Report on

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Presentation Report on
Opportunities for the Pakistani IT industry
within Bioinformatics
by
September 14, 2005
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Objectives of the Workshop

• To introduce PSEB and Gallups report on
  Opportunities for Pakistan IT Industry in
• Bioinformatics Outsource
• Hear your opinion/ critique on the report.
• Formulate a plan to develop bioinformatics
  business in Pakistan.

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Overview of Bioinformatics

• Dr. Ahmed Gilani

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What is Bioinformatics?

• Bioinformatics is the application of computer
  technology and statistics to the management of
  biological information.
• In the past decade bioinformatics has become an
  integral component of research and development in
  biological sciences.
• The need for bioinformatics stems from a
  fundamental change that is taking place in
  biology.

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Bioinformatics Is a Merging of Disciplines
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Application Areas of Bioinformatics

• Genomics
• Proteomics
• Pharmacogenomics
• Comparative Genomics/ Phylogenetics
• Forensics

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Genomics

• In genome projects, bioinformatics includes the
  development of methods to search databases
  quickly, to analyze DNA and protein sequence
  information, and to predict protein sequence and
  structure from DNA sequence data.

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• Sequences and structure of Genes and Proteins.
  Sequences are the simplest way to represent a
  macromolecule. This sequence codes for the
  sequence of amino acids in proteins and is
  produced in this form by genome sequencing
  projects. Protein sequences are usually obtained
  via computer-based translation of genomic data.
• 3-D Molecular Structures. These are obtained by
  physical measurements (X-ray, Nuclear Magnetic
  Resonance) combined with computer modeling.

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• Finding Genes in the DNA sequence of various
  organisms (Gene Annotation)

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• Developing methods to predict the structure
  and/or the function of newly discovered proteins
  and structural RNA sequences 
• Clustering Proteins into families of related
  sequences and the development of protein models 

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• Aligning similar proteins and generating
  phylogenetic trees to examine evolutionary
  relationship between different organisms. 
• Systems biology- that looks at life as an
  integrated and interrelated system of genes,
  proteins and other chemicals instead of studying
  each of these components in isolation.

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• Bibliographic data, such as abstracts of
  scientific articles. The amount of scientific
  literature in biology has increased exponentially
  in recent years, especially after the onset of
  genome projects. This information is organized
  into a few large public databanks available
  through the internet.

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Industry Characteristics

• 1 billion in 2004 ( growing at 17 per annum)
• Over all it is estimated that the pharmaceutical
  industry spends around 6 of its 9 billion drug
  discovery budget on IT, i.e. US.500 million per
  year.
• Indian Market 17 million in 2004

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Market share of different Segments of
Bioinformatics
 
Genomic 50 Proteomics 20 Chemiinformatics 19
Pharmacogenomics 11
 
 
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Steps involved in bringing a drug to market

• Identifying drug target Genomic, Functional
  Genomic, Proteomics
• Screening for an affective chemical High
  throughput screening, virtual screening,
  combinatorial chemistry
• Animal Trials in-silico prediction of metabolic
  pathways effected by the drug
• Drug Development and Clinical Trials data
  management, analysis

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The Role of IT in Bioinformatics

• 1. Electronic Data Capture
• 2. Data Mining
• 3. Data Warehousing
• 4. Data Visualization
• 5. Customized Software

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Data Pipeline in Microarray Anaysis
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At the Periphery of Bioinformatics

• Medical Informatics
• Clinical Trials (around 6 billion annually)

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• The gap between medical informatics and
  bioinformatics is closing. Patient data is being
  integrated with genomic data.
• Data mining in clinical trials, patient data for
  adverse effects, efficacy of drugs, etc
• Represents a major opportunity for outsource.

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Challenges for Bioinformatitians

• Provide efficient tools for research
• Provide services for analysis, data integration,
  visualization
• Develop better, more useful algorithms

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Company Profile IMAGINA BIOTEK

• A leading technology company providing software
  development and system integration services for
  companies and institutions working in the pharma,
  health and life science sectors.Solutions
  offered range from data integration platforms for
  genomics and proteomics, to gene expresion data
  analysis algorithms, gene network reconstruction
  and simulation software, knowledge discovery
  tools, supercomputing and communications
  infrastructure, etc.

