Various Career Options Available - Imtech

weinerthreeforksBiotechnology

Oct 2, 2013 (3 years and 10 months ago)

72 views


Opportunities in Bioinformatics





Presented By


Dr G. P. S. Raghava

Co
-
ordinator, Bioinformatic Centre

IMTECH, Chandigarh


Email: raghava@imtech.res.in

Web: http://imtech.res.in/raghava/


What is Bioinformatics (BI) ?

More About Bioinformatics


Historical Background

Media Hype & Confusion

Important Applications of BI

Bioinformatics in India

Demand of BI Professionals

How to Enter in BI (Course & Degrees)

What is Bioinformatics


Biocomputing: Application of Computer in
Biosciences


Biocomputing started in 1960’s


Explosion of Genomic Data


Access and Management of Data


Biocomputing+Information Science


Role of Internet in BI


Relationships between











sequence


3D structure protein functions



Properties and evolution of genes, genomes,
proteins, metabolic pathways in cells



Use of this knowledge for prediction, modelling, and
design

Core of Bioinformatics

TDQAAFDTNIVTLTRFVM
EQGRKARGTGEMTQLLNS
LCTAVKAISTAVRKAGIA
HLYGIAGSTNVTGDQVKK
LDVLSNDLVINVLKSSFA
TCVLVTEEDKNAIIVEPE
KRGKYVVCFDPLDGSSNI
DCLVSIGTIFGIYRKNST
DEPSEKDALQPGRNLVAA
GYALYGSATML
V

In 1995, the number of genes in the database started to exceed
the number of papers on molecular biology and genetics in the
literature!

(
Boguski, 1999
)

The challenge

More About Bioinformatics

Sequence

Analysis

Database

Homology

Searching

Multiple

Sequence

Alignment

Homology

Modeling

Docking

Protein

Analysis

Proteomics

3D

Modeling

Sample

Registration &

Tracking

Integrated

Data

Repositories

Common

Visual

Interfaces

Intellectual

Property

Auditing

Bio


Informatics

Genome

Mapping

Computational Biology

in the High
-
Throughput Era

The Genome and Beyond





Scientific Challenges


Algorithmic Challenges


Computational Challenges


Historical Background


Life Science
-

young compared to
physics and chemistry


1953 Structure of DNA


1960s Understanding of “code of life”


1970s Genetic manipulation technology


1980s Widespread innovation
-
biotechnology/genetic revolution


1990s Human Genome Project


2000s Structural Genomics ?

Media Hype and Confusion


Anybody can do BI


BI can do anything


Colleges/Courses/Training


No Quality Check


Limited Knowledge of Subject


More user than developer

Why Bioinformatcs is Required


Data growth is exponential


Difficult to understand life without BI


Detection of new diseases


BI tools allow to save expr. Expend.


Rational Drug design



Computer
-
aided vaccine design

Application of Bioinformatics


Genome Annotation


Protein Structure Prediction


Proteomics


DNA Chip technology


Disease Diagnostics


Fingerprinting Technique


Drug/Vaccine Design

Genome Annotation

The Process of Adding Biology Information and

Predictions to a Sequenced Genome Framework

Protein Structures



Protein Structure Prediction


Experimental Techniques


X
-
ray Crystallography


NMR


Limitations of Current Experimental
Techniques


Protein DataBank (PDB)
-
> 17000 protein structures


SwissProt
-
> 90,000 proteins


Non
-
Redudant (NR)
-
> 800,000 proteins


Importance of Structure Prediction


Fill gap between known sequence and structures


Protein Engg. To alter function of a protein


Rational Drug Design

Traditional Proteomics


1D gel electrophoresis (SDS
-
PAGE)


2D gel electrophoresis


Protein Chips


Chips coated with proteins/Antibodies


large scale version of ELISA


Mass Spectrometry


MALDI: Mass fingerprinting


Electrospray and tandem mass
spectrometry


Sequencing of Peptides (N
-
>C)


Matching in Genome/Proteome Databases

Overview of 2D Gel


SDS
-
PAGE + Isoelectric focusing (IEF)


Gene Expression Studies


Medical Applications


Sample Experiments


Capturing and Analyzing Data


Image Acquistion


Image Sizing & Orientation


Spot Identification


Matching and Analysis

Comparision/Matcing of Gel Images


Compare 2 gel images


Set X and y axis


Overlap matching spots


Compare intensity of spots


Scan against database


Compare query gel with all gels


Calculate similarity score


Sort based on score

Mass Fingerprinting


Add protease (e.g. trypsin)


Get fragment size of peptides



Scan against peptides of a protein
obtained theortically by that protease



Scan against all proteomes

Differential Proteomics:


