Systems Biology

Systems biology is the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions, which give rise to life.

Image courtesy of US Department of Energy

Instead of analyzing individual components or aspects of the organism, such as sugar metabolism or a cell nucleus, systems biologists focus on all the components and the interactions among them, all as part of one system.

These interactions are ultimately responsible for an organism's form and functions. For example, the immune system is not the result of a single mechanism or gene. Rather, the interactions of numerous genes, proteins, mechanisms and the organism's external environment, produce immune responses to fight infections and diseases.

Systems biology emerged as the result of the genetics "catalog" provided by the Human Genome Project, and a growing understanding of how genes and their resulting proteins give rise to biological form and function.

"Systems biology...is about putting together rather than taking apart, integration rather than reduction. It requires that we develop ways of thinking about integration that are as rigorous as our reductionist programs, but different. It means changing our philosophy, in the full sense of the term." - Denis Noble (2006). The Music of Life: Biology beyond the genome. Oxford University Press.

As an analogy, if you wanted to study an automobile, and only focused on identifying the engine, seat belts, and tail lights, and studied their specific functions, - you would have no real understanding of how an automobile operates. More important, you would have no understanding of how to effectively service the vehicle when something malfunctioned.

 

Systems Biology In Action (The Whole is Greater Than the Sum of the Parts)

The goal of systems biology is to discover new emergent properties in order to better understand the entirety of processes that happen in a biological system. Some of the areas of study are listed below, along with the associated 'omic.

Systems Biology Combines:

• Genomics (Genome)
  • Pharmacogenomics: pharmaco-relevant genes
  • Spliceomics: splicing codons
  • Transcriptomics: Whole cell or tissue gene expression measurements by
    DNA microarrays or serial analysis of gene expression

• Epigenomics: epigene

• Proteomics (Proteins): Identification of proteins and protein expression patterns
• Metabolomics: Identification and measurement of all small-molecules metabolites within a cell or tissue
• Bioinformatics: Use of computers to find and then integrate data

Systems Biology Projects or Efforts

		“To understand systems, and to be able to fully understand a system's emergent properties, systems need be studied as a whole. This recognition that complex systems, especially life, are truly understood from knowledge of the interactions of their component parts is fundamental to systems biology and all the research at the Institute for Systems Biology.” - Quote from Institute for Systems Biology

Researchers are busy working with various organizations and agencies to put all the pieces together.

A few organizations working to accomplish this are listed below:

1) The Institute for Systems Biology (ISB)

The Institute for Systems Biology was co-founded in 2000 in Seattle, Washington. It has since grown to more than 220 staff members, including eleven faculty members and laboratory groups. It has established facilities for DNA sequencing, genotyping, DNA arrays and cell separations.

The Institute developed as a result of the new research model called systems biology, a revolutionary approach to analyzing biological complexity and understanding how biological systems function.

		The Institute has brought together a multidisciplinary group of scholars and scientists, from biologists, mathematicians and engineers, to computer scientists and physicists, in an interactive and collaborative environment.

2) The Cancer Biomedical Informatics Grid (caBIG®):

As systems biology continues to move forward, the National Cancer Institute (NCI) identified the need in 2003 for an informatics initiative of unprecedented scope for the biomedical community in recognition of three factors:

• The growing clinical and economic burden of cancer;
• The transformation of research catalyzed by the molecular revolution and multiple genomics technologies that were generating massive amounts of data; and
• The recognition that the "essential unity" of research and clinical care had powerful potential to improve the outcomes of all cancers, as it had done in the field of pediatric oncology.

For more information on the history of caBIG®, http://cabig.cancer.gov

3) GeneGo's MetaCore is an integrated "knowledge-based" platform for pathway analysis of OMICs data and gene lists with easy to use, intuitive tools for data visualization and analysis plus workflows with reports. This is a systems biology and pathway analysis approach to drug discovery and the software can be purchased online.

4) Systems Biology (A Portal Site for Systems Biology): This is a website aimed to provide information and tools needed to understand systems biology. Examples of information on this website are:

(1) Links to biological databases, research groups, conferences

(2) Software tools

(3) Protocols of biological experiments

(4) Publications.

5) BMC Systems Biology: This is an open access journal publishing original peer-reviewed research articles in systems-level analysis of biological events, whether experimental or theoretical, at the level of molecules, cells or organisms.

CISN Summary:

"Looking at the genome won't tell you much about the downstream function, but looking at the metabolome won't tell you much about the underlying regulation. It's the whole integration (system biology) that's important". - Teresa Fan, University of Louisville, Kentucky