Bioinformatics color

Transcription

Preface
It gives me immense pleasure and honor to compile and present the booklet on the
Bioinformatics National Certification (BINC) examination and the DBT-BINC-JRF programme
on behalf of the Department of Biotechnology (DBT), Government of India. The booklet is
designed with an objective to serve as a single point reference to all the stakeholders of the
BINC examination in general and the BINC fellowship awardees and their imminent
supervisors in particular. The BINC examination was introduced in 2005 to identify and certify
professionals in the area of Bioinformatics as the subject has emerged as an independent
discipline over the years and is assuming an increasingly important role in the Life Sciences
research in the post-genomic era.
There are two major aspects of conducting the BINC examination viz. academic and
administrative. The academic component has been spearheaded and mentored by Prof. A. S.
Kolaskar (Former Vice Chancellor, University of Pune; Founder Director, Bioinformatics Centre
and Chairman, BINC National Coordination Committee), and the esteemed members of the
BINC National Coordination Committee. The Coordination Committee has been the driving
force in setting and maintaining high standards of the BINC examination. This examination is
novel and unique in the sense that it employs a three-tier system including an objective,
subjective and practical examination to evaluate the knowledge and skill set of the candidates.
The Bioinformatics community in India has been extremely supportive by contributing as
paper setters, moderators, and evaluators.
With a modest beginning as a Distributed Information Center under the BTIS network of
DBT in the year 1987, the Bioinformatics center has evolved as a Center of Excellence. Despite
the decline in the faculty strength in 2008-09, the centre is able to embark on various activities
mainly due to wholehearted support extended not only by the staff of the centre and but also
the associated faculty members, some of who also served as the Observers for BINC examination
held at various examination centers. Coordinating and conducting any examination at the
national level is a huge responsibility and demands the cooperation of many. The administrative
support extended by the various sections of University of Pune and the SET unit in particular
is acknowledged for timely help. Contributions of erstwhile coordinators of BINC examinations,
Prof. Indira Ghosh, Dr. Chaitanya Hiremath and Late Dr. V. Shankar are gratefully acknowledged.
Dr. S.R.R. Reddy deserves a special mention for adding value to various aspects of BINC
examination, specially the post-examination analyses, which served as a feedback for
subsequent examinations. I appreciate the wide range of contributions made by my colleague,
Dr. Sangeeta Sawant. The BINC website has been developed and is maintained by our scientific
and technical staff members. The actors behind the scene who worked relentlessly for making
each of the BINC examination a success are all the members of our staff.
I am short of words to thank Dr. M. K. Bhan, Secretary, DBT, for the message specially
written for this booklet. I am grateful to Dr. A. D. Adsool, Vice Chancellor (Acting), University
of Pune, for supporting various activities of the center. The preamble written by
Prof. A. S. Kolaskar reveals the genesis of the BINC examination. Foreword to the booklet
written by Dr. T. Madhan Mohan (Advisor, DBT), underlines the continued support for
strengthening Bioinformatics activities in India.
I urge the reader to help DBT in popularization of BINC examination by sharing the
information with students, colleagues and society at large. Your suggestions, if any, to improve
the readability of the booklet are most welcome.
Dr. Urmila Kulkarni-Kale
Coordinator, BINC
Index
Contents
BINC – General information
Page
No.
1
•
List of examination centers
1
•
Pattern of BINC examination & question papers
3
BINC website
3
BINC – Sample Application Form
5
BINC – Sample Admit Card
6
Frequently asked questions
7
DBT-BINC-JRF Award: Terms and Conditions
9
DBT-BINC-JRF Data Sheet /Candidate Information Form
12
DBT-BINC-JRF/SRF Grant Claim Form
14
DBT-BINC-JRF/SRF Grant Utilization Certificate
15
DBT-BINC-JRF/SRF Grant - Statement of Expenditure
16
BINC Coordinator – Contact details
17
List of successful candidates – 2007, 2008 & 2009
18
Annexure I: Syllabus of BINC examination 2009
20
.
BINC: General Information
BioInformatics National Certification (BINC) examination was instituted by the Department
of Biotechnology, Government of India in the year 2005 with an objective to certify Bioinformatics
professionals. Any science graduate with or without formal training in Bioinformatics can
appear for this examination. A national coordination committee under the chairmanship of
Prof. A. S. Kolaskar consisting of Bioinformatics experts from all over the country, decides the
mode, frequency, syllabus, centers of examination, question paper setters, evaluators, etc.
Frequency of BINC
BINC examination is conducted annually in the first half of the calendar year.
Eligibility
Graduates/post-graduates/Ph.D. in Science, Technology, Pharmacy, Engineering,
Agriculture, Veterinary Science and Medicine (including Ayurveda and Homeopathy) from
recognised Indian universities and institutions with or without formal training in Bioinformatics
are eligible to appear for the examination. Students in the final year of the Bachelor’s degree
course can also apply.
Age limit & attempts
There is no age limit to appear for the BINC examination. Also, there is no limit on the
number of attempts to qualify for BINC certification. However, candidates who have cleared
BINC examination in a maximum of three attempts only are eligible for BINC research
fellowship, if other criteria are satisfied. (See FAQs on pages 7-8 and the section on ‘DBTBINC-JRF Award: Terms and Conditions’ on pages 9-11.)
Examination Centers
BINC examination was held in 2009 at the seven centers listed below:
•
University of Pune, Pune
•
Jawaharlal Nehru University, New Delhi
•
Anna University, Chennai,
•
West Bengal University of Technology, Kolkata
•
Institute of Bioinformatics and Applied Biotechnology, Bangalore
•
North-Eastern Hill University, Shillong
•
University of Hyderabad, Hyderabad
Up-to-date information regarding BINC examination centers is available on BINC website.