Fingerprints of Disease

Phenotypic

Changes

Normal Cells

Disease Cells


Differential protein expression



Protein nitration patterns


Altered phosporylation


Altered glycosylation profiles

Utility


Target discovery


Disease pathways


Disease biomarkers

Fingerprinting Technique


What is fingerprinting


It is technique to create specific pattern for a given
organism/person


To compare pattern of query and target object


To create Phylogenetic tree/classification based on pattern



Type of Fingerprinting


DNA Fingerprinting


Mass/peptide fingerprinting


Properties based (Toxicity, classification)


Domain/conserved pattern fingerprinting


Common Applications


Paternity and Maternity


Criminal Identification and Forensics



Personal Identification


Classification/Identification of organisms


Classification of cells

Drug Design based on Bioinformatics Tools


Detect

the

Molecular

Bases

for

Disease


Detection

of

drug

binding

site


Tailor

drug

to

bind

at

that

site


Protein

modeling

techniques


Traditional

Method

(brute

force

testing)



Rational

drug

design

techniques


Screen

likely

compounds

built



Modeling

large

number

of

compounds

(automated)


Application

of

Artificial

intelligence


Limitation of known structures


Search of Target protein


Search of Lead compound


History of Bioinformatics in India


Biocomputing started in 1950’s


IISc Banglore (Prof G Ramachandran)


Mostly analysis of protein structure


Distributed information center (DIC)


DBT initiate 9 DICs during 1986
-
7


National Facilities (IMT,IISc,IARI,JNU,MKU)


Sub
-
DICs started (around 50)


Mirror sites in 1999 (IMT,Pune,JNU,IISc)

Education in Bioinformatics


Role of BIC’s in education


Workshops, training, course etc started


Facilities/Infrastructure in BI


Advanced diploma in BI (Pune,JNU,MKU)


M.Sc. In bioinformatics


Private Sector


Number of courses initiated


Dedicated training centers


Universities


R&D Institutes


Ph.D in Bioinformatics (IMT)

Business Comparisons

Company

Revenues

IT Budget

Pct

Bristol
-
Myers Squibb

15,065,000,000

440,000,000

2.92 %

Pfizer

11,306,000,000

300,000,000

2.65 %

Pacific Gas & Electric

10,000,000,000

250,000,000

2.50 %

K
-
Mart

31,437,000,000

130,000,000

0.41 %

Wal
-
Mart

104,859,000,000

550,000,000

0.52 %

Sprint

14,235,000,000

873,000,000

6.13 %

MCI

18,500,000,000

1,000,000,000

5.41 %

United Parcel

22,400,000,000

1,000,000,000

4.46 %

AMR Corporation

17,753,000,000

1,368,000,000

7.71 %

IBM

75,947,000,000

4,400,000,000

5.79 %

Microsoft

11,360,000,000

510,000,000

4.49 %

Chase
-
Manhattan

16,431,000,000

1,800,000,000

10.95 %

Nation’s Bank

17,509,000,000

1,130,000,000

6.45 %



Typical Bioinformatics

Multi
-
Disciplinary Training


Scientists


Biology, Molecular Genetics, Clinical Biochemistry,
Protein Structure Chemistry



Mathematicians


Statistics, Algorithms, Image processing



Computer Scientists


Database, User Interface/Visualizations, Networking
(Internets/Intranets), Instrument Control





Typical Bioinformatics

Multi
-
Disciplinary Functions



Scientists


Experimental Design & Interpretation


Laboratory Protocols & Standards/Controls



Mathematicians


Analysis & Correlation of Data


Validation methodologies



Computer Scientists


Information Storage / Control Vocabulary


Data Mining



External

Public

Databases

Bioinformatics Architecture

External

Proprietary

Databases

Unix

servers

&

Specialized

Hardware

Users

Workstation

Java & Desktop

Programs

Web

Browser

Active

Server

Livewire

CGI

NT

servers

Proprietary

Internal

Databases

Web

Server

Shared

Access

Databases

MS

Access

Business Opportunities in BI


Software development


Web servers development


Train manpower in Field of BI



Database management


Rational Drug design


Develop Diagnostic kits


Assist user in Vaccine development


Consultant to Biotech Companies

Bioinformatics at IMT, Chandigarh

http://imtech.res.in/bic/

http://imtech.res.in/


Mirror Sites (http://www.imtech.res.in/mirror_sites/)


Public Domain Resources in Biology (www.imtech.res.in/)


IMTECH Library on Internet (/lib/)


Concept of vaccine design


Protein Structure Prediction (Olympic
-
2000)


Gene Prediction


Software for general use


GNU software


SUN Freeware


PostgreSQL


Site:
http//:imtech.res.in/raghava/www.html

THANK YOU!