Computational Biology

12/21/2017 Computational biology - Wikipedia
Computational biology
Computational biology involves the development and application of data-
analytical and theoretical methods, mathematical modeling and computational
simulation techniques to the study of biological, behavioral, and social
systems.[1] The field is broadly defined and includes foundations in computer
science, applied mathematics, animation, statistics, biochemistry, chemistry,
biophysics, molecular biology, genetics, genomics, ecology, evolution,
anatomy, neuroscience, and visualization.[2]
Computational biology is different from biological computation, which is a

subfield of computer science and computer engineering using bioengineering
and biology to build computers, but is similar to bioinformatics, which is an
interdisciplinary science using computers to store and process biological data.
Contents
Introduction
Subfields
Computational anatomy
Computational biomodeling
Computational genomics (Computational genetics)
Computational neuroscience
Computational pharmacology
Computational evolutionary biology
Cancer computational biology
Computational neuropsychiatry
Software and tools
Open source software
Conferences
Journals
https://en.wikipedia.org/wiki/Computational_biology 1/14
Related fields
See also
References
External links
Introduction
Computational Biology, which includes many aspects of bioinformatics, is the
science of using biological data to develop algorithms or models to understand
among various biological systems and relationships. Until recently, biologists
did not have access to very large amounts of data which have become
commonplace, particularly in molecular biology and genomics. Researchers
were able to develop analytical methods for interpreting biological
information, but were unable to share them quickly among colleagues.[3]
Bioinformatics began to develop in the early 1970s. It was considered the

science of analyzing informatics processes of various biological systems. At this
time, research in artificial intelligence was using network models of the human
brain in order to generate new algorithms. This use of biological data to
develop other fields pushed biological researchers to revisit the idea of using
computers to evaluate and compare large data sets. By 1982, information was
being shared amongst researchers through the use of punch cards. The amount
of data being shared began to grow exponentially by the end of the 1980s. This
required the development of new computational methods in order to quickly
analyze and interpret relevant information.[3]
Since the late 1990s, computational biology has become an important part of
developing emerging technologies for the field of biology.[4] The terms
computational biology and evolutionary computation have a similar name, but
are not to be confused. Unlike computational biology, evolutionary
computation is not concerned with modeling and analyzing biological data. It
instead creates algorithms based on the ideas of evolution across species.
Sometimes referred to as genetic algorithms, the research of this field can be
applied to computational biology. While evolutionary computation is not

inherently a part of computational biology, Computational evolutionary
biology is a subfield of it.[5]
Computational biology has been used to help sequence the human genome,
create accurate models of the human brain, and assist in modeling biological
systems.[3]
Subfields
Computational anatomy
Computational anatomy is a discipline focusing on the study of anatomical
shape and form at the visible or gross anatomical scale of
morphology. It involves the development and application of computational,
mathematical and data-analytical methods for modeling and simulation of
biological structures. The field is broadly defined and includes foundations in
anatomy, applied mathematics and pure mathematics, machine learning,
computational mechanics, computational science, medical imaging,
neuroscience, physics, probability, and statistics; it also has strong connections
with fluid mechanics and geometric mechanics. It focuses on the anatomical
structures being imaged, rather than the medical imaging devices. It is similar
in spirit to the history of Computational linguistics, a discipline that focuses on
the linguistic structures rather than the sensor acting as the transmission and
communication medium(s).Due to the availability of dense 3D measurements
via technologies such as magnetic resonance imaging (MRI), Computational
anatomy has emerged as a subfield of medical imaging and bioengineering for
extracting anatomical coordinate systems at the morphome scale in 3D.
In computational anatomy, the diffeomorphism group is used to study

different coordinate systems via coordinate transformations as generated via
the Lagrangian and Eulerian velocities of flow from one anatomical
configuration in to another. Computational anatomy intersects the study of
Riemannian manifolds where groups of diffeomorphisms are the central focus,
intersecting with emerging high-dimensional theories of shape emerging from