DBT-BINC Junior Research Fellowship Programme
1
Mode of Selection
Candidates are selected on the basis of a written test consisting of three papers viz., Paper
I (objective type), Paper II (subjective type) and Paper III (practical examination). Candidates
scoring overall 40% marks or above in each paper will be certified. Thus, this is the most
comprehensive examination for certification and award of fellowship conducted in this country.
Details of the Award
All successful candidates are awarded certificates of proficiency in Bioinformatics. The
certificate is generally considered equivalent to the Advanced Diploma in Bioinformatics
conducted by several universities and DBT-supported institutions. Further •
Cash awards of Rs. 10,000/- are given to the top ten candidates in the merit list who have
passed and are eligible for BINC certification.
•
Junior research fellowships (DBT-BINC-JRF) are awarded to top fifteen BINC certified
candidates having a Master’s degree in Science, Technology, Pharmacy, Engineering,
Agriculture, Veterinary Science and Medicine (including Ayurveda and Homeopathy)
and have taken admission to Ph.D. programme in Bioinformatics offered by recognised
Indian Universities/Institutes. Refer to pages 9-11 of the booklet for more information.
Tentative calendar of activities
2
BINC advertisement in news papers
1st week of December
BINC advertisement on website
1st week of December
Online registration period
December 1 st week – January 2nd week
Display of the list of eligible candidates on
the website
Last week of January
Availability of admit cards on the website
for download
Last week of January
BINC examination (Paper I): Objective
February 3rd week (Day 1, morning)
Results of Paper I
February 3rd week (Day 1, 6.00 P.M.)
BINC examination (Paper II): Short answers
February 3rd week (Day 2, morning)
BINC examination (Paper III): Practicals
February 3rd week (Day 2, afternoon)
BINC final result
Last week of March
Result of qualifying examination to be sent by
the candidates to the Coordinator, BINC
By third week of August
Distribution of BINC certificates, DBT-BINC-JRF
award letter & booklet
By second week of September
Intimation of acceptance / rejection of
DBT-BINC-JRF by awardees
By end of October
Distribution of DBT-BINC-JRF award letters to
wait listed candidates
First week of November
BioInformatics National Certification (BINC) Examination
Pattern of BINC Examination & Question papers
The examination consists of THREE papers as mentioned below. BINC is the only national
certification examination, which evaluates candidates for their knowledge in Bioinformatics
and problem solving ability and therefore, includes a practical component also. Sample
questions and syllabi for both, Paper I (Basic) & Paper II (Advanced) are available online.
Paper III consists of questions/problems to test both, the analytical ability as well as
programming skills necessary for a Bioinformatician and is based on basic and advanced topics
in Bioinformatics.
Paper
Type
Day of Examination
No. of questions
Marks
Paper I
Objective
Paper II
Paper III
Duration
Day 1 (Morning)
100
100
2 hours
Short answers
Day 2 (Morning)
15
150
3 hours
Practicals
Day 2 (Afternoon)
2
100
2 hours
Important points to note
•
There will be negative marking of 0.25 marks for each wrong answer in Paper I.
•
Candidates securing 40% or above marks in Paper I will be eligible to appear for Papers
II and III.
•
Results of Paper I will be announced at the respective examination centers as well as on
BINC website by 6:00 P.M. on Day 1 of the examination.
•
Candidates scoring overall 40% marks or above in each paper will be certified.
Syllabus
The syllabus consists of four sections viz. Biology; Physical & Chemical Sciences (Basic
Mathematics, Statistics, Physics & Chemistry); Information Technology and Bioinformatics.
Visit http:// bioinfo.ernet.in/binc/syllabus for updates and revisions. Syllabus of BINC
2009 examination is included for reference (see Annexure I). Each year experts review the
existing syllabus and revise it so that it is up-to-date and relevant to the needs of academia
& industry. This revised syllabus is then made available on the BINC website before 1st
week of December.
BINC website:
•
http:// bioinfo.ernet.in/binc
•
BINC website provides links to important information viz. eligibility, syllabus, sample
questions, application procedure, important dates, list of examination centers, and FAQs.
•
Candidates applying for BINC examination should register online. Printed & duly signed
application form along with the DD and other relevant documents should be sent by post
to the BINC Coordinator.
•
Candidates can track progress of their application and download admit cards using the
same login ID and password generated at the time of registration.
•
Candidates can also reach the BINC administration by sending email to:
[email protected]
•
BINC website is developed and maintained in house by the Bioinformatics Centre,
University of Pune.
3
Snapshot of BINC website
4
BINC - Sample Application form
5
BINC - Sample Admit Card
6
Frequently Asked Questions (FAQs)
1)
What is the objective of BINC examination?
There is a growing need for trained manpower in the area of Bioinformatics. Currently,
various universities and institutions, both government and private, impart Bioinformatics
education in India. However, there exists a large variation in the course contents, training
period and method of training. The Department of Biotechnology (DBT), Government of
India has instituted BINC examination with the objective of evaluating the Bioinformatics
knowledge & skills of students. The qualifying candidates will be awarded a certificate.
This certification would facilitate industries and potential employers in recruiting
Bioinformatics professionals.
As an added incentive, DBT has decided to grant
2)
•
Cash awards to the top ten candidates in the merit list
•
DBT – BINC junior research fellowships (DBT-BINC-JRF) to top fifteen candidates
who have a Master’s degree and are willing to enter into the Ph.D. programme
offered by recognised Indian universities/institutes in the area of Bioinformatics/
Computational Biology.
What is the minimum qualification required to appear for the BINC examination?
