Assignment

On
Applications of Computer Science in Biology

Contents

1. Introduction
2. Types and Applications of Computational Biology
 Types of computational biology
- Network Biology
- Darwinian Biology
- Neuroscience
 Applications of computational biology
- Anatomy
- Models & data
 Associated fields
3. Application of computer and statistics in biology
 Genomics
- Comparative Genomics
 Proteomics
 Structural Genomics/Bioinformatics
 Drug Designing
 Functional Genomics
 Pharmacogenomics
4. Conclusion
5. Reference
 Types and Applications of Computational Biology

Description
In order to comprehend biological systems and relationships, computational biology uses
data analysis, mathematical modeling, and computer simulations. The area has roots in
applied mathematics, chemistry, and genetics and is a nexus of computer science, biology,
and big data. Biological computing, a branch of computer engineering that applies
bioengineering to the construction of computers, is distinct from it.

The study of informatics processes in biological systems, or bioinformatics, first emerged in

the early 1970s. In order to create new algorithms, artificial intelligence research at the time
used network models of the human brain. Due to the utilisation of biological data, biological
researchers are now evaluating and comparing massive data sets within their own field
using computers.

By 1982, researchers were exchanging data using punch cards. By the end of the 1980s,
the volume of data had increased dramatically, necessitating new computational techniques
for quickly evaluating pertinent data.

The Human Genome Project, arguably the best-known illustration of computational biology,
was underway in 1990. The project had achieved its primary objectives by 2003, having
mapped approximately 85% of the human genome. Nevertheless, work persisted, and by
2021, level "full genome".

Types of computational biology

Network biology: The purpose of systems biology is to identify emergent features by

computing the interactions between various biological systems, from the cellular level to
large populations. Cell signalling and metabolic pathway networking typically takes place
during this process. Systems biology frequently applies computational methods from
biological modeling and graph theory to examine these intricate cellular relationships.

Darwinian biology: Evolutionary biology has benefited from computational biology by:

1. Using computational phylogenetics to recreate the tree of life using DNA data.

2. Using DNA data and population genetics models to estimate demographic or selection
history (either in the forward or backward time directions.

3. Constructing population genetics models of evolutionary systems from the ground up to

forecast what is likely to change.

Neuroscience: The study of brain function in terms of the nervous system's information

processing capabilities is known as computational neuroscience. It is a branch of
neuroscience that focuses on modeling the brain to look at particular features of the
nervous system. Examples of brain models are:
1. Realistic brain models these models aim to capture every feature of the brain, down to
the molecular level, in great detail. The most accurate models offer the most knowledge
about the brain, but they also have the greatest room for error.

2. A brain model with more variables can potentially make more mistakes. These models do
not take into account the unknown components of cellular structure.

Applications

Anatomy: The study of anatomical form and shape at the visible or large anatomical scale
(displaystyle 50-100 mu) of morphology is known as computational anatomy. For modeling
and simulating biological structures, it entails the development of computer, mathematical,
and data-analytical techniques. Instead than concentrating on the medical imaging
equipment, it emphasizes the anatomical structures being examined. In order to extract
anatomical coordinate systems at the morphome scale in 3D, computational anatomy has
arisen as a subfield of medical imaging and bioengineering due to the availability of dense
3D observations through technologies like magnetic resonance imaging.

Computational anatomy was first conceptualized as a generative model of shape and form
from exemplars that were then transformed.

Models and data: The study of the processes that control the structure, development, and
behavior of biological systems is known as mathematical biology. Mathematical models of
live organisms are used in this field. In contrast to experimental biology, which is more
emphatically minded, this requires a more theoretical approach to problems. Discrete
mathematics, topology (which is helpful for computational modeling), Bayesian statistics,
linear algebra, and Boolean algebra are all used in mathematical biology.

Associated fields

The interdisciplinary fields of computational biology, bioinformatics, and mathematical

biology all use quantitative fields like information science and mathematics to the study of
life. Computational and mathematical approaches are used in computational and
mathematical biology to answer theoretical and experimental problems about biology. In
contrast, bioinformatics is the use of information science to comprehend complicated data
from the life sciences.

