As you worked your way through high school, or otherwise worked to prepare
yourself for college, you were probably unaware that an information
explosion was taking place in the field of biology. This explosion, brought on
by advances in biotechnology and communicated by faster, more powerful
computers, has allowed scientists to gather data more quickly and disseminate
data to colleagues in the global scientific community with the click of a
The Brazilian Symposium on Bioinformatics (BSB) 2008 was held at Santo
Andr´e (S˜ao Paulo), Brazil, August 28–30, 2008. BSB 2008 was the third symposium
in the BSB series, although BSB was preceded by the Brazilian Workshop
on Bioinformatics (WOB). This previous event had three consecutive editions in
2002 (Gramado, Rio Grande do Sul), 2003 (Maca´e, Rio de Janeiro), and 2004
(Bras´ılia, Distrito Federal). The change from workshop to symposium reflects
the increasing quality and interest behind this meeting.
Bioinformatics ? Biology and Computers ? What do they have to do with each other?
I suppose that this question could have been raised even in 19th century when
technologies of computers and biology were just emerging. At one city in France the
great Louis Pasteur (1822-1895) was studying how fermentation of alcohol was
linked to the existence of a specific microorganism. In another city in England,
equally great Charles Babbage (1791-1871) was oiling his Analytical Engine in which
Ada Lovelace, a mathematician who understood Babbage's vision, was trying to
calculate the Bernoulli numbers.
Immediately after the first drafts of the human genome sequence were reported almost
a decade ago, the importance of genomics and functional genomics studies became
well recognized across the broad disciplines of biological sciences research.
Computational chemistry and molecular modeling is a fast emerging area which is used for the modeling and simulation of small chemical and biological systems in order to understand and predict their behavior at the molecular level. It has a wide range of applications in various disciplines of engineering sciences, such as materials science, chemical engineering, biomedical engineering, etc.
Nowadays it is difficult to imagine an area of knowledge that can continue developing
without the use of computers and informatics. It is not different with biology, that has
seen an unpredictable growth in recent decades, with the rise of a new discipline,
bioinformatics, bringing together molecular biology, biotechnology and information
Computational biology is undergoing a revolution from a traditionally compute-intensive science conducted by individuals and small research groups to a high-throughput, datadriven science conducted by teams working in both academia and industry. It is this new biology as a data-driven science in the era of Grid Computing that is the subject of this chapter.
Biological signal analysis1 encompasses several interdisciplinary topics that deal with analysing
signals generated by various physiological processes in the human body. These signals could be
electrical, chemical or acoustic in origin and an analysis of these signals are often useful in
explaining and/or identifying pathological conditions of the human body. However, these signals in
their rawest form do not provide much information and therefore, the motivation behind biological
signal analysis is to extract (i.e. to reveal) the relevant information.
This book synthesizes current research in the integration of computational intelligence and pattern analysis techniques, either individually or in a hybridized manner. The purpose is to analyze biological data and enable extraction of more meaningful information and insight from it. Biological data for analysis include sequence data, secondary and tertiary structure data, and microarray data.
Physicists pretend not only to know everything, but also to know everything bet-
ter. This applies in particular to computational statistical physicists like US. Thus
many of our colleagues have applied their computer simulation techniques to
ﬁelds outside of physics, and have published sometimes in biological, economic
or sociological journals, and publication ﬂow in the opposite direction has also
At one time, computational chemistry techniques were used only by experts
extremely experienced in using tools that were for the most part di½cult to
understand and apply. Today, advances in software have produced programs
that are easily used by any chemist. Along with new software comes new
literature on the subject. There are now books that describe the fundamental
principles of computational chemistry at almost any level of detail.
The fields of biological and medical physics and biomedical engineering are
broad, multidisciplinary and dyanmic. They lie at the crossroads of frontier research
in physics, biology, chemistry, and medicine. The Biological & Medical
Physics/Biomedical Engineering Series is intended to be comprehensive,
covering a broad range of topics important to the study of the physical, chemical
and biological sciences. Its goal is to provide scientists and engineers with
textbooks, monographs, and reference works to address the growing need for
This book is a practical introduction to scientific computing and offers
BPSIC subroutines, suitable for use on a perscnal complter, for solving a
number of important problems in the areas of chmistry, biology and
pharmacology. Althcugh our text is advanced in its category, we assume only
that you have the normal mathmatical preparation associated with an
undergraduate degree in science, and that you have some familiarity with the
S I C programing language.
There are many issues that should be considered in examining the implications of the imminent ﬂood of data that will be generated both by the present and by the next generation of global ‘e-Science’ experiments. The term e-Science is used to represent the increasingly global collaborations – of people and of shared resources – that will be needed to solve the new problems of science and engineering . These e-Science problems range from the simulation of whole engineering or biological systems, to research in bioinformatics, proteomics and pharmacogenetics.
Bioinformatics is an interdisciplinary field which addresses biological problems using computational techniques, and makes the rapid organization and analysis of biological data possible. The field may also be referred to as computational biology, and can be defined as, "conceptualizing biology in terms of molecules and then applying informatics techniques to understand and organize the information associated with these molecules, on a large scale.
An ultimate goal of modern biology is to understand how the genetic blueprint of
cells (genotype) determines the structure, function, and behavior of a living organism
(phenotype). At the center of this scientific endeavor is characterizing the biochemical
and cellular roles of proteins, the working molecules of the machinery of life. A
key to understanding of functional proteins is the knowledge of their folded structures
in a cell, as the structures provide the basis for studying proteins’ functions
and functional mechanisms at the molecular level....
Systems biology has received an ever increasing interest during the last
decade. A large amount of third-party funding is spent on this topic, which
involves quantitative experimentation integrated with computational
modeling. Industrial companies are also starting to use this approach more
and more often, especially in pharmaceutical research and biotechnology.
A computer program has been evaluated for subsite map
calculations of depolymerases. The program runs inWIN-DOWSanduses the experimentallydeterminedbond cleavage
frequencies (BCFs) for determination of the number of
subsites, the position of the catalytic site and for calculation
of subsite binding energies. The apparent free energy values
were optimized by minimization of the differences of the
measured and calculated BCF data.
This series is directed to healthcare professionals who are leading the transformation of
health care by using information and knowledge. Launched in 1988 as Computers in
Health Care, the series offers a broad range of titles: some addressed to specific professions
such as nursing, medicine, and health administration; others to special areas of
practice such as trauma and radiology. Still other books in the series focus on interdisciplinary
issues, such as the computer-based patient record, electronic health records,
and networked healthcare systems....