Graduation in Science, Technology, Pharmacy, Engineering, Agriculture, Veterinary
Science and Medicine (including Ayurveda and Homeopathy) from a recognised Indian
university/institution with or without formal training in bioinformatics.
Students in the final year of Bachelor’s / Master’s degree programme are eligible to appear
for BINC. Individuals possessing Ph.D. degree who intend to obtain certification in the
area of Bioinformatics are also eligible.
3)
Is it necessary for students with formal training in Bioinformatics (Bachelor’s, Master’s
degree holders as well as diploma holders) to appear for this exam?
Even those with formal training in Bioinformatics are encouraged to appear for the exam
since BINC certification would serve as a benchmark for the training they had received
and the skills they acquired. However, no formal training in Bioinformatics at any level is
needed to appear for the BINC examination.
4)
How many attempts are permitted for BINC examination?
Currently there is no limit on the number of attempts to appear for the BINC examination.
However, to avail the DBT-BINC junior research fellowship (DBT-BINC-JRF) for pursuing
Ph.D. in Bioinformatics, a maximum of three attempts are allowed.
5)
Is there any age limit to appear for BINC?
There is no age limit to appear for the BINC examination.
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6)
How many times is the BINC examination held every year?
At present it is held once in a year.
7)
Are there any prescribed text/reference books?
There are no reference books or textbooks prescribed. Examinees are advised to refer to
standard books that cover the different topics included in the syllabus prescribed for the
BINC examination.
8)
Do you provide a sample question paper?
As of now we do not provide any sample question paper. However, sample questions
with answers are provided on the BINC website.
9)
What does qualifying the BINC examination mean? What are the advantages of qualifying
BINC examination?
•
Your knowledge in the area of Bioinformatics is certified by the Department of
Biotechnology (DBT), Govt. of India.
•
Top ten successful candidates in the BINC merit list receive cash prizes of
Rs.10,000/- each.
•
Top fifteen candidates will be awarded DBT-BINC-JRF to pursue Ph.D in
Bioinformatics at recognised Indian universities and institutes.
10) What is the difference between BINC certification and DBT-BINC-JRF award?
While anyone with a Bachelor’s degree in Science, Medicine, Engineering etc. is eligible
to appear in the BINC examination and receive a certificate, the fellowships are given
only to those who have a Master’s degree and are enrolled in the Ph.D. programme in
Bioinformatics in any recognized institute/university in India. The fellowships, fifteen in
number at present, are awarded to eligible candidates strictly on the basis of the merit list
in the BINC examination.
BINC qualified candidates would be called ‘DBT Certified Bioinformaticians’ while the
individuals availing the fellowship would be called as DBT-BINC Junior Research Fellows
(DBT-BINC-JRF).
11)
8
Are foreign students eligible to appear for BINC?
•
Foreign nationals intending to have certification are eligible to appear for BINC
examination.
•
Minimum qualification includes a degree from a recognized university/institute
in the areas listed in FAQ 2.
•
Formal training in the area of Bioinformatics is not a prerequisite.
•
Note that the foreign students will only be certified by DBT and are not eligible
for the cash award as well as junior research fellowship.
DBT-BINC-JRF Award: Terms and Conditions
DBT-BINC-JRF award is a corollary of the BINC examination being conducted by the DBT.
This fellowship will be awarded to top 15 BINC candidates in the merit list who meet the
following criteria:
•
Indian national with a post graduate degree in Science, Technology, Pharmacy, Engineering,
Agriculture, Veterinary Science and Medicine (including Ayurveda and Homeopathy) etc.,
who are interested in pursuing research leading to Ph.D. degree in Bioinformatics/
Computational Biology in any recognized Indian university/institute.
•
Candidates receiving the BINC fellowship will have to satisfy all the rules/requirements of
the university/institute where they are enrolled in the Ph.D. programme hereafter referred
to as ‘host institution’. The research supervisor should tacitly certify that the fellow would
carry out research in the area of Bioinformatics/Computational Biology.
•
Candidates should join the host institution under the BINC fellowship programme within
the time limit prescribed by the coordinating institution, namely, University of Pune, Pune.
No TA/DA will be admissible for joining the host institution.
•
The DBT-BINC research fellowship is awarded initially for a period of two years and
extended on yearly basis thereafter for another three years, based on the progress, overall
importance of the research project of the fellow and recommendations of the research
supervisor as well as a monitoring expert committee. The evaluation and recommendation
for the extension of the fellowship will be made by the host institution as per their internal
procedures and guidelines.
•
Each fellow is entitled to a fellowship of Rs. 12,000/- per month (during the first and second
year) and 14,000/- per month (during the third and subsequent years). The fellowship
payable to each candidate would be at par with CSIR/UGC JRFs and SRFs. In addition, the
Fellow is also entitled to HRA (as applicable at the host institution) and other benefits
including medical allowance of Rs. 250/- per month as per DBT norms.
•
Each fellowship would also carry a research contingency grant of Rs. 30,000/- per annum.
The amount is primarily meant for meeting the cost of consumables and minor equipment
required (computer peripherals/ license fees for databases and software) for the research
work of the Fellow. However, with the consent of the research supervisor, a portion of the
grant, not exceeding Rs. 10,000/- per annum, may be utilized towards the cost of attending
major conferences/ symposia/seminars/workshops held in India in the area related to
research of the fellow. The same amount can also be utilized for payment of the registration
fees of online international workshop/international conference. The grant should not be
utilized for international travel or for meeting the cost of attending conferences held abroad.