the field of shape statistics. The metric structures in Computational anatomy
are related in spirit to morphometrics, with the distinction that Computational
anatomy focuses on an infinite-dimensional space of coordinate systems
transformed by a diffeomorphism, hence the central use of the terminology
diffeomorphometry, the metric space study of coordinate systems via
diffeomorphisms. At Computational anatomy's heart is the comparison of
shape by recognizing in one shape the other. This connects it to D'Arcy
Wentworth Thompson's developments On Growth and Form which has led to
scientific explanations of morphogenesis, the process by which patterns are
formed in Biology. The original formulation of Computational anatomy is as a
generative model of shape and form from exemplars acted upon via
transformations.[6]
The spirit of this discipline shares strong overlap with areas such as computer
vision and kinematics of rigid bodies, where objects are studied by analysing
the groups responsible for the movement in question. It is a branch of the
image analysis and pattern theory school at Brown University[7] pioneered by
Ulf Grenander. Making spaces of anatomical patterns in Pattern Theory,
into a metric space is one of the fundamental operations since being able to
cluster and recognize anatomical configurations often requires a metric of
close and far between shapes. The diffeomorphometry metric[8] of
Computational anatomy measures how far two diffeomorphic changes of
coordinates are from each other, which in turn induces a metric on the shapes
and images indexed to them. The models of metric pattern theory,[9][10] in
particular group action on the orbit of shapes and forms is a central tool to the
formal definitions in Computational anatomy.
Computational biomodeling
Computational biomodeling is a field concerned with building computer
models of biological systems. Computational biomodeling aims to develop and
use visual simulations in order to assess the complexity of biological systems.
This is accomplished through the use of specialized algorithms, and
visualization software. These models allow for prediction of how systems will
react under different environments. This is useful for determining if a system
is robust. A robust biological system is one that “maintain their state and
functions against external and internal perturbations”,[11] which is essential for
a biological system to survive. Computational biomodeling generates a large
archive of such data, allowing for analysis from multiple users. While current
techniques focus on small biological systems, researchers are working on
approaches that will allow for larger networks to be analyzed and modeled. A
majority of researchers believe that this will be essential in developing modern
medical approaches to creating new drugs and gene therapy.[11] A useful
modelling approach is to use Petri nets via tools such as esyN [12]
Computational genomics (Computational genetics)

Computational genomics is a field
within genomics which studies the
genomes of cells and organisms. It
is sometimes referred to as
Computational and Statistical
Genetics and encompasses much of
Bioinformatics. The Human
Genome Project is one example of
computational genomics. This
project looks to sequence the entire
human genome into a set of data.
Once fully implemented, this could
allow for doctors to analyze the A partially sequenced genome.
genome of an individual patient.[13]
This opens the possibility of
personalized medicine, prescribing treatments based on an individual’s pre-
existing genetic patterns. This project has created many similar programs.
Researchers are looking to sequence the genomes of animals, plants, bacteria,
and all other types of life.[14]
One of the main ways that genomes are compared is by homology. Homology
is the study of biological structures and nucleotide sequences in different
organisms that come from a common ancestor. Research suggests that
between 80 and 90% of genes in newly sequenced prokaryotic genomes can be
identified this way.[14]
This field is still in development. An untouched project in the development of

computational genomics is the analysis of intergenic regions. Studies show that
roughly 97% of the human genome consists of these regions.[14] Researchers in
computational genomics are working on understanding the functions of non-
coding regions of the human genome through the development of
computational and statistical methods and via large consortia projects such as
ENCODE (The Encyclopedia of DNA Elements) and the Roadmap
Epigenomics Project.
Computational neuroscience
Computational neuroscience is the study of brain function in terms of the
information processing properties of the structures that make up the nervous
system. It is a subset of the field of neuroscience, and looks to analyze brain
data to create practical applications.[15] It looks to model the brain in order to
examine specific types aspects of the neurological system. Various types of
models of the brain include:
Realistic Brain Models: These models look to represent every aspect of