The National Institutes of Health (NIH) defines computational biology as, the production and
use of data-analytical and theoretical approaches, mathematical modeling, and
computational simulation techniques to research biological, behavioral, and social systems.
Research, development, or use of computational tools and methods for extending the use of
biological, medical, behavioral, or health data, including those to collect, save, organize,
archive, process, or display such data, is known as bioinformatics.
Application of computer and statistics in biology

There is a vast and broad application of both computer technology and statistics in
biology. Few of the important fields of biology are as mentioned below, briefly
explaining the application of both computer technology and statistics.

Genomics
Genomics is an attempt to analyze or compare the complete genetic compliment of
an organism. Modern high-density experimental studies on various genomes
produce huge amounts of data. Interpretation of this data into a biologically
meaningful knowledge is nowadays a major challenge. This challenge is
answerable only by the implementation of computer technology and statistics. It
requires a development of robust analytical methods which are applicable and
useful. Various statistics and algorithms are also used for the comparison of
sequenced genome. Principles of Genomics synthesize the state-of-the-art
statistical methodologies applied to genome study.
Comparative Genomics is a collection of robust protocols formolecular biologists
beginning to use comparative genomic analysis tools in a variety of areas. It
involves Comparison of human genetics with model organisms such as mice, fruit
fly, E. coli. Computational approaches to genome comparison have recently
become a common research topic in computer science. A public collection of case
studies and demonstrations is growing, ranging from whole genome comparisons
to gene expression analysis. This has increased the introduction of different ideas,
including concepts from systems and control, information theory, strings analysis
and data mining. It is anticipated that computational approaches will become and
remain a standard topic for research and teaching, while multiple courses will
begin training students to be fluent in both topics.

Proteomics
The term "proteome" refers to the entire complement of proteins, including the
modifications made to a particular set of proteins, produced by an organism or a
cellular system. This will vary with time and distinct requirements, such as
stresses, that a cell or organism undergoes. The term "proteomics" is a large-scale
comprehensive study of a specific proteome, including information on protein
abundances, their variations and modifications, along with their interacting
partners and networks, in order to understand cellular processes. “Clinical
proteomics” is a sub-discipline of proteomics that involves the application of
proteomic technologies on clinical specimens such as blood.

Structural genomics or structural bioinformatics

It refers to the analysis of macromolecular structure particularly proteins; the main
goal of structural genomics is the extension of idea of genomics, to obtain accurate
three dimensional structural models for known proteins. Structural genomics
proceeds through increasing levels of analytic resolution, starting with the
assignment of genes and markers to individual chromosomes, then the mapping of
these genes and markers within a chromosome, and finally the preparation of a
physical map culminating in sequencing. Structural genomics takes advantage of
completed genome sequences in several ways in order to determine protein
structures. The gene sequence of the target protein can also be compared to a
known sequence and structural information can then be inferred from the known
protein’s structure. Structural genomics can be used to predict novel protein folds
based on other structural data. Structural genomics can also take modeling-based
approach that relies on homology between the unknown protein and a solved
protein structure.

Drug designing
Drug design is the inventive process of finding new medications based on the
knowledge of a biological target. The drug is most commonly an organic small
molecule that activates or inhibits the function of a biomolecule such as a protein,
which in turn results in a therapeutic benefit to the patient. In the most basic sense,
drug design involves the design of small molecules that are complementary in
shape and charge to the biomolecular target with which they interact and therefore
will bind to it. Drug design frequently but not necessarily relies on computer
modeling techniques. This type of modeling is often referred to as computer-aided
drug design. Finally, drug design that relies on the knowledge of the three-
dimensional structure of the biomolecular target is known as structure-based drug
design.

Functional genomics
Functional genomics refers to the development and application of global
experimental approaches to assess gene function by making use of the information
and reagents provided by structural genomics. It is characterized by high-
throughput or large-scale experimental methodologies combined with statistical or
computational analysis of the results (Hieter and Boguski 1997).
 

Pharmacogenomics
It is an application of genomic approaches and technologies to the identification of
drug targets. In other words knowing whether a patient carries any of the genetic
variations which can help to prescribe and individualize drug therapy, decrease the
chance for adverse drug events, and increase the effectiveness of drugs.
Pharmacogenomics combines traditional pharmaceutical sciences such as
biochemistry with an understanding of common DNA variations in the human
genome.