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•
The fellowship and the contingency grant will be paid to the DBT-BINC-JRF/SRF through
the host institution where he/she is working. DBT will release the money to University of
Pune and University of Pune in turn will transfer it to the host institution after receiving
the joining report of JRF. The fellowship and grant for subsequent years will be released
by University of Pune to the host institution after the receipt of progress report of the JRF
and Utilization Certificate (UC) and Statement of expenditure (SE) in DBT format duly
signed by the Guide/Supervisor and Finance/Accounts Officer of the respective host
institution. (See pages 12-16 for the DBT-BINC-JRF Data Sheet / Candidate Information
Form, DBT-BINC-JRF/SRF Grant Claim Form, DBT-BINC-JRF/SRF Grant Utilization
Certificate and DBT-BINC-JRF/SRF - Statement of Expenditure. These forms can also be
downloaded from the BINC website.)
•
Certification by the Guide and HOD stating that the student was working full time as JRF/
SRF in the Department and has not availed leave for more than 30 working days in the
calendar year is also required.
•
The fellows should devote full time to their research and training for which they have been
awarded the fellowships. They shall abide by the rules and regulations of the host institutions
applicable to research fellows.
•
The fellows will be entitled to 30 days leave per year with fellowship. Any period of absence/
leave beyond 30 days in a year will be treated as leave without fellowship.
•
The candidate who has been awarded the DBT-BINC Junior Research Fellowship must
convey his / her acceptance of the same within six weeks from the date of award. Otherwise,
it would be awarded to the next candidate in the order of merit. However, the fellowship
offer, if accepted by a candidate shall remain valid for a period of one year, within which
he/she must avail the fellowship and subsequently join a Ph.D. programme.
•
Bioinformatics Centre, University of Pune, Pune will coordinate and administer the
implementation of the fellowship programme on behalf of the Department of Biotechnology,
Government of India.
Points to note for prospective supervisors of DBT-BINC-JRFs
•
A supervisor would be permitted to take no more than two DBT-BINC-JRFs in his/her
laboratory at any given time.
•
The recipients of the DBT-BINC-JRF should be citizens of India.
•
The supervisors should provide their details along with those of the candidate at the time
of registration. See the ‘DBT-BINC-JRF Data Sheet/Candidate Information Form’.
•
The research supervisor should ensure that the fellow would carry out research in the area
of Bioinformatics/Computational Biology and provide an endorsement letter to this effect.
10
•
The progress report should be sent to the Coordinator, BINC programme annually. The
consolidated report on completion of the tenure of the fellowship should also be sent. The
supervisor and the host institution will be responsible for submission of such reports and
also submission of UC/SE to the University of Pune (Coordinator of this programme) for
the grant received.
•
In all the publications resulting out of the research work carried out during the period of
the fellowship, the DBT should be acknowledged for support through the award of the
fellowship.
Mode of Activation and Continuation of the Fellowship
•
Upon receiving the award letter, the candidate needs to select his/her research supervisor
from a University/Institute/Centre where he/she can register for Ph.D. In cases where
there is a separate Ph.D. admission procedure of the institution, candidates have to go
through that procedure.
•
The fellowship is activated only when the candidate, after fulfilling all the requirements,
sends his biodata, duly filled DBT-BINC-JRF Data Sheet/ Candidate Information Form (in
the format given on page 12) and joining report through the host institution to the
Coordinator, DBT-BINC-JRF programme.
•
The candidate who has been awarded the BINC Junior Research Fellowship must convey
his / her acceptance of the same within six weeks from the date of award. Otherwise, it
would be awarded to the next candidate in the order of merit. However, the fellowship
offer, if accepted by a candidate shall remain valid for a period of one year, within which
he/she must avail the fellowship and subsequently join a Ph.D. programme.
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DBT-BINC-JRF Data Sheet / Candidate Information Form
(Note : This form can also be downloaded from http://bioinfo.ernet.in/binc/forms)
12
13
DBT-BINC-JRF/SRF Grant Claim Form
14
DBT-BINC-JRF/SRF Grant Utilization Certificate
(for the year financial year
-
)
1.
Certified that the amount of Rs. ______________ has been utilized on the fellowship and
contingency for which it was sanctioned and that the balance of Rs.______________
remaining unutilized at the end of the year has been surrendered to Govt. (vide
No._________dated____________)/will be adjusted towards the grants-in-aid payable
during the next year _________.
2.
Certified that I have satisfied myself that the conditions under which the grants-in-aid
was sanctioned have been duly fulfilled and that I have exercised the following checks to
see that the money was actually utilized for the purpose for which it was sanctioned.
Kinds of checks exercised :
1.
Cash Book
2.
Ledger
3.
4.
5.
Research Supervisor
(Signature with seal)
Head of the Department
Finance & Account Officer
Place:
Date:
(Note : This certificate can also be downloaded from http://bioinfo.ernet.in/binc/forms)
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DBT-BINC-JRF/SRF Statement of Expenditure
for the period from _________ to _________
Name of the Research Fellow (JRF / SRF):
Date of Joining:
Institute / University:
Department:
DBT-BINC-JRF Reference Letter No:
Grant released: Rs.
Expenditure details:
Month
Fellowship
House Rent
Allowance
Medical
Allowance
Total Rs.
April
May
June
July
August
September
October
November
December
January
February
March
Total Fellowship Rs.
Contingency Expenses Rs.
Total Expenditure Rs.
Grant Released
Total Expenditure Rs.
Balance Rs.