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• IMAGINA BIOTEK brings together knowledge from
  different technological fields (supercomputing,
  artificial intelligence, signal and image
  processing, data mining, open source software,
  etc) to provide solutions and new insights to the
  problems of data management and data analysis
  related to biomedical and biotechnological
  research.
• biowav is an integrated collection of function
  for analysis of electrophysiological signals
  (EEG, ECG, EMG) which provides the latest signal
  processing technologies (ICA, wavelet, etc).

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Opportunities in Bioinformatics Business for
Pakistan
Prof. Zafar Iqbal Malik
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Outsourcing Model in Technology Businesses

• Outsourcing has developed as an important
  concept in today's business.
• 1) Focus on core strength - the opportunity cost
  of adding a new segment of services to an
  existing business is high. Companies prefer to
  not diverge from their focus on their core
  competencies, and stay competitive.
• 2) Improve operational efficacy and stay
  competitive the outsourcing partner can be
  relied upon to choose the best technology for
  automation

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Outsourcing cont. 3) Leverage top talents from
the bioinformatics companies companies can
make use of the best resources engaged in IT
services without having to worry about
recruiting, training and retaining
professionals   4) Minimize on total cost of
ownership the rate of obsolescence is very
high in the IT sector. Companies who outsource
do not have to bear the replacement costs that
accompany obsolescence.
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Outsourcing cont. 5) Improve service delivery
to customers the company can dictate to the
outsourcing partner the timelines it is required
to meet. 6) Reduce cost and time the time
spent otherwise on planning and development is
saved and better utilized to managing the
existing resources. 7) Expand service portfolio
companies can extend their services without
having to invest on building in house
capabilities
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• Outsourcing
• Inspite of a tremendous increase in demand, the
  US educational stream has not significantly
  increased the production of scientific
  workforce.
• As a result cost of research has gone higher.
• Many companies are realizing that they can get
  their research done abroad, at cheaper cost,
  without any compromise in quality.
• In clinical trials for example, GSK (Glaxo smith
  Kline) has announced that it will shift 30 of
  its clinical trials to countries like India and
  China.

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Research Scientists and Internal Bioinformatics
Would Like

• Integration of public, proprietary, and 3rd party
  data through one interface.
• Ability to perform cross-database queries.
• Rapid searching of large volumes of data with
  the ability to control filtering.
• Indication that new, relevant information is
  available.

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Types of Bioinformaticspeople
Bioinformatics Scientist-a laboratory scientist
who has skills with Unix, Perl, SQL, etc., knows
the limitations of available bioinformatics
tools, and uses these tools and his/her
scientific knowledge to help the validation
process in the lab. Bioinformatics
Programmer/DBA-a programmer/DBA who understands
the biological questions being asked and has
expertise in Unix, Perl, SQL, C, Java, XML,
etc. in order to build bioinformatics databases
and applications. Bioinformatics IT
Administrator a system administrator who is able
to create and maintain a hardware infrastructure
that can handle the data formats, file sizes, and
application requirements for essential and
high-throughput bioinformatics endeavors.
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Bioinformatics Companies

• Companies purely focusing on software
  development / provision of IT services
• Companies integrating Biotech with
  bio-informatics

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Company Profile LIONs Services

• LIONs professional services department provides
  customized solutions for clients specific
  needs.
• These tailor-made solutions can include
  integrating proprietary and third- party
  databases and applications developing
  customized views and interfaces and integrating
  internal data visualization resources.
• LION also offers training courses for users and
  administrators

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Company Profile MicroDiscovery
Focuses on providing analysis of high-throughput
data from biochip and microarray experiments as
well as on the integration of genomic and
proteomic data.The range of services and
software encompasses the whole data processing
pipeline from image analysis to advanced data
mining. A high transparency of data quality
throughout each processing step is guaranteed by
consistent data integration.
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Micro-array data is recorded via an automatic
image processing software with the key task of
determining reliable and intuitive quality
parameters. Elaborated data mining methods allow
the most significant results to be filtered out
swiftly and reliably.
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What Is a Bioinformatics Company Like?

