scientific questions or properties in
  Systems Biology
• Basic measurement technologies and experimental
  methods in systems biology research
• System Structures Identification
• System Behavior or Function Analysis
• Test system for systems biology
• Hostpathogen systems biology
• Future directions or open issues in systems
  biology

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A Brief History of Systems Biology

• Two important concepts of biology by the end of
  the 19th century
• Reductionist complex situations can be analyzed
  by reducing them to manageable pieces, examining
  each in turn, and reassembling the whole from the
  behavior of the pieces
• Mechanist All biological behavior was
  predetermined, forced, and identical between all
  individuals of a particular species organisms
  were thus merely complex machines.

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• RENE DESCARTES (1595-1650)
• "I am thinking therefore I exist."
• Rene Descartes was a famous French mathematician,
  scientist and philosopher. He was arguably the
  first major philosopher in the modern era to make
  a serious effort to defeat skepticism. His views
  about knowledge and certainty, as well as his
  views about the relationship between mind and
  body have been very influential over the last
  three centuries.

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• Jacques Loeb 18591924
• American physiologist, b. Germany, M.D. Univ. of
  Strasbourg, 1884. He came to the United States in
  1891 and taught at Bryn Mawr, the Univ. of
  Chicago, and the Univ. of California. From 1910
  he was a member of the Rockefeller Institute (now
  Rockefeller Univ.).
• Best known for his tropism theory and for his
  experiments in inducing parthenogenesis and
  regeneration by chemical stimulus, he also
  propounded the mechanistic philosophy that all
  ethics were the outgrowth of humanity's inherited
  tropisms. He was a founder and editor of the
  Journal of General Physiology. His works include
  The Mechanistic Conception of Life (1912),
  Artificial Parthenogenesis and Fertilization
  (1913), and The Organism as a Whole (1916).

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A Brief History of Systems Biology

• from Jan Smuts' holism to Ludwig von
  Bertalanffys General Systems Theory
• Holism (from the Greek Holos, whole) is the
  theory, which makes the existence of "wholes" a
  fundamental feature of the world
• wholes are more than the sum of their
  parts
• the mechanical putting together of their
  parts will not produce them or account for their
  characters and behaviour

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• SMUTS, JAN CHRISTIAAN 18701950 South African
  statesman
• Smuts in retirement wrote Holism and Evolution
  (1926, 3d ed. 1936), in which he developed the
  view that evolution is a sequence of ever more
  comprehensive integrations
• wholes are the real units of nature and as a
  unity wholes are self-organizing systems and
  synergistic, thus cooperating units. For him
  every organism, every plant or animal, and every
  person is a whole that has a certain internal
  organization and measure of self direction as
  well as an individual specific character of its
  own

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A Brief History of Systems Biology

• from Jan Smuts' holism to Ludwig von
  Bertalanffys General Systems Theory
• General Systems Theory
• concepts of organization, non-summative
  wholeness, control, self-regulation,
  equifinality, and self-organization, are as valid
  in the social and behavioral sciences as they are
  in the biological. This led Von Bertalanffy to
  postulate a new discipline, its subject matter
  being the formulation and derivation of those
  principles which are valid for systems in
  general.

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• Ludwig von Bertalanffy (1901-1972)
• in the 1930's Bertalanffy formulated the
  organismic system theory that later became the
  kernel of the GST
• His starting point was to deduce the phenomena of
  life from a spontaneous grouping of system
  forces--comparable, for instance, to the system
  developmental biology nowadays. He based his
  approach on the phenomenal assumption that there
  exists a dynamical process inside the organic
  system.
• In the next step he modelled the heuristic
  fiction of the organism as an open system
  striving towards a steady state.
• Then he postulated two biological principles,
  namely, the maintenance of the organism in the
  non-equilibrium, and the hierarchic organization
  of a systemic structure. Finally he furnished
  this biological system theory with a research
  program that dealt with the quantitative kinetic
  of growth and metabolism

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A Brief History of Systems Biology

