M.Sc. in BIOINFORMATICS FOR WOMEN (MAHILA MAHAVIDYALAYA)FACULTY OF SCIENCE

ORDINANCES GOVERNING M.Sc., M.Sc. (Tech.) GEOPHYSICS, AND M.C.A. DEGREE COURSE

(Effective from 2004-05)

Under the powers conferred by Section 4A of the Banaras Hindu University Act, 1915, as amended, and under the provisions of Clause 3 of Section 18 of this Act, the University hereby institutes the four semester course of the degree of Master of Science, six semester course of the degree of Master of Science (Tech.) Geophysics and Master of Computer Applications and makes the following ordinances governing admission, course of study, examinations and other matters relating to these Degrees under the Faculty of Science of the Banaras Hindu University.

1. ADMISSION OF THE M.Sc./M.Sc. (Tech.) GEOPHYSICS/M.C.A. COURSE

(a) Admission to M.Sc., M.Sc. Bioinformatics in MMV , M.Sc. (Tech.) Geophysics courses shall be made on merit in the PET.

(b) Admission to M.Sc. Biotechnology shall be made on merit through an All India Combined Entrance Examination.

(c) Admission to M.Sc. course in Molecular and Human Genetics and M.Sc. in Environmental Science shall be made on merit as per criteria laid down by the Faculty of Science.

(d) Admission to M.C.A. course shall be made on merit through an All India M.C.A. Common Entrance Test (AIMCET).

(ii) Each Postgraduate Department of the Faculty of Science shall have an Admission Committee constituted under Statute (xviii) of the Academic Council consisting of the Head of the Department and two senior members of the staff of the department in station.

(iii) Admission cannot, be claimed by any candidate as a matter of right. The admission or re-admission of a candidate shall be entirely at the discretion of the Admission Committee, which may refuse or admit any student without assigning any reason therefor.

(iv) On his/her selection for admission to the M.Sc/M.Sc. (Tech.)/M.C.A. course, the candidate shall within the time fixed by the Dean/ Principal, MMV (in case of Bioinformatics) deposit the tuition and other fees prescribed for the course. If the candidate fails to deposit the fees within the stipulated time, his/her selection shall automatically stand cancelled. Such a candidate shall not be admitted to the concerned course unless a fresh order of selection or extension of date for payment of fees is issued by the Dean / Principal, MMV (in case of Bioinformatics)/ of the Faculty concerned.

(v) There is no provision of re-admission for entry classes i.e. Ist semester of M.Sc., M.Sc. (Tech.) / MCA Courses (Except as stated in promotion rules).

(vi) Foreign Students – Admission of foreign nationals shall be governed by the rules passed by the Academic Council applicable to the Faculty of Science from time to time.

2. M.Sc./M.Sc. (Tech.) GEOPHYSICS/M.C.A. DEGREE COURSE (i) The course of study leading to Master of Science/Master of Science (Tech.) Geophysics and

Master of Computer Application degree of the University shall be conducted by the constituent Departments of the Faculty and shall be of the duration of 4 semesters for M.Sc. and 6 semesters for M.Sc. (Tech) Geophysics and M.C.A.

(ii) A student of the M.Sc./M.Sc. (Tech.) Geophysics/M.C.A. degree course shall not be permitted to seek admission concurrently to any other degree or diploma examination in the University unless otherwise provided for in the Ordinances hereinafter defined.

(iii) To qualify for the M.Sc./M.Sc. (Tech.) Geophysics/M.C.A. degree, the candidate must:

(a) satisfy the minimum requirement for entrance as prescribed hereinafter for the M.Sc./M.Sc. (Tech.) Geophysics/M.C.A.Degree Course.

(b) attend a regular course of lectures, and do to the satisfaction of the University, seminars, sessionals and practicals as may be prescribed for the M.Sc./M.Sc. (Tech.) Geophysics/M.C.A. Examinations in the relevant prospectus of studies.

