A NEED FOR ASIAN BIOINFORMATICS CENTRE AND NETWORK - A
STUDY
A.S. KOLASKAR Bioinformatics Centre, University of Pune, PUNE 411 007.
Abstract In last two decades biology has become more quantitative. Biophysical and
Biochemical
techniques are commonly used in biological research to understand ultrastructure of
biological
system at cellular, sub-cellular and molecular level. Advancements in sequencing
techniques for
nucleic acids and proteins and their application to carry out large scale sequencing
have emerged
into mega-projects such as genome projects. Among the genome project through
human genome
project, sequencing of full human genome, has attracted attention of public from
every walk of
life. In addition, genomes of other organisms, which are important commercially and
for basic
research, are being sequenced. Today complete genome sequence information from
more than
ten organisms is available. The large genome projects such as rice, human etc. are
progressing
as co-operative multinational and multilaboratory projects. All these genome projects
are
producing large biological data. Similarly, proteome projects, those will be started
soon, will also
produce large data (Prof. A.Tsugita). Three dimensional structural data of
biomacromolecules
and metabolic pathways related information are also getting accumulated much faster
than what
was expected few years back. Biochemical and Biophysical data on mutant proteins
and enzymes
is also accumulated. The interest in cataloguing various plants, animals and microbial
species
along with their habitat and wherever possible the inclusion of molecular data under
the projects
such as Species 2000, makes the size and number of biological databases very large.
These
biological databases are multimedia in nature. Modern tools developed by the
database experts
and communication technologists needs to be used in manipulating biological
information. Newer
tools are required to develop to carry out data mining and data warehousing in the
area of
biology. The multimedia nature and large size of biological databases in outstripping
the
advantage that one gets due to the availability of larger data communication band
widths in
today's computer networks. Similar is the case in data storage. The cost of
computerised data
databases and their sizes, in the area of biology, has increased more rapidly than the
rate of
decrease in data storage cost per unit. Thus, there is an urgent need to develop tools
for data
compression and decompression. Biological data is critical for developing new
biotechnological
process and to manage environment. It can be also used to develop biological
warfares. Thus,
data security has become a major issue in present day Bioinformatics. Use of multiple
databases
to arrive at meaningful solution to the problem or to gain the knowledge of the
biological
processes/systems is not uncommon. It is imperative that one must be able to travel
seemlessly
from one database to other database and must be able to analyse these different
databases
simultaneously. Though JAVA interfaces allows seemless travel among the databases
as well as
among very different computer systems, simultaneous analysis of different databases
require use
of controlled vocabulary. Development of such controlled vocabulary directory, the
word in
which have unique meaning for biologists in different sub-disciplines is essential.
Bioinformatics
which is popular in molecular biologists today will become more relevant for those
biologists
which are working at the cellular and species level and studying the functionality of
biological
process. Thus, in short, the complexity and importance of Bioinformatics will grow in
next
couple of years.
In northern hemisphere Biotechnology industry is growing at much faster rate, though
it's
products are more useful and essential to the southern hemisphere. In Asian region,
growth of
the Biotechnology industry and research is not upto the mark with the exception of
Japan.
Among several reasons which affect the growth of Biotechnology in Asia, one of the
main reason
is non-availability of critical number of scientists and laboratories to carry out quality
research in
specific area of biotechnology. In fact, this has been realised by several national
agencies which
have increased their funding to Biotechnology in last few years. Though, the results
are
encouraging, the gap between southern and northern hemisphere in terms of
development of new
products using biotechnology is not decreasing.
The Second approach which might result in better through-put will be development of
International Institute in Asian region on the pattern some what similar to The
International
Vaccine Institute in Seoul, Korea. For multidisciplinary area such as Bioinformatics,
establishment
of International Institute becomes essential.
In this paper an attempt has been made to provide a blue print for such a Institute
which will take
the leadership role in Bioinformatics area and will complete and provide solution
better than
European Biological Institute (EBI), Cambridge, UK, or National Centre for
Biotechnology
Information (NCBI). The Asian Bioinformatics Institute (ABI) will have close links
with
Bioinformatics Centres in Asian countries and will also interact with EBI and NCBI
and other
international centres working in the area of Bioinformatics.
THE NEED FOR ASIAN BIOINFORMATICS CENTRE :
Most of the countries in Asian region may be characterized as developing countries.
The
industrial growth rate in last couple of years in each of this country is above 5%
showing buoyant
economy. Even the recent fall in share market had little effect on this buoyancy. The
growth of
nontraditional industries such as those which make use of high environmentally clean
technology
will affect considerably the GDP of these nations. Several biotechnology based
products makes
use of such high and clean technologies for the growth of biotechnology industry, one
requires
not only a strong biotechnology research and development laboratories but even more
important
is the availability of upto-date and accurate information and data. The scientific
research and
product development in Biotechnology is highly dependent on data and modelling
studies than
in other conventional areas of science and technology. Development of new vaccine
or drug
requires on an average investment 1-2 billion dollars over a period of ten years.
Similarly
development of a new hybrid plant which will be resistant to common viral and
bacterial
infections, but will have high productivity with acceptable nutrition values also
requires sustain
investment for a long period. Reduction in product development time, by even one or
two years
will have major impact on the industry and society. To develop new drugs against
diseases which
arise due to faulty genes or from regulations it is necessary to understand the function
of the
whole genome. Functional genomics thus has become one of the very important area
of
Bioinformatics. In near future one will have to also understand how different genes
communicate
with each other. Analysis of data from quantitative gene expression also helps in
identifying
quickly genes involved in diseases. This and other factor mentioned above have
prompted
multinational pharmaceutical companies and large biotechnology oriented industries
to develop
their own Bioinformatics research and development group. Smaller and medium
companies have
realised that their financial resources does not make it viable to have Bioinformatics
section within
its own structure. To overcome such difficulty European Biotechnology Institute (EBI)
has
established a consortium of biotechnology industries, the members of which can carry
out data
mining, modelling studies, data analysis with the help of scientists in the EBI at low
cost. On the
other hand NCBI gets full support from the government to carry out its activities.