• Consists of Biologists, Computer Scientists,
  Mathematicians and Marketing people.
• Active participation of client in the
  development stag
• Bioinformatics companies should expect revenues
  in a few million dollars only.
• Only those companies who are able to adapt and
  innovate will survive.

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• A great deal of competition exists in the field.
• For any new company offering bioinformatics
  services or products, proof of concept, will
  be essential. This means that a nascent company
  will need to demonstrate its ability before
  getting business.

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The Pakistani Perspective

• Pakistan offers unique genetic resources in
  human population, crops and other species.
• In several areas such as crop varieties
  development, Pakistan offers a genuine promise.
• In certain areas such as, drug development,
  protein expression assays, population genetics
  and clinical trials, there are pockets of
  expertise in the country, which can be utilized
  to develop bioinformatics business.

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• Service provision in bioinformatics is possible,
  although human resources would have to be
  channeled towards that stream.
• At the moment, most researchers are not
  exploring their luck in knowledge based economy
  due to lack of awareness, interest, or IT and
  management support system. This trend is
  however detrimental to academic research as well.

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Bioinformatics Relevant to Pakistan

• Classification of Plant Species
• Genetic modification of crop species
• Design of Biological Catalysts
• Drug designing, vaccine development for
  neglected, prevalent diseases, screening of
  natural molecules (herbs) for medicinal activity

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IT Expertise Available in Pakistan

• Database and Allied
• Specialized Tools
• E Commerce
• Networking
• GIS
• Image Processing
• Information Systems

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Indian Companies

• Indian IT companies such as Tata Consultancy
  Services (TCS), Cognizant Technologies, Infosys,
  Wipro, and Satyam have already set up their
  bioinformatics divisions. 
• TCS, for instance, is entering the
  bio-informatics market with its indigenously
  developed computing platforms and applications
  within this year. The company is nurturing a
  40-member team that is working on developing
  bio-informatics software solutions.

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• A database application, specially created for the
  bioinformatics segment is in the pipeline. TCS is
  also looking at developing bio-informatics
  software applications in collaboration with
  biotech and pharma companies 

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• Satyam's Center of Excellence has identified Data
  warehousing and Datamining as a key initiative
  area in the field of bio-informatics since the
  field is an emerging domain where data
  warehousing and datamining techniques and
  concepts are used extensively for deciphering
  complex patterns and to correlate and analyze the
  vast volumes of data generated.

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• Pharmaceutical companies too, are making moves
  into the bioinformatics arena. GVK Biosciences,
  Dr. Reddy's Laboratories, Biocon, Astra Zeneca,
  Ranbaxy, Biological E, and Nicholas Piramal are
  some of the names that have either opted for the
  joint venture route or have tied up with start-up
  companies. 

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Research Methodology
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Research Methodology
The objectives of the study were achieved by
using a combination of Primary and Secondary
data. The primary data was collected by
conducting In-depth interviews while secondary
data was collected by conducting desk research.
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Research Methodology
Desk Research
An initial desk research was carried out to gain
background knowledge of the subject as well as to
identify the stakeholders. Major part of
objective were covered by conducting desk
research. For this purpose published reports and
statistics either electronic or in hardcopy were
utilized through scientific journals, business
reports, industry and technological magazines and
online databases. A multidisciplinary team of
researchers having background in Bioinformatics,
computer Science, Social Sciences and Biology was
deployed for the purpose
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Research Methodology
In-depth Interviews
A survey of potential stakeholders of
bioinformatics business was done to estimate the
current state of biological research in the
country, research interests of different groups,
opinion on bioinformatics, use of bioinformatics
software and identification of opportunities in
local and international markets. For the
in-depth interview sample was divided into 4
groups. Group 1. Scientists working in
biological sciences / medicine. Group 2.
Information Technology (IT) Companies. Group
3. Educational Institutions imparting
bioinformatics education at various levels.
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Research Methodology
The respondents were selected using snow balling
sampling method. Literature search was done to
identify prominent research institutes in the
country. The stakeholders were also identified
during the preliminary workshop.
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Results