Signature of the
Supervisor
(with seal)
Director/Head
of the Department
(with seal)
Finance and Accounts Officer
(with seal)
(Note : This statement can also be downloaded from http://bioinfo.ernet.in/binc/forms)
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BINC Coordinator: Contact details
Coordinator:
Dr. Urmila Kulkarni-Kale
Director, Bioinformatics Centre
University of Pune
Pune 411 007
Telephone: 020-25692039
020-25690195
Fax:
020-25690087
e-mail:
[email protected] (primary)
[email protected]
URL:
http://bioinfo.ernet.in
http://bioinfo.ernet.in/binc
Accountant:
Mr. Mahesh Joshi
Assistant Coordinator :
Advertised (under process)
(Technical)
BINC Assistant:
Advertised (under process)
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Annexure I
Syllabus for BINC examination 2009
The syllabus consists of four sections viz. Biology; Physical & Chemical Sciences (Basic
Mathematics, Statistics, Physics & Chemistry); Information Technology and Bioinformatics.
Visit http://bioinfo.ernet.in/binc/syllabus.html for updates and revisions. The syllabus for
BINC 2009 is included for reference.
Paper I (Basic)
Subject: Biology
Cell Biology & Genetics
•
Basic aspects of prokaryotic and eukaryotic cells (plant and animal cells); membranes
and cellular compartments, cell organelles, structure and function.
•
Cell motility and shape: cytoskeletal elements, cilia and flagella; motor proteins.
•
Cell-cell interactions: Intercellular junctions.
•
Photosynthesis, transportation of proteins in cells, transpiration, respiration.
•
Cell cycle and its regulation; events during mitosis and meiosis.
•
Mendelian principles of inheritance, sex linked inheritance.
•
Concept of linkage, linkage maps and recombination.
•
Mutations – molecular, gene/point and chromosomal types.
•
Phenotype and genotype relationships, role of environment, from gene to phenotype,
gene interactions. Study of quantitative traits.
•
Genetics of populations, genetics and evolution.
•
Concepts of generation of diversity and specificity in immune system; Immunological
methods.
Molecular Biology
•
Prokaryotic genome organization and structure.
•
Prokaryotic gene expression, factors involved in gene regulation.
•
Eukaryotic genome organization and structure, Mechanism of gene expression in
eukaryotes, Basic mechanism of transcription and translation.
•
Mechanisms by which genome undergoes changes, recombination, mutation, inversion,
duplication, transposition.
Biochemistry
20
•
Carbohydrates and lipids, their importance in cells.
•
Proteins: Amino acids and peptides; primary, secondary, tertiary and quaternary
structures.
•
Nucleic acids: Bases, nucleotides, RNA and DNA. Different structural form of DNA,
denaturation and renaturation of DNA.
•
Enzymes: Units of activity, coenzymes and metal cofactors, temperature and pH effects,
Michaelis-Menten kinetics, inhibitors and activators, active site.
•
Organization of metabolic systems: enzyme chains, multienzyme complexes and
multifunctional enzymes & regulatory enzymes.
•
Concept of biochemical regulation, feed back and feed forward systems, biochemical
oscillations.
Paper I (Basic)
Subject: Basic Mathematics, Statistics, Physics & Chemistry
•
Functions and Graphs: Functions, Relations, notation and representation. Graphs. Review
of basic functions. Functions of several variables.
•
2D coordinate geometry: Equations of line, circle, ellipse, parabola, hyperbola.
•
3D geometry: Equations of sphere and cone.
•
Basic trigonometric functions.
•
Matrix algebra: Addition, subtraction, multiplication, transpose, inverse.
•
Introduction to principles of statistical sampling from a population, random sampling
•
Frequency distributions and associated statistical measures, Probability distributions –
normal and binomial.
•
Concept of pH, pK, chemical equilibrium, Henderson-Hasselbach equation, structure
of water, chemical forces, hydrophilic and hydrophobic forces, electronic structure of
molecules, chemical bonds, ionic bonds, covalent bonds, hydrogen bonds and coordinate
bonds.
•
First law of thermodynamics, isothermal process, entropy and second law of
thermodynamics, reversible and irreversible processes; free energy and chemical
potential; Gibbs free energy.
Paper I (Basic)
Subject: Information Technology
Concepts in Computing
•
Overview and functions of a computer system.
•
Input and output devices.
•
Storage devices: Hard Disk, Diskette, Magnetic Tape, RAID, ZIP devices, Digital Tape,
CD-ROM, DVD, etc (capacity and access time).
•
Main Circuit Board of a PC: Chips, Ports, Expansion slots, etc.
•
Memory: Register, buffer, RAM, ROM, PROM, EPROM, EEPROM (comparison).
21
•
Types of Processing: Batch, Real-Time, Online, Offline.
•
History of computers: Evolution, Generation of computers (I, II, III, IV, V), Classification
of computers (mainframes, mini computers, microcomputers, special purpose) –
comparison with respect to memory, power, cost, size - then and now.
•
Types of modern computing: Workstations, Servers.
•
An overview of computer viruses: What is a virus? Virus symptoms, How do they get
transmitted? What are the dangers? General Precautions.
•
Introduction to operating systems: Operating System concept, Windows 2003/XP,
Windows Vista, UNIX/LINUX.
•
The Internet and its resources, World Wide Web (WWW): Associated tools, services,
resources and various terminologies.
•
Programming in C.
Introduction to Database Systems
•
Concepts of various types of databases
•
Data Abstraction.
•
Data Models.
•
Instances & Schemes.
•
E R Model:
o Entity and entity sets.
o Relations and relationship sets.
o E R diagrams.
o Reducing E R Diagrams to tables.
•
Network Data Model: Basic concepts.
•
Hierarchical Data Model: Basic Concepts.
•
Multimedia Databases Basic Concepts and Applications.
o Indexing and Hashing.
•
Text Databases.
Paper I (Basic)
Subject: Bioinformatics
•
Major Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB
The knowledge of various databases and bioinformatics tools available at these resources, the
major content of the databases, purpose and utility in Life Sciences.
•
Open access bibliographic resources and literature databases:
Open access bibliographic resources related to Life Sciences viz., PubMed, BioMed Central,
Public Library of Science (PLoS).
