BIOINFORMATICS: THE RISING SCIENCE OF THE 20th CENTURY

2014 - 19109

MR. JUDE VINCENT E. PARCON

UNIVERSITY OF THE PHILIPPINES - VISAYAS

 Bioinformatics is a field of science that utilizes information technology to store,
distribute and analyze an extensive amount of biological data. The term was first used
by a Dutch system - biologist named Paulien Hogeweg in 1970. It is an interdisciplinary
field that also combines knowledge in computer science, biology, mathematics and
statistics to correlate and process large sets of data. In the early 2000s, the term
“bioinformatics” served commonly as a collective term that encompasses proteomics,
which is the study of proteins and their biological functions, genomics which is mainly
concerned in sequencing and analyzing an organism’s genome. Nowadays,
bioinformatics is more than just data analyzing (Mandal, 2014; Whelan, Yap, Surette,
Golding & Bowdish, 2013). Bioinformatics aims to organize data that will allow
researchers to easily access existing information and to be able to submit new entries.
The field also aims to develop tools and resources that aids in the analysis of data.
Lastly, with the aid of the tools created, data analysis should be done with accuracy and
can interpret the results in a biologically meaningful manner (Luscombe et al., 2001).
Bioinformatics is being used in a number of fields such as in pharmacology
where resources are important to comprehend and predict toxicity, metabolism and
excretion of existing drugs and potential drug leads (Shah et al., 2014). Bioinformatics is
also a crucial part of agriculture wherein full genomic information about plant species
provide sufficient data to enable scientists produce and come up with enhanced plant
species that are drought and pesticide resistant (Elanchezhian, 2012). DNA profiling
and analysis is the main core of forensic sciences wherein bioinformatics can be of a
big help as it makes the work easier for the experts to cross check DNA profiles (Bianchi
and Lio, 2007). These are some of the few applications of bioinformatics in different
scientific fields.
As of June 2017, there are approximately 3.2 zettabytes of data in the
cybersphere wherein one zettabyte is equivalent to one million petabyte (Pritchard et
al., 2017). Along with this data explosion scientists are also producing and storing more
biological data in their databases taking only less than a year to double up genetic
sequencing data. One of the world’s largest biology - data repositories, the European
Bioinformatics Institute in Hinxton, United Kingdom currently stores 20 petabytes of
biological data such as genes, proteins and small molecules (Marx, 2017). With this,
scientists have come up with a way to store data in DNA. One gram of a single stranded
DNA can store up to 455 exabytes or equivalent of 250 million DVDs (Castillo, 2014).
The DNA having a data density that it can hold and its high durability makes it an
efficient medium of data storage (Erlich and Zielinski, 2017).
Bioinformatics specialists process biological information at the molecular level by
using computers, and focus on managing and analyzing the enormous amount of data
that is being created. They create and maintain databases that make use of algorithm
and analytical techniques for data storage such as DNA sequences. Specialists also
team up with biologists, scientists and biotechnologist (Bioinformatics Specialist, 2014).
The Philippine Genomic Center (PGC) located in the University of the Philippines
Diliman is the Core Facility of Bioinformatics in the country. As the field of bioinformatics
and density of data continue to arise, there is a need to produce more bioinformatics
specialists. In the Philippines, the field of bioinformatics is still not widely known as there
are only three bioinformatics specialists in the country as other Filipinos engaged in the
field are working overseas (Tablizo, 2017; Reyes 2015). In addition, primary knowledge
about this field is not yet felt and used and in the different institutions in our country.
Furthermore, only few Filipinos know about the field of bioinformatics.
One way of disseminating information about this biotechnology is by conducting
seminars and workshops, not only to students, but to other professionals as well. The
Philippine Genomic Center along with the National Institute of Molecular Biology and
Biotechnology conducts a number of workshops and forums across the country to
further publicize the importance and applications of bioinformatics. One of which was
the Genome Assembly, Annotation, and Variant Calling held last January 18 - 19, 2016
in the Computational Science Research Center, National Science Complex, UP Diliman.
This training offered a step - by - step execution of a simple data analysis workflow that
covers the genome assembly, variant calling and annotation.
A seminar titled “Enhancing Local Agrigeconomics through Ultramodern
Sequencing Tools and Bioinformatics” was held last November 10, 2017 at the Venus
Park View Hotel in La Trinidad, Benguet. The said seminar was spearheaded by the
Benguet State University teamed up with the Philippine Genomic Center (PGC) and the
University of the Philippines Los Banos and was co-sponsored by the Philippine -
California Advanced Research Institute (PCARI). As a country with agriculture as one of
the main sources of income for the rural areas, it is important that we understand the
core compounds and behaviour of plant crops in order to come up with ways of
developing products that could not harm and affect the crop itself. One example of
which is the identification of pesticide resistant genes that could aid and serve as
models for developing new pesticides. Senior Researcher Analyst, Dr. Benedict Maralit
of the PGC states that the use of bioinformatics in handling genetic data aid researchers
gain less human errors and to come up with more quality data (Benguet State
University, 2017).