Most Asian
countries are facing two types of problems to develop an established Bioinformatics
Centre which
are on par with NCBI or EBI. These are : (1) Non-availability of trained man-power,
and
(2) Computer networks are slow and less reliable in many asian countries with
exception that of
Japan, Singapore, Korea. The problem of non-availability of sufficient bandwidth for
international
communication from government owned networks such as CHINAPACK (China),
NICNET
(India) etc. affects its users and Bioinformatics researchers. The access of data from
web sites
in west and its use to develop models gets restricted. In fact, even today very few
institutes in
asian regions in the area of biology and biotechnology in particular, have online
databases which
can be accessed through Internet. Raw data produced in asian regions though small
compared
to northern hemisphere does not get full analysed and looses its real value. On the
other hand it
can be seen from yeast genome sequence data project that no data was available to
researchers
till the yeast genome project scientists analysed it completely. This increases further
the gap
between northern hemisphere and southern hemisphere scientists and technologists.
Some of
these problems were visualised and tackled by individual countries by initiating
Bioinformatics
activities. India was one of the first asian country to establish national Bioinformatics
system
which was followed by Japan and Taiwan and now Singapore. The lead gained
through such
planned Bioinformatics activity could not have maintained due to small investments
by individual
countries and non-availability of trained man-power, network infrastructure, etc. To
overcome
the lacunae and to provide the leadership, it is essential to have Bioinformatics Centre
where there
is critical number of scientists working on different aspects of Bioinformatics. Such a
centre thus
will be able to provide upto-date training in Bioinformatics to scientists from various
disciplines.
Major functions and objectives of such international Bioinformatics Centres are listed
below :
MAIN OBJECTIVES :
(1) Development of mirror sites for all major biotechnological databases and provide
the accessibility.
(2) Development of key batabases in collaboration with Institutes/Bioinformatics
Centres from member countries.
(3) Development of tools for on-line data analysis and modelling, data warehousing
and data mining etc.
(4) Development of network tools by taking into consideration regional/local
infrastructure.
(5) To provide expertise in developing multi-media database and management system,
analysis and model.
(6) To carry out short term/long term training to scientific workers from member
countries.
(7) To develop education material on WEB, CD's or in printed form interacting with
domain experts and Bioinformatics experts.
(8) To help the industry in formulating data needs and answering their needs in the
area, data, information and modelling.
(9) To act as a liaison between various national Bioinformatics Centres and Institutes
in this area.
(10) To work to be leader in the Bioinformatics.
STRUCTURE :
The host country will provide space building and initial funds for developing
infrastructure.
Member countries will initially put one time grant as entry fee and then a small
amount as a yearly
fee will be charged which will be utilised to update the infrastructure. The United
Nation agencies
such as UNIDO, UNESCO, UNDP etc. will provide grants initially for five years
period and then
on project basis. Industries from all Asian region pay membership fees and can
become a member.
The members will get all their queries answered at no additional cost for a period of
five years.
After five years industries will pay annual membership fees as decided by the Board
of Directors.
Other non-member industries will be provided services on charge. All the funds raised
in this
fashion will be used to form a trust and the interest from these funds will be utilised
for running
the Institute. The Executive Director will run the Institute by taking the advise from
the members
of Board of Trustees and Scientific Advisory Committee. The member of the Board of
Trustees
will be drawn from representatives of member countries as well as representatives of
member
industries. Representatives from international agencies such as UNDP, UNEP,
UNIDO,
UNESCO will also be represented on the Board of Trustees. These trustees will meet
at least
once a year and discuss the policies related issues and guide the Executive Director.
There will
be also a Scientific Advisory Committee (SAC). The SAC will consist of active
scientists in the
area of Bioinformatics, computer science and technology, communication technology
and few
biologists. These scientists will be drawn from various parts of the world. SAC will
decide the
priority areas in which the Institute should carry out work and will assess the work
carried out
by resident as well as visiting scientists. The SAC will prepare a futuristic workable
scientific plan
for the Institute for a period of five years. The Institute will have core resident
scientists and large
number of visiting scientists. A small part of these core scientists will form a group
which will
help the member industries in solving their problems and needs in Bioinformatics.
The centre will
have a strong research and training component which will be carried out resident and
visiting
scientists as well as with the help of young researchers. The student will be selected
internationally. Thus, the funds of the Institute will be utilised to provide the
subsistence and
travel to these researchers and visiting scientists. Upto-date infrastructure with all
facilities will
be established in this Institute. The member on the Board of Trustees/SAC as well as
visiting
scientists will serve for a specific duration - normally 3-5 years term. Only in rare
cases these
members will get second term but in no case any member will continue beyond ten
years. Several
Bioinformatics Centres in the country will form a part of the virtual Institute. These
associate
members will be given certain facilities to upgrade their infrastructure and to carry out
effectively
high quality research in Bioinformatics. They will also be provided small honorarium
for a period
when they are associated with the Institute.
India will work, in general, to provide the leadership in Bioinformatics and will
catalyse the
growth of biotechnology in asian region in particular and the whole world in general.
It will not
work in isolation but will have close interactions with large number of Institutes in
biology,
biotechnology and informatics..