22
•
Sequence databases: Formats, querying & retrieval
o Nucleic acid sequence databases: GenBank, EMBL, DDBJ
o Protein sequence databases: SWISS-PROT, TrEMBL, PIR-PSD
o Repositories for high throughput genomic sequences: EST, STS GSS, etc.
o Genome Databases at NCBI, EBI, TIGR, SANGER
Viral Genomes
Archeal and Bacterial Genomes.
Eukaryotic genomes with special reference to model organisms (Yeast,
Drosophila, C. elegans, Rat, Mouse, Human, plants such as Arabidopsis
thaliana, Rice, etc.)
•
Structure Databases:
o PDB, NDB, PubChem
•
Derived Databases
Knowledge of the following databases with respect to: basic concept of derived databases, sources
of primary data and basic principles of the method for deriving the secondary data, organization
of data, contents and formats of database entries, identification of patterns in given sequences
and interpretation of the same.
o Sequence: Prosite, Pfam
o Structure: CATH, SCOP, DSSP, PDB Goodies.
•
Extraction of knowledge from databases on Immunology, Plant, animal & infectious
diseases: search new databases & servers using NAR Database & Web server Issue,
BMC Bioinformatics etc.
•
Sequence Analysis
o File formats : Various file formats for bio-molecular sequences: GenBank, FASTA,
GCG, MSF, NBRF-PIR etc.
o Basic concepts: Sequence similarity, identity and homology, definitions of
homologues, orthologues and paralogues.
o Scoring matrices: basic concept of a scoring matrix, Matrices for scoring nucleic
acid and proteins sequence alignments, PAM and BLOSUM series, principles
based on which these matrices are derived.
o Database Searches:
keyword-based Entrez and SRS
Sequence-based: BLAST & FASTA
Use of these methods for sequence analysis including the on-line use of
the tools and interpretation of results from various sequence and structural
as well as bibliographic databases.
23
o Pairwise sequence alignments: basic concepts of sequence alignment, Needleman
& Wunsch, Smith & Waterman algorithms for pairwise alignments, use of pairwise
alignments for analysis of Nucleic acid and protein sequences and interpretation
of results.
o Multiple sequence alignments (MSA): the need for MSA, basic concepts of
various approaches for MSA (e.g. progressive, hierarchical etc.). Algorithm of
CLUSTALW and PileUp and their application for sequence analysis (including
interpretation of results), concept of dendrogram and its interpretation.
o Sequence patterns and profiles: Basic concept and definition of sequence patterns,
motifs and profiles, various types of pattern representations viz. consensus,
regular expression (prosite-type) and profiles; profile-based database searches
using PSI-BLAST, analysis and interpretation of profile-based searches.
o Taxonomy and phylogeny: Basic concepts in systematics, taxonomy and
phylogeny; molecular evolution; nature of data used in Taxonomy and Phylogeny,
Definition and description of phylogenetic trees and various types of trees.
o Protein and nucleic acid properties: Computation of various parameters using
proteomics tools at the ExPASy server, GCG utilities and EMBOSS.
o Comparative genomics: Basic concepts and applications.
•
Structural Biology
o Proteins: Principles of protein structure; anatomy of proteins – Hierarchical
organization of protein structure - Primary. Secondary, Super secondary, Tertiary
and Quaternary structure; Internal coordinates of proteins; Derivation and
significance of Ramachandran Map, protein folding.
o DNA and RNA: types of base pairing – Watson-Crick and Hoogstein; types of
double helices A, B, Z and their geometrical as well as structural features; structural
and geometrical parameters of each form and their comparison; various types of
interactions of DNA with proteins and small molecules.
RNA secondary and tertiary structures; t-RNA tertiary structure.
o Carbohydrates:
The various building blocks (monosaccharides), configurations and conformations
of the building blocks; formations of polysaccharides and structural diversity
due to the different types of linkages.
Glyco-conjugates: various types of glycolipids and glycoproteins.
•
3-D structure visualization and simulation
o Visualization of structures using Rasmol or SPDBV or CHIME.
o Basic concepts in molecular modeling: different types of computer representations
of molecules.
o Concepts of force fields: representations of atoms and atomic interactions,
potential energy representation.
24
•
Classification and comparison of protein 3D structures:
o
Purpose of 3-D structure comparison and concepts, Algorithms such as FSSP,
VAST and DALI, Fold Classes.
•
Secondary structure prediction: Algorithms of Chou and Fasman, GOR methods;
analysis of results and measuring the accuracy of predictions using Q3, Segment overlap,
Mathew’s correlation coefficient.
•
Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction
(sequence similarity / identity of target proteins of known structure, fundamental
principles of protein folding, etc.) Homology Modeling; fold recognition, threading
approaches, and ab-initio structure prediction methods.
•
Fundamentals of docking small and macromolecules to proteins and nucleic acids.
Paper II (Advanced)
Subject: Biology
Cell Biology & Genetics
•
Vesicular transport and protein traffic in cells.
•
Second messenger, different mechanisms of signal transduction, concepts in signal
network, molecules involved in various signaling pathways such as G-protein coupled
receptors, protein kinases, calcium binding proteins.
•
X-linked and autosomal diseases, mitochondrial related disease, QTL methods for
diagnostics.
•
Extra chromosomal inheritance.
•
Immune response, autoimmune disorders, ELISA method.
•
Molecular genetics and genetic disorders.
Molecular Biology
•
Genome organization, Initiation, elongation and termination of transcription – template
& enzyme properties, Promoter & regulatory sequences.
•
Methods for studying gene expression and regulatory sequences, large-scale expression
analysis, use of microarrays.