Another seminar hosted by the PGC is the introductory molecular biology
workshop at the Department of Science and Technology - PCAARRD Innovation and
Technology Center in Los Banos, Laguna last March 3, 2017. This enabled
bioinformatics specialists and biologists to impart their knowledge to various strategic
plan managers of the department about the possible services that can be rendered and
achieved with the proper use and application of genomics in agriculture, forestry, marine
science and biodiversity. Moreover, the Director of PGC - DNA Sequencing and
Bioinformatics Facility (DSBF) Dr. Ma. Anita Bautista mentioned that the Genomic
Center would like to fill in gaps between genomics and bioinformatics. Workshops and
trainings regarding bioinformatics are designed to facilitate the development of local
expertise but more importantly, it is a step addressing the country’s need for manpower
development (PGC, n.d.).
The introduction of an undergraduate study majoring in bioinformatics is also one
way of raising awareness about the field and its uses in different sectoral department in
our country. Currently, there is only one post graduate program in the country that offers
a Masters in Health Informatics (MSHI) in the University of the Philippines Manila which
is divided into two tracks: the Medical Informatics track handled by the College of
Medicine - Medical Informatics Unit and the Bioinformatics track that is being offered by
the College of Arts and Sciences. Generally, the MSHI curriculum aims to provide
leaders and competent professionals in Health Informatics that will be able to apply
informatics concepts, skills and principles for the solution of health informatics
problems, provide valuable insights in the field that can be used in critical study of all
levels of health information systems and to be able to provide technical services to both
private and public sectors of the country (College of Medicine, 2013).
Some of the major courses under the Bioinformatics curriculum are the Database
Modeling and Design for Bioinformatics, Nucleic Acid and Protein Architecture
Dynamics and Structure and Representations and Algorithms in Bioinformatics. Under
the Representations and Algorithms course, methods and computational issues in
molecular biology and algorithms are discusses. On the other hand, concepts, design
and management of bioinformatics database are introduced along with the stochastic
processes and modeling discussed under the course Stochastic Models in
Bioinformatics (National Graduate Office for the Health Sciences, 2010). However, this
graduate program is open only to those who have a baccalaureate degree in computer
science, biochemistry, molecular biology, information sciences and medicine or allied
health professions. Graduates from other fields are required to have at least a working
experience in health sciences field before they can apply for the curriculum (University
of the Philippines Manila, n.d.).
As bioinformatics is an interdisciplinary field, there is a need to introduce the
overlapping sciences of the said field such as chemistry, statistics, biology, computer
science and engineering. The Bachelor of Science in Bioinformatics curriculum offered
by the Brigham Young University in Utah, USA has included subjects such as Biology,
Molecular Biology, Introduction to Computer Programming and Genetics, as introductory
subjects to higher divisions of the field. Computational Biology, one of the higher
courses under the bioinformatics curriculum, provides the extensive knowledge and
experience in developing computational approaches to address biological needs such
as DNA data and the introduction to bioinformatics databasing using various programs
like the Perl and the SQL. In addition to that, the course Stat 201 or the Statistics for
Engineers and Scientists is included to be able to practice hypothesis testing and to
interpret data using different professional statistical tools. One important course that
must be taken up is the Bioethics class wherein in - depth lecture of various ethical and
philosophical issues are discussed and emphasized. Along with that, lectures regarding
proper tools and approaches needed to come up with bioethical decisions are also
inculcated in the course (Brigham Young University, n.d.).
 Virginia Commonwealth University (VCU) in Richmond, Virginia offers a
bachelor’s degree in bioinformatics with a major in computational sciences. The
curriculum of the program consists of introductory courses such as biology, chemistry,
and statistics to serve as a backbone for core subjects focusing on the bioinformatics in
the areas of genomics and quantitative or statistical bioinformatics. Molecular Biology
through Discovery is one of the fundamental courses in the study as molecular biology
is known to be the raw material or the essential groundwork for bioinformatics. The
Biological Sciences course also serves as an essential introductory course to the field,
as it tackles the basic biological concepts that are important in bioinformatics such as
DNA replication, gene expression and cell structure. One major course in the curriculum
track is the Applications in Bioinformatics which integrates the student’s biological,
computational, quantitative skills with applicable strategies, methods and technologies
further applying it in conducting researches. Apart from that, the VCU also offers
Computer Graphics as one of the concentration cores in the curriculum. Graphic
development and modeling are the primary objectives of the lecture as it makes use of
mathematical techniques in order to analyze and come up with graphic models
representing data structures (Virginia Commonwealth University, 2016). These are
some of the subjects that could be introduced and included in an undergraduate degree
in bioinformatics here in the Philippines.