(c) pass in required number of papers/courses taught during 4 or 6 semesters as the case may be for the degree. An Examination shall be held at the end of each semester in various courses/papers taught during that semester. The overall performance in sessionals, practicals and written examinations in the prescribed number of courses/papers shall determine the result of the candidate for the M.Sc./M.Sc. (Tech.) Geophysics/M.C.A. degree in accordance with the rules and regulations prescribed for the purpose.

(d) sessionals shall include work done in laboratory, field, library, house work and seminar relevant to the course, as prescribed by the various Boards of Studies.

Explanations:

An odd and an even semester shall comprise an academic year, the academic year in these ordinances shall mean the year from July to June.

(iv) (a) A student is expected to have full i.e. 100% attendance and condonation upto 30% only can be considered for the specified cogent reasons. However, student shall be deemed to have pursued a regular course of study in a subject during each year provided he/she has attended atleast 70% of the classes actually held in each subject of higher examination. A maximum of 30% condonation in attendance can be considered for the cogent grounds. The Dean of the Faculty /Principal, MMV (incase of Bioinformatics) be authorized to condone attendance upto 30% only on the following grounds:

i. Participation in N.C.C./N.S.C./N.S.O. camps duly supported by a certificate. ii. Participation in University or College/Faculty Team Games or Inter University

tournaments, duly supported by a certificate from the Secretary of the University Athletic Association Concerned;

iii. Participation in Educational Excursions conducted on working days certified by the Dean of the Faculty or the Head of the Department / Principal, MMV (for Bioinformatics). These excursions shall not include those organized for a class as a whole. No credit will be given for excursions conducted on holidays;

iv. University deputation for Youth Festival certified by The Dean of theFaculty /Principal, MMV (for Bioinformatics) and

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v. Prolonged illness duly certified by a Registered Medical Practitioner or the Superintendent, S.S. Hospital of the Banaras Hindu University.

(b) For the purpose of this Ordinance a subject shall be deemed to be one borne on the list of subjects laid down in the prospectus of the examination concerned and shall consist of a paper or a group of papers or thesis or practicals, if any.

3. ADMISSION AND ENTRANCE TEST QUALIFICATIONS

(i) The minimal eligibility condition for admission to various Master's Degree courses shall be as under+:

(a) M.Sc. in Physics, Chemistry, Zoology, Botany, Geology, Computer Science, Geography, Mathematics, Statistics, Psychology and Home Science (2 Year)

B.Sc. (Hons.)*/B.Sc.*, under 10+2+3 pattern, securing a minimum of 50% marks in the aggregate in Science subjects (considering all the three years of B.Sc. Course). The subject in which admission is sought must be a Hons. Subject at B.Sc. (Hons.) level/subject studied in all the three parts at Graduate level. However, for admission to M.Sc. in Botany/Zoology, a candidate must also have offered Chemistry as one of the subjects at the Graduate level.

(b) M.Sc. in Biochemistry (2 Year)

B.Sc. (Hons.)* in Biochemistry/B.Sc.* under 10+2+3 pattern with Biochemistry as a subject in all the three years of graduation course, securing a minimum of 50% marks in the aggregate in Science subjects (considering all the three years of B.Sc. Course),

ORB.Sc. (Hons.)* in Chemistry/Botany/Zoology/B.Sc.* under 10+2+3 pattern with Chemistry as a subject in all the three years of Graduation Course securing a minimum of 50% marks in the aggregate in Science subjects (considering all the three years of B.Sc. Course). The candidate must also have studied any two of the following subjects viz., Biochemistry, Botany, Zoology, Mathematics, Physics, Geology, Physiology, Microbiology, Biotechnology and Industrial Microbiology at least for two years at Graduate level.

(c) M.Sc. (Tech.) in Geophysics

B.Sc. (Hons.)*/B.Sc.* under 10+2+3 pattern securing a minimum of 50% marks in the aggregate in Science subjects (considering all the three years of B.Sc. Couse) with Physics, Maths and one more Science subject.

(d) M.Sc. in Biotechnology

Bachelor's degree* under 10+2+3 pattern of education in Physical, Biological, Agricultural, Veterinary and Fishery Sciences, Pharmacy, Engineering/Technology, 4-years B.S. (Physician Assistant Course); OR Medicine (M.B.B.S.) OR B.D.S. with at least 55%.