• The sample consists of 3 groups
• Information Technology Companies (n10)
• 2) Scientists working in biological sciences /
  medicine (n20)
• 3) Educational Institutions imparting
  Bioinformatics Education at various levels (n7)

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Recommendations
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Recommendation
Suggestions on how to develop bioinformatics
business in Pakistan can be divided into three
broader categories. 1. Raising
Awareness 2. Development of Human
Resource 3. Business Model Development
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Recommendation

• Awareness
• ? Raising Awareness about Bioinformatics
  Opportunities.
• Workshop for promotion of Bioinformatics Business
  in Pakistan
• Business Model and Policy Initiatives
• Bioinformatics will develop along with
  biotechnology
• First focus on local market
• a. Collaboration with local researchers and
  industry
• b. Collaboration with the bioinformatics
  supplier Contract Research might be the first
  step
• Support to the manpower
• Public Private partnership

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Recommendation
In the field of bioinformatics and biotechnology
, the partnership between industry and academia
would take two forms. 1. The academic
institution outsources translational work,
development of a marketable products, any
database or software product to a commercial
company, the copy right is maintained by the
academic institutions. 2. The academic
institution and the industry collaborate in the
entire project and share the copy right / patent.
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Recommendation
Following steps have been recommended in BPI-2004
to facilitate industry-academia
partnership ? Understanding the industry
environment and market environment through
techno-economic market surveys ? Inventorying
the transferable technologies available within
the BTIS network and making them available on
the public domain ? Developing an
Industry-Institution Partnership programme at
national, regional and international level.
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Recommendation
? Promoting the growth of business incubators in
the field of bioinformatics ? Provision for
industrial and entrepreneurial consultancy
services ? Encourage enterprise creation
through liberalized flow of foreign capital,
outsourcing, infrastructure generation
etc. ? Adequate emphasis on human resource
development that suits the requirement of the
industries.
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Recommendation

• Seeding Grants to develop bioinformatics
  Expertise
• Creation of a Model Bioinformatics Company
• HEC support for bioinformatics education and
  startups
• Clearing House
• A web based clearing house, comprising the list
  of projects (provided) and IT tools/ softwares
  (also provided) should be maintained by PSEB.
  This would serve 2 purposes.
• 1. It will allow Pakistani practitioners to form
  a community of their own, where they can share
  information with each other.
• 2. It will publicize their competence to attract
  customers for both local and international
  market.

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Recommendation

• Private entrepreneurship model for
  Bioinformatics
• Foreign Assistance for Human Resource
  Development
• Need for Resource Integration
• Development of Human Resources
• What sort of bioinformatics experts would be
  needed by Industry
• Collaboration between Bioinformatics
  Educational Institutes and Researchers

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Recommendation
Funding of Bioinformatics Research
Government support of Bioinformatics
programs Combine scientific expertise with
Entrepreneurial Skills Advocacy for
improvement in School level Education General
directions and suggestions can be given but the
field will develop once Bioinformatics will
require IT experts and biologists to sit together
and collaborate with one another.
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Acknowledgements

• We wish to thank our team
• Gallup Fatima Idrees, Sadia Zaidi
• Interns Sanna Aizad, Mahreen Ali, Shumaila
  Sayyab, Hina Naz (Bioinformatics students MAJ
  University)
• Interviewers Dr. Farhan Cyprian, Dr. Shehryar
  Hussain, Khurram Mir
• Mentors Dr. Qasim Sheikh, Dr. Ozair ul Ghani
• PSEB Team Salahuddin Yusuf, Omar Hassan,
  Sabahat Majeed