The Philippine Genome Center is an institution that emphasizes both basic and
applied research for the development of health diagnostics, DNA forensics, therapeutics
and better crop cultivation. It was established at the University of the Philippines during
the 1246th Board of Regents meeting last July 31, 2009 under the supervision of former
UP President Emerlinda R. Roman and was formally launched on the November 8,
2011(Philippine Genome Center, n.d.). The Philippine Genomic Center aims to fulfill two
major functions: first, is to provide computing systems that will serve as resources to
enable researchers to efficiently process, manage, share and analyze massive amounts
of genomic data. These will enable them to transform complex data into more
understandable and useful information to both experts and the general public; secondly,
to host trainings, workshops, meetings and conferences for bioinformatics and related
topics in high performance computing (Philippine Genome Center, n.d.).
 Two years after the opening of the Philippine Genome Center, the PGC DNA
Sequencing Core Facility (DSCF) was launched and formally opened to the public. The
PGC-DSCF provides a wide array of DNA sequencing of small genomes to various
academic research groups in the scientific community most especially to the research
group in the country (Saloma, 2017; Philippine Genome Center, 2014). Then six
months after the DSCF opened, the PGC - Core Facility for Bioinformatics (CFB)
opened its doors to the academe and the general public (Ronda, 2014). The CFB aims
to render genome-scale data generation and analysis to both local scientists and
researchers. It was established to facilitate the transition of knowledge in genomics into
applications that are beneficial to the society. The Core Facility for Bioinformatics also
works on research programs that are related to PGC’s research thrusts, including
software development and computational techniques, as well as collaborate research
projects that aim at finding solutions to complex and computing - intensive problems of
interest to PGC researchers (Saloma, 2017).
Bioinformatics specialists are trained to become experts in different fields of
science and thus having a solid foundation in chemistry, molecular biology, computer
science and statistics. Specialists are needed in the field of molecular medicine, energy
development, animal science field, forensic science and agriculture. As bioinformatics is
considered as a challenging and intellectual field, pursuing the course will help one
become an expert in the field that can actually contribute to research, learn and be on
the top of a field that is constantly advancing. Bioinformatics can be a big help in the
pharmaceutical industry as it lessens the workload and number of experiments to be
conducted in order to produce a new drug. Drug discovery, designing and development
along with product formulation, polymer modeling and pharmacology are the important
aspects of pharmaceutical industry that utilizes bioinformatics. As only 10% of drug
molecules in the research area pass through the development case, using simulations
and informatics can significantly help improve the efficiency of drugs. In the aspect of
pharmacology, bioinformatics is used in drug target identification and in the
development of biomarkers and pharmacogenic tools to maximize the therapeutic
benefit of drugs (Shah, Rathod, Basuri, Modi & Parmar, 2015).
 The field of forensic science also utilizes bioinformatics techniques. Forensic
DNA analysis is the core foundation of the said field. Personal identification and
relatedness to other individuals are the two major subjects of forensic DNA analysis.
This aids the law enforcement officers to connect DNA profiles to individuals that are
prosecuted by the law. As the DNA become the most important personal identification
characteristic, bioinformatics tools are needed to accurately identify and detect genetic
variation between samples that can be useful in court and even in mass disaster
identification. Agriculture on the other hand utilizes bioinformatics in a way that it
provides a full run through of a specific plant organism’s genome. Moreover, studying
and locating specific genes and codon in the genome will help scientists to not only
come up with products that will not harm the organism, but as well as enhance the
organism itself making it pesticide, drought and toxic resistant (Elanchezhian, 2012).
Overall, the field of bioinformatics is one of the most recent and continually
growing industry in the scientific world, especially in the Philippines. As it continues to
be a widely known field, the need of for bioinformatics specialist also continues to grow.
But before that, disseminating information about bioinformatics is the crucial stage in
order to educate and let researchers, scientists, professionals, students and the general
public know what this science is about and its application and importance in the
country’s setting. Some of the few ways in raising awareness is by conducting
workshops, symposiums and trainings that could get the interest of the people; by the
possible introduction of bioinformatics as an undergraduate course here in the
Philippines and by strengthening further the role of the Philippine Genome Center as
the Core Facility of Bioinformatics here in the country.
Philippines is one of the countries that is slowly engaging in the field of research
and biotechnology. And with this, a large number of career opportunities in the field of
bioinformatics are waiting for the majority of Filipinos that are willing to learn and serve
for the benefit of the country. With the vast number of applications of bioinformatics in
the society, it is anticipated that more sectoral department will utilize the resources and
services that can be rendered by bioinformatics. As the establishment of the PGC - CFB
was only three years ago, bioinformatics still has a long way to go but through the
proper promulgation of the field with the help of the government and its departments, it
is expected that bioinformatics will soon be a well known and developed science here in
the country.
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