•
Genetic information transfer, details of regulation in eukaryotes & prokaryotes,
horizontal gene transfer.
•
Operons – positive & negative regulation, Processing of RNA and Proteins - Transport
and Stability
•
Organization of eukaryotic genome, Methods for studying variation and polymorphism
at genome level, PCR, northern, southern, western blotting, RFLP, Fingerprinting,
RAPDs, DNA and protein sequencing methods.
•
Epigenetic mechanisms of inheritance and regulatory RNA molecules (RNA; miRNA,
siRNA), antisense RNA and their applications.
•
GFP- Green Fluorescent Protein and application in Molecular Biology.
25
Biochemistry
•
Enzyme kinetics, Lineweaver-Burk plot, Competitive and non competitive inhibition.
•
Molecular mechanisms of interactions of small and large molecules including ions,
regulation of protein pathways, mechanism of enzyme action, ribozyme and abzymes.
•
Isoenzymes, allosteric enzymes, regulation by covalent modification.
•
Carbohydrate metabolism: Glycolysis, gluconeogenesis, glycogenolysis, glycogenesis,
TCA cycle and oxidative phosphorylation.
•
Pentose phosphate pathway; hormonal control, β-oxidation and biosynthesis of fatty
acids.
•
Transamination and deamination of amino acids, ketogenic and glycogenic amino acids,
urea cycle.
•
Purine and pyrimidine biosynthesis
Paper II (Advanced)
Subject: Basic Mathematics, Statistics, Physics & Chemistry
26
•
Number integration. Interpolation and approximate methods. Concept of Eigen vectors
and eigen values. Poisson and extreme value distributions.
•
Vector addition, subtraction, dot, cross, scalar triple product, divergence and curl.
•
Methods of least squares, chi-square test, systematic and random sampling, accidental
and systematic errors, correlation and regression analysis.
•
System of linear equations.
•
Mathematical modeling and simulation, Multivariate analysis, Hypothesis testing,
Markov process.
•
Methods for determining free energy changes, coupled reaction, kinetics of reaction,
activation energy. Polar molecules, molar refraction and polarization. Dipole moment,
potentiometric determination of pK of amino acids. Free energy of charged metal ions;
Hydration and solvation number. Non-covalent bonding in protein structure.
•
Biophysical Techniques for determining size and shape of macromolecules – ultra
centrifugation, electrophoresis and chromatography. Application of spectroscopy
(fluorescence and absorption spectroscopy) and X-ray diffraction for determination of
biomolecular secondary and tertiary structure – CD, NMR, X-ray crystallography, mass
spectroscopy of biological molecules.
•
Basic principle of chemical kinetics – Zero order and first order kinetics, energy of
activation, Derivative and differential
•
Basics of classical mechanics and quantum mechanics.
•
Laws of motion
•
Principles of lasers.
Paper II (Advanced)
Subject: Information Technology
•
Parallel Processing and Computing, Cluster computing, Grid computing, etc
•
Java and Perl Programming.
•
Introduction to Distributed Database Processing; Understand, appreciate and
implement relational database design.
SQL and Front End Development
•
Select Statements.
•
Data Definition Statements.
•
Data Manipulation Statements.
•
Data Control Statements.
•
Other Database Objects
o Views
o Sequences
o Synonyms
•
Introduction to Application Development using Visual Basic.
•
Working with Code and Forms.
•
Variables, Procedures and Controlling Program Executor.
•
Standard Controls.
•
Data Access Using Data Control.
•
Connecting to Oracle Database using Visual Basic.
•
Acquiring the skills of using Oracle DBMS as backend, SQL skills and basic skill in
using VB as a front end.
Computer Graphics and Visualisation
•
Introduction.
•
Scientific & Engineering Opportunities.
•
Visualization techniques
o Software.
o Hardware.
•
Graphics.
•
Interactive graphics.
•
Interaction devices & techniques.
•
Geometric transformations.
•
Viewing in three dimensions.
•
Rendering.
•
Standards CGI, GKS, PHIGS.
27
Programming in C
•
Concepts of flowcharting, algorithm development, pseudo codes etc.
•
Computer assignments based on the following topics in ‘C’ programming: Data types,
operators and expressions, Hierarchy of operators, control statements including decision
(if, if-else), loops (while, do-while, for), branching (switch, break, continue), functions,
arrays (1D, 2D- all matrix operations including inverse of a matrix), strings, file handling,
data structures etc.
Or
Programming in Object Oriented Languages
JAVA
28
•
An introduction to JAVA programming.
•
Object oriented programming and Java.
•
Java Basics.
•
Working with objects.
•
Arrays, Conditionals and Loops.
•
Creating Classes and Applications in Java.
•
More about methods.
•
Java Applets Basics.
•
Graphics, Fonts and Color.
•
Simple Animation and Threads.
•
Advanced Animation, Images and Sound.
•
Managing Simple Events and Interactivity.
•
Creating User Interfaces with AWT.
•
Windows, Networking and other Tidbits.
•
Modifiers, Access Control and Class Design.
•
Packages and Interfaces.
•
Exception.
•
Multithreading.
•
Streams and I/O.
•
Using Native Methods and Libraries.
•
Under the Hood.
•
Java Programming Tools.
•
Working with Data Structures and Java.
•
Image Filters.
Or
Perl
•
Introduction: What is Perl? Why use Perl in Bioinformatics? History of Perl, Availability,
Support, Basic Concepts.
•
Scalar Data: What is Scalar Data? Numbers, Strings, Scalar Operators, Scalar Variables,
Scalar Operators and Functions.
•
Arrays and List Data: What is a List or Array? Literal Representation, Variables, Array
Operators and Functions, Scalar and List Context.
•
Control Structures: Statement Blocks.