+ A candidate admitted to or having qualified for a Degree in, a General Course of study from BHU or any other University/Institution shall be entitled to appear in the Entrance Test for, and admission to, the next higher Courses/Degree in that line or to a Professional Course only. Further a candidate admitted to, or having qualified for a Degree in, any Professional Course from BHU or any other University/Institution shall be entitled to appear in the Entrance Test for, and admission to, the next higher Course/Degree only in the same professional discipline (Provided further that a candidate applying for M.Sc. in Bioinformatics course is exempted from applicability of this clause) .

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Furthermore, a candidate who is registered for/already awarded doctoral Degree from BHU or any institution in India shall not be entitled to appear in any of the Entrance Tests held for any Course in the University.

(e) M.Sc. in Molecular and Human Genetics (Special Course)

B.Sc. (Hons)*/B.Sc.* (10+2+3) OR B.Sc. (Ag) OR M.B.B.S. with a minimum 55% aggregate marks OR equivalent GPA and with a minimum 55% marks (or equivalent grade point) with not less than 55% marks at 10 & 10 + 2 levels.

(f) M.Sc. in Environmental Science (Special Course)

B.Sc. (Hons)*/B.Sc.* (10+2+3) OR M.B.B.S. OR B.E./B. Tech. with a minimum 50% marks (Equivalent GPA) with a minimum 50% aggregate at 10 & at 10+2 levels.

(g) M.Sc. in Applied Microbiology (Special Course)

B.Sc. (10+2+3) with any two of the following subjects Botany, Microbiology, Chemistry, Zoology, Industrial Microbiology, Life Science or Biotechnology or Microbiology or Industrial Microbiology or Life Sciences with a minimum 50% aggregate marks (or equivalent grade points).

(h) M.C.A.

Bachelor's degree* under 10+2+3 pattern in any discipline with a minimum of 50% marks in the aggregate with mathematics as one of the subjects at either intermediate or +2 (10+2) or equivalent examination or at Bachelor's level (as a main or subsidiary subject).

(i) M.Sc. Bioinformatics (for women)

(a) 10+2 with Science and Bachelor's degree under at least 10+2+3 pattern in Science/ Engineering/Technology/Agriculture/Medicine/Veterinary Science/Pharmaceutics with at least 50% in the aggregate.

(ii) Candidates selected for admission to the concerned course of study shall submit the following certificates:

(a) Migration certificate from the University last attended indicating that he/she has passed qualifying examination from another University.

(b) Certificate of character from the Principal of the College last attended.

(iii) If the Head of the Department concerned is satisfied that there are genuine difficulties in the production of the above certificates he/she shall at the request of the candidate give him/her time to submit the above certificate within the prescribed period. In case he/she is unable to do so, his/her admission shall be cancelled.

______________________________________________________________________________

* Or an equivalent examination recognized by the Banaras Hindu University

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4. INTER-UNIVERSITY ORDINANCES

(i) Notwithstanding anything contained in these ordinances a student, who is qualified under the foregoing ordinances for admission to University and who is a member of some other Indian University shall not be admitted to the University or any constituent faculty without the production of:

(a) leaving or transfer certificate signed by the Principal of the College last attended and certifying to the satisfactory conduct of the student mentioning the highest examination he/she has passed, and;

(b) a certified copy of all the entries against his/her name in the enrolment register of University if such a copy is obtainable.

(ii) A student of some other Indian University shall in any case be admitted only at the beginning of the particular course which he/she proposes to take in the University.

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5. SCALE OF TUITION AND OTHER FEES

(i) All regular candidates preparing for the M.Sc. in Bioinformatics course shall pay the following fees per Academic Year (Subject to change):

Item Day Scholar HostlerRoom Rent 0 160Fan Charges 0 100HDMF 0 2000Fan Caution Money 0 1000Mess Caution Money 0 800Hostel/Amnt. Fees 0 50Tuition Fees 250 250Fac/Inst Dev Fund 3250 3250Lab Fee & Dev Fund 3500 3500Acad Assessment Charges 700 700Libr Fee & Dev Fund 2500 2500Comp. & Internet Fac. 500 500Students Health Welfare 280 280Extra Curr. Activities Fund 170 170Boarders/Delegacy Un. Fee 10 10Student’s Union Fee 0 0Students Welfare Fund 1000 1000Admission 50 50Enrollment 50 50Id Card & Pass Book 26 26Alumni Actvt. Fund 50 50Training & Placement 1500 1500Libr. Caution Money 500 500Cyber Hut Membership 200 200Grand Total 14536 18646

(ii) The fees for Special Courses shall be charged as decided by the Academic Council from time to time.