the brain, including as much detail at the cellular level as possible.
Realistic models provide the most information about the brain, but also
have the largest margin for error. More variables in a brain model create
the possibility for more error to occur. These models do not account for
parts of the cellular structure that scientists do not know about. Realistic
brain models are the most computationally heavy and the most expensive
to implement.[16]
Simplifying Brain Models: These models look to limit the scope of a model
in order to assess a specific physical property of the neurological system.
This allows for the intensive computational problems to be solved, and
reduces the amount of potential error from a realistic brain model.[16]
It is the work of computational neuroscientists to improve the algorithms and

data structures currently used to increase the speed of such calculations.
Computational pharmacology
Computational pharmacology (from a computational biology perspective) is
“the study of the effects of genomic data to find links between specific
genotypes and diseases and then screening drug data”.[17] The pharmaceutical
industry requires a shift in methods to analyze drug data. Pharmacologists
were able to use Microsoft Excel to compare chemical and genomic data
related to the effectiveness of drugs. However, the industry has reached what is
referred to as the Excel barricade. This arises from the limited number of cells
accessible on a spreadsheet. This development led to the need for
computational pharmacology. Scientists and researchers develop
computational methods to analyze these massive data sets. This allows for an
efficient comparison between the notable data points and allows for more
accurate drugs to be developed.[18]
Analysts project that if major medications fail due to patents, that

computational biology will be necessary to replace current drugs on the
market. Doctoral students in computational biology are being encouraged to
pursue careers in industry rather than take Post-Doctoral positions. This is a
direct result of major pharmaceutical companies needing more qualified
analysts of the large data sets required for producing new drugs.[18]
Computational evolutionary biology

Computational biology has assisted the field of evolutionary biology in many
capacities. This includes:
Using DNA data to reconstruct the tree of life with computational

phylogenetics
Fitting population genetics models (either forward time[19] or backward
time) to DNA data to make inferences about demographic or selective
history
Building population genetics models of evolutionary systems from first

principles in order to predict what is likely to evolve.
Cancer computational biology

Cancer computational biology is a field that aims to determine the future
mutations in cancer through an algorithmic approach to analyzing data.
Research in this field has led to the use of high-throughput measurement. High
throughput measurement allows for the gathering of millions of data points
using robotics and other sensing devices. This data is collected from DNA,
RNA, and other biological structures. Areas of focus include determining the
characteristics of tumors, analyzing molecules that are deterministic in causing
cancer, and understanding how the human genome relates to the causation of
tumors and cancer.[20]
Computational neuropsychiatry
Computational neuropsychiatry is the emerging field that uses mathematical
and computer-assisted modeling of brain mechanisms involved in mental
disorders. It was already demonstrated by several initiatives that
computational modeling is an important contribution to understand neuronal
circuits that could generate mental functions and dysfunctions.[21][22][23]
Software and tools
Computational Biologists use a wide range of software. These range from
command line programs to graphical and web-based programs.
Open source software

Open source software provides a platform to develop computational biological
methods. Specifically, open source means that every person and/or entity can
access and benefit from software developed in research. PLOS cites four main
reasons for the use of open source software including:
Reproducibility: This allows for researchers to use the exact methods used
to calculate the relations between biological data.
Faster Development: developers and researchers do not have to reinvent
existing code for minor tasks. Instead they can use pre-existing programs
to save time on the development and implementation of larger projects.
Increased quality: Having input from multiple researchers studying the
same topic provides a layer of assurance that errors will not be in the
code.
Long-term availability: Open source programs are not tied to any
businesses or patents. This allows for them to be posted to multiple web
pages and ensure that they are available in the future.[24]
Conferences
There are several large conferences that are concerned with computational
biology. Some notable examples are Intelligent Systems for Molecular Biology
(ISMB), European Conference on Computational Biology (ECCB) and
Research in Computational Molecular Biology (RECOMB).
Journals
There are numerous journals dedicated to computational biology. Some
notable examples include Journal of Computational Biology and PLOS
Computational Biology. The PLOS computational biology journal is a peer-
reviewed journal that has many notable research projects in the field of
computational biology. They provide reviews on software, tutorials for open
source software, and display information on upcoming computational biology
conferences. PLOS Computational Biology is an open access journal. The
publication may be openly used provided the author is cited.[25] Recently a new
open access journal Computational Molecular Biology (http://biopublisher.ca/
index.php/cmb) was launched.
Related fields
Computational biology, bioinformatics and mathematical biology are all