•
Hashes: What is a Hash? Hash Variables, Literal Representation of a Hash, Hash
Functions, Hash Slices.
•
Basic I/O.
•
Regular Expressions: Concepts About Regular Expressions, Simple Uses of Regular
Expressions, Patterns, More on the Matching Operator, Substitutions, The split and
join Functions.
•
Subroutines: System and User Functions, The local operator, Variable-length Parameter
Lists, Notes on Lexical Variables.
•
Miscellaneous Control Structures.
•
Filehandles and File Tests: What Is a Filehandle? Opening and Closing a Filehandle,
Using Pathnames and Filenames, A Slight Diversion: die, Using Filehandles, The -x
File Tests, The stat Function.
•
Formats: What Is a Format? Defining a Format, Invoking a Format.
•
Directory Access: Moving Around the Directory Tree, Globbing, Directory Handles,
Opening and Closing a Directory Handle, Reading a Directory Handle.
•
File and Directory Manipulation.
•
Process Management: Using system and exec, Using Backquotes.
•
Other Data Transformation: Finding a Substring, Extracting and Replacing a Substring.
•
Formatting Data: Sorting, Transliteration.
•
System Information: Getting User and Machine Information, Packing and Unpacking
Binary Data, Getting Network Information.
•
Database Manipulation: DBM Databases and DBM Hashes, Opening and Closing DBM
Hashes, Fixed-Length Random-Access Databases, Variable-Length (Text) Databases,
Win32 Database Interfaces.
•
CGI Programming: The CGI.pm Module, Your CGI Program in Context, Simplest CGI
Program, Passing Parameters via CGI, Perl and the Web.
•
Object oriented perl: Introduction to modules, Creating Objects.
•
Bioperl: Introduction, Installation procedures, Architecture, Uses of bioperl.
29
Paper II (Advanced)
Subject: BioInformatics
•
Sequence Analysis
o Scoring matrices: Detailed method of derivation of the PAM and BLOSUM
matrices.
o Pairwise sequence alignments: Needleman & Wuncsh, Smith & Waterman
algorithms for pairwise alignments and their implementation.
o Multiple sequence alignments (MSA):
Use of HMM-based Algorithm for MSA (e.g. SAM method).
o Taxonomy and phylogeny: Phylogenetic analysis algorithms such as Maximum
Parsimony, UPGMA, Transformed Distance, Neighbors-Relation, NeighborJoining; Probabilistic models and associated algorithms such as Probabilistic
models of evolution and Maximum likelihood algorithm, Bootstrapping method,
use of tools such as Phylip, Mega, PAUP.
o Sequence patterns and profiles: Algorithms for generation of sequence profiles:
Profile Analysis method of Gribskov, PSI-BLAST; HMMer.
o Protein and nucleic acid properties: e.g. Proteomics tools at the ExPASy server
and GCG utilities and EMBOSS.
•
Genomics and Proteomics
o Prediction of genes, promoters, splice sites, regulatory regions: basic principles,
application of methods to prokaryotic and eukaryotic genomes and interpretation
of results.
o DNA microarray, the databases and basic database tools.
o Protein arrays: basic principles.
o Basic concepts on identification of disease genes, role of bioinformatics- OMIM
database, reference genome sequence, integrated genomic maps, gene expression
profiling; identification of SNPs, SNP database (dbSNP).
o Metabolic pathways: databases such as KEGG, EMP.
o DNA microarray- SAGE database.
o Plant, animal and pathogen databases.
•
30
Comparative genomics: Basic concepts and applications, MUMmer, BLAST2, MegaBlast
algorithms, applications of Suffix tree in comparative genomics, synteny and gene order
comparisons.
•
Identification / assignment of secondary structural elements from the knowledge of 3D structure of macromolecule.
•
Structural Biology
o Prediction of protein structure
Secondary structure prediction: PHD and PSI-PRED methods.
•
Molecular modeling and simulations
o Geometry optimization algorithms: Steepest descent, conjugate gradient.
o Various Simulation Techniques: MD, Monte Carlo, docking strategies etc.
o Molecular mechanics, conformational searches.
•
Genomics and Proteomics
o Large scale genome sequencing strategies.
o Genome assembly and annotation.
o Metagenomics.
o Gene networks: basic concepts, computational model such as Lambda receptor
and lac operon.
o Functional genomics: application of sequence based and structure-based
approaches to assignment of gene functions - e.g. sequence comparison, structure
analysis (especially active sites, binding sites) and comparison, pattern
identification, etc. Use of various derived databases in function assignment, use
of SNPs for identification of genetic traits.
o DNA microarray: understanding of microarray data and correlation of gene
expression data to biological processes and computational analysis tools
(especially clustering approaches).
o Protein arrays: bioinformatics-based tools for analysis of proteomics data (Tools
available at ExPASy Proteomics server); databases (such as InterPro) and analysis
tools.
o Protein-protein interactions: databases such as DIP, PPI server and tools for
analysis of protein-protein interactions.
•
Bioinformatics Resources at the species level
o ICTV Database, AVIS, VirGen, Viral genomes at NCBI, VBRC, VBCa, PBRC and
Subviral RNA database, Species 2000, TreeBASE etc.
•
Advanced and specialized databases:
o COG, KEGG.
31
•
Computational methods for identification of polypeptides from mass spectrometry.
•
Drug design
o
Drug discovery process.
o
Role of Bioinformatics in drug design.
o
Target identification and validation, lead optimization and validation.
o
Structure-based drug design and ligand based drug design.
o
Modeling of target-small molecule interactions.
Paper III
•
32
Questions based on the syllabi of Papers I and II for the subjects of Bioinformatics & IT.

Bioinformatics color

Transcription

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