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6. SYSTEM OF EXAMINATION

1. The examinations of M.Sc./M.Sc.(Tech.) Geophysics/M.C.A Course in the Faculty of Science shall be conducted in four/six semesters, ordinarily in December/May or on such dates as may be fixed by the Dean in the various courses/papers taught during that academic year.

2. The academic performance of the candidate shall be evaluated in respect of the course of study prescribed for each semester through the examinations held in that semester.

3. The Credit System

Each course shall have a specified number of credits. These credits describe the weightage of the course. The number of credits that the student has satisfactorily completed measures the performance of the student. Satisfactory progress of a student is subject to his maintaining a minimum Grade Point Average (GPA). A certain minimum number of credits as specified in the syllabus must be earned by the student to qualify for the degree.

Course Structure for the M.Sc./M.Sc. (Tech.) Geophysics/M.C.A. Degree

There shall be three /two (for Bioinformatics) categories of course:

(a) Core Courses(b) Major Electives (Specialization)(c) Minor Electives(not applicable for Bioinformatics)

The minimum credit requirement for the two year M.Sc. Degree in the Faculty of Science be 90 credits and for a 3-year degree 135 credits. A student would be permitted to register for a minimum of 20 credits and a maximum of 28 credits/semester. There shall be three types of courses with distribution of credits as given below:

Two Year DegreeSuggested Credits *

(i) Core Courses 54(ii) Major Elective (Specialization) 27(iii) Minor Electives (from other Departments within the 09

Faculty or within the same Department)* see course contents for credit distribution in Bioinformatics Three Year Degree

Suggested Credits(i) Core Courses 81(ii) Major Elective (Specialization) 40(iii) Minor Electives (from other Departments within the 14

Faculty or within the same Department)

The option of the major and minor electives shall be exercised by the student at the beginning of the semester. Dissertation may partly or wholly replace the major electives.

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Evaluation of Credits:

Credits of a course shall be evaluated in the following manner:

(a) For all theory (lecture) courses one credit per hour per lecture per week per semester will generally be adopted with the restriction of a maximum of 3 credits per course or more subject to the approval of Board of Studies.

(b) Each laboratory hour for semester will be assigned half credit. Courses with odd number of lab hours are acceptable, e.g. courses having 1 hour contact per week per semester or 3 hours contact per alternate week per semester will be rationalized to have integer number of contact hours per week so that fraction smaller than 0.5 are not involved in credit assignment of lab courses.

.Calculation of Semester Grade Point Average (SGPA) and Cumulative Grade Point Average (CGPA)

n Ci.Pi

i = 1SGPA = ---------------------

n Ci

i = 1Where,

Ci = Number of credits assigned for the ith course of a semester for which SGPA is to be calculated.

Pi = Grade point earned in ith coursei = 1, …….n, represent the number of courses in which a student

is registered in the concerned semester

m Cj..Pjj = 1

CGPA = ---------------------n Ci.

j = 1Where,

Cj = Number of credits assigned for jth course, up to the semester for which CGPA is to be calculated.

Pj = Grade point earned in jth course.

j = 1, ……..m; represent the number of courses in which a student was registered, up to the semester for which CGPA is to be calculated.

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Grading System: The grading system, as detailed hereunder will be applicable.

