In order to understand life phenomena you have to combine :
bioinformatics : the organization and use of biological information,
particularly computer-driven processing and analysis of data and databases
in the fields of molecular biology and genetics
One of the ultimate goal of life science is to gain a comprehensive
understanding of the cell, the smallest unit of life. Realistically speaking,
however, it is probably impossible for human intelligence to map out how
the metabolites inside of the cell act, because understanding the cell
means knowing how each part functions in coordination with the system as
a whole, and under what conditions, and how much change occurs. Just thinking
about how the thousands of metabolites in different locations inside of
the cell interact, under these conditions, is enough to make you dizzy.
Whether or not computer simulation is the most appropriate way of doing
this, I think that at present time there are no other options. It is also
important to conduct experiments for the sake of quantification and simulation
of the dynamic changes in cells. In short, various information is required
for making models of cells by computer, and this information can only be
corroborated experimentally. Biology is set to become highly quantitative
in the 21st century. It will become a computer-intensive discipline. Software
infrastructure is another critical component of system biology research.
Although attempts have been made to build simulation software and to make
use of the many analysis and computing packages originally designed for
general engineering purposes, there is no common infrastructure or standard
to enable integration of these resources :
XML-based computer-readable model
definition that enables models to be exchanged between software tools.
developed by the Bioengineering Institute at the University of Auckland,
incorporates existing languages including MathML and RDF to encode mathematical
Systems Biology Mark-up Language
(SBML) : a "species" is a term defined by SBML as "an entity that
takes part in reactions", and it distinguishes the different states that
are caused by enzymatic modification, combination, dissociation, and translocation.
To distinguish the different states of a component in the same compartment
in detail, we only need to assign a unique name to each state using suitable
subscripts. For example, states of the protein that translocates from cytosol
to plasma membrane can be distinguishable by names such as "XXcyt"
and "XXpm". Since SBML is a machine-readable format, all the
information can be used for a range of computational analysis, including
ERATO Systems Biology Workbench
(SBW) is built on SBML and provides a framework of modular open-source
software for systems biology research. With the ongoing rapid increase
in both volume and diversity of 'omic' data (genomics, transcriptomics,
proteomics, and others), the development and adoption of data standards
is of paramount importance to realize the promise of systems biology. A
recent trend in data standard development has been to use extensible markup
language (XML) as the preferred mechanism to define data representations.
But the syntactic and document-centric XML cannot achieve the level of
interoperability required by the highly dynamic and integrated bioinformatics
applications. Semantic web technologies (RDF), as recommended by the World
Wide Web consortium (W3C), expand current data standard technology for
biological data representation and managementref.
Abstraction Layer for Simulation Analysis (BALSA) is a project of the
Cell Systems Initiative of the University of Washington. BALSA is a symbolic
language for representing biological processes, including cell signaling.
One of the examples includes the canonical Wnt/beta-catenin Pathway from
STKE. BALSA is currently a prototype of a Java-based cell systems modeling
environment prototype. A cursory explanation of BALSA and its support software,
CellDesigner : modeling tool
for biochemical networks. Designed to be compliant with SBML format
Cytoscape : an open-source bioinformatics
software platform for visualizing molecular interaction networks. Can integrate
the network interactions with gene-expression profiles
: a desktop or client-server software package for visualization and analysis
of biological pathways. Works with the company's ResNet database of over
1,000,000 functional relationships
How quickly data can be written to your hard drive ? about 435,000 million
bits a second. Electron pulses lasting 2.3 picoseconds or less are too
short to reliably record a bit of computer information. But such a rate
is still a thousand times faster than we can achieve in state-of-the-art
magnetic devices today.
information theory : a system for analyzing, chiefly by statistical
methods, the characteristics of communicated messages and the systems that
encode, transmit, distort, receive, and decode them.
Facility for the Analysis
of Chemical Thermodynamics (FACT) : started in 1976 as a collaboration
of chemical properties and thermodynamics in metallurgy, FACT has expanded
over the last 25-plus years to become a fully integrated thermodynamic
database employing the FACTSage software now in use in hundreds of laboratories
around the world. With FACTsage, users can predict reaction directions,
calculate thermodynamics in solution, and plot phase diagrams, among many