interdisciplinary approaches to the life sciences that draw from quantitative
disciplines such as mathematics and information science. The NIH describes
computational/mathematical biology as the use of
computational/mathematical approaches to address theoretical and
experimental questions in biology and, by contrast, bioinformatics as the
application of information science to understand complex life-sciences data.[1]
Specifically, the NIH defines
Computational biology: The development and application of

data-analytical and theoretical methods, mathematical modeling
and computational simulation techniques to the study of
biological, behavioral, and social systems.[1]
Bioinformatics: Research, development, or application of

computational tools and approaches for expanding the use of
biological, medical, behavioral or health data, including those to
acquire, store, organize, archive, analyze, or visualize such
data.[1]
While each field is distinct, there may be significant overlap at their

interface.[1]
See also
International Society for Computational history
Computational Biology Computer simulation
List of bioinformatics institutions Mathematical biology
List of biological databases Monte Carlo method
Bioinformatics Molecular modeling
Biostatistics Network biology
Computational chemistry Structural genomics
Computational science Synthetic biology
Systems biology
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2. "About the CCMB" (http://www.brown.edu/research/projects/computational
-molecular-biology/). Center for Computational Molecular Biology.
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5. Foster, James (June 2001). "ionary Computation". Nature Reviews.
6. Grenander, Ulf; Miller, Michael I. (1998-12-01). "Computational Anatomy:
An Emerging Discipline" (http://dl.acm.org/citation.cfm?id=309082.30908
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10. U. Grenander and M. I. Miller (2007-02-08). Pattern Theory: From
Representation to Inference. Oxford: Oxford University Press.
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11. Kitano, Hiroaki (14 November 2002). "Computational systems biology" (htt
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(https://doi.org/10.1371%2Fjournal.pone.0106035). PMC 4152123 (https://
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(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851118). Current
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21. Dauvermann, Maria R., Heather C. Whalley, André Schmidt, Graham L.
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External links
bioinformatics.org (http://www.bioinformatics.org)
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12/21/2017 Computational biology - Wikipedia

Computational biology is different from biological computation, which is a

Bioinformatics began to develop in the early 1970s. It was considered the

applied to computational biology. While evolutionary computation is not

In computational anatomy, the diffeomorphism group is used to study

intersecting with emerging high-dimensional theories of shape emerging from

Computational genomics (Computational genetics)

This field is still in development. An untouched project in the development of

Realistic Brain Models: These models look to represent every aspect of

It is the work of computational neuroscientists to improve the algorithms and

Analysts project that if major medications fail due to patents, that

Computational evolutionary biology

Using DNA data to reconstruct the tree of life with computational

Building population genetics models of evolutionary systems from ﬁrst

Cancer computational biology

Open source software

Computational biology, bioinformatics and mathematical biology are all

Specifically, the NIH defines

Computational biology: The development and application of

Bioinformatics: Research, development, or application of

While each field is distinct, there may be significant overlap at their

8. Miller, Michael I.; Younes, Laurent; Trouvé, Alain (2014-03-01).

Retrieved from "https://en.wikipedia.org/w/index.php?

This page was last edited on 13 December 2017, at 16:31.

Text is available under the Creative Commons Attribution-ShareAlike License;

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