• Paradigm shift in biology from component to
  systems analysis
• during the latter half of the 20th century
  focused on the generation of information about
  individual cellular components, their chemical
  composition, and often their biological
  functions( by reductionist approaches)

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A Brief History of Systems Biology

• Paradigm shift in biology from component to
  systems analysis
• Over the past decade, the advent of
  high-throughput experimental technologies is
  forcing biologists to view cells as systems,
  rather than focusing their attention on
  individual cellular components. over the coming
  years and decades biological sciences will be
  increasingly focused on the systems properties of
  cellular and tissue functions

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• Hiroaki Kitano(????)Ph.D Project Director. Sony
  Computer Science Laboratories
• Standardize and develop software platforms for
  systems biology researches
• Theorization and Demonstration of Molecular
  Reaction In Cellular System
• Understanding Robustness of Cellular System and
  its Control Mechanism

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• Leroy Hood (MD PhD) is recognized as one of the
  worlds leading scientists in molecular
  biotechnology and genomics.
• In 2000, Hood co-founded, and is currently
  President of, the Institute for Systems Biology
  in Seattle which pioneers systems approaches to
  biology and medicine.
• His professional career began at Caltech where he
  and his colleagues pioneered four instruments,
  sequencers and synthesizers for DNA and protein.
  Hood was also one of the first advocates of, and
  a key player in, the Human Genome Project.
• In 1992, he moved to the University of Washington
  to create the cross-disciplinary Department of
  Molecular Biotechnology as the William Gates III
  Professor of Biomedical Science. He has played a
  role in founding numerous biotechnology
  companies, including Amgen, Applied Biosystems,
  Systemix, Darwin, Rosetta and MacroGenics.

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What is Systems biology ?

• Systems biology is a new field of biology that
  aims to develop a system-level understanding of
  biological systems. System level understanding
  requires a set of principles and methodologies
  that links the behaviors of molecules to system
  characteristics and functions.
• Systems biology is a comprehensive quantitative
  analysis of the manner in which all the
  components of a biological system interact
  functionally over time

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Basic Concepts in Systems Biology

• There are three basic concepts that are crucial
  to understanding complex biological systems
• Emergence that are not demonstrated by their
  individual parts and cannot be predicted even
  with full understanding of the parts alone

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Basic Concepts in Systems Biology

• There are three basic concepts that are crucial
  to understanding complex biological systems
• Robustness Biological systems maintain
  phenotypic stability in the face of diverse
  perturbations imposed by the environment,
  stochastic events, and genetic variation

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Basic Concepts in Systems Biology

• There are three basic concepts that are crucial
  to understanding complex biological systems
• Modularity a module in a network is a set of
  nodes that have strong interactions and a common
  function

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Basic scientific questions or properties in
Systems Biology

• System structures. These include the network of
  gene interactions and biochemical pathways, as
  well as the mechanisms by which such interactions
  modulate the physical properties of intracellular
  and multicellular structures.

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Basic scientific questions or properties in
Systems Biology

• System dynamics. How a system behaves over time
  under various conditions metabolic analysis,
  sensitivity analysis, dynamic analysis

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Basic scientific questions or properties in
Systems Biology

• System control Mechanisms that systematically
  control the state of the cell can be modulated to
  minimize malfunctions and provide potential
  therapeutic targets for treatment of disease

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Basic scientific questions or properties in
Systems Biology

• System design Strategies to modify and construct
  biological systems having desired properties can
  be devised based on definite design principles
  and simulations, instead of blind trial-and-error.

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Basic measurement technologies and experimental
methods in systems biology research

• Comprehensive Factor, Time-series, Item
• Accurate such specific parameter values as
  binding constant, transcription rate, translation
  rate, chemical reaction rate, degradation rate,
  diffusion rate, speed of active transport, etc.
• Systematic means that measurement is performed in
  such a way that obtained data can be consistently
  integrated

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Basic measurement technologies and experimental
methods in systems biology research

• High-throughput genomic and proteomic platforms
• integration Computer science, mathematics, and
  statistics Model organisms Comparative or
  functional genomics
• Automation and micromation

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