% of marks Letter Grade Grade Points Greater than or equal to 90 (> 90) S 10Greater than or equal to 80 & less than 90 (> 80 <90) A 9Greater than or equal to 70 & less than 80 (> 70 <80) B 8Greater than or equal to 60 & less than 70 (> 60 <70) C 7Greater than or equal to 50 & less than 60 (> 50 <60) D 6Greater than or equal to 40 & less than 50 (> 40 <50) E 5Passed with Grace P 4Below 40 F 0Non-appearance in examinations (Incomplete) I -Incomplete Project/Dissertation/Training X -Non-completion of Course Z -

Explanation:

'F' Grade

The "F" grade denotes poor performance, i.e. failing a course. A student has to appear at supplementary examination/subsequent examination, if provided under the Ordinance in all courses in which he/she obtains "F" grades, until a passing grade is obtained.

'X' Grade

An "X" grade is awarded to a student if he does not complete Project/Dissertation or Training. This will be converted to a regular grade on the completion of the Project/Dissertation/ Training work and its evaluation. Notwithstanding anything stated above, in case a candidate gets "X" grade in a project he/she will have to complete the project within the next semester.

Grace Rules:

The Tabulators shall award grace marks as per the following guidelines:

(1) A student who fails in not more than 3 theory papers by total marks of not more than ½ the number of total theory papers of the semester (any fraction is rounded off to the next higher number), shall be awarded grade "P" (in place of grade "F") of Grade Point 4.

(2) Grace mark will not be awarded for making up shortfall in minimum SGPA/CGPA or improving the Grade.

Examination System

For evaluation, the overall structure of the distribution of marks shall be such that 30% marks are allotted to various assessments during the semester, while 70% marks shall be allotted for the end semester examinations.

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The assessments could comprise (a) class tests for theory papers and (b) seminar/Sessionalfor practicals. Some subjects such as Geology may need to allot a specific number of credits to Filed Work.

(i) The distribution of sessional marks out of 30 will be as under

(a) Class assignment & Regularity … 10(b) Sessional Tests / Presentation … 20

(ii) At the discretion of concerned HOD, a student who could not appear in the internal test(s) already conducted on account of some cogent reasons, such as late admission, illness etc., may be allowed to appear in one internal assignment/test.

(iii) All HOD's shall ensure that all internal assessment marks of sessional are sent to Controller of Examinations, prior to commencement of End Semester Exam.

There will not be any sessional marks for courses, which involve Seminar/Field Work/ Project work.

Class Tests

The class tests shall be conducted by each teacher conducting the course and the marks shall be displayed on the Notice Board.

Supplementary Examination

Supplementary examinations shall be held usually two weeks before the succeeding odd semester.

7. PROMOTION RULES AND SUPPLEMENTARY EXAMINATIONM.Sc. 2-YEAR (FOUR SEMESTER) COURSES

(A) FIRST Semester COURSE & EXAMINATION

The candidates who have taken admission in M.Sc. First Semester in a session can be put in the following two categories on the basis of their attendance in the Semester.

(I) (1) Those who have put in the required minimum percentage of attendance for appearing in First Semester Examination and filled up examination form in time for appearing at the First Semester Examination;

(2) Those who did not put in the required minimum percentage of attendance for appearing at the First Semester Examination or did not fill up examination for in time for appearing at the First Semester Examination.

Candidates under Category (1) are eligible for appearing at the examination of First Semester while candidates under Category (2) are not allowed to appear at the Examination of the Semester. However such candidates are allowed to reappear at the Entrance Test (PET) of subsequent year(s) for seeking admission afresh. This implies that no re-admission is permissible to those who do not put in the required percentage of attendance for taking the examination.

(II) After appearing at the Examination of First Semester the candidates can be put in the following Categories in the context of declaration of the results of First Semester Examination.

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i) Passed i.e. who have passed in all courses of the Examination of the Semester

ii) Promoted i.e. who have not passed in all the courses of the Examination of the Semester

iii) Minimum Passing Grade – Grade 'E' for each course.

iv) Promotion to SECOND Semester

All students who have put in the minimum required percentage of attendance in I Semester and filled up the examination form in time will be promoted to II Semester.

(B) SECOND Semester COURSE & EXAMINATION

As in the First Semester Course, in all Semesters, all the candidates who have put in the minimum percentage of attendance for appearing at the Examination and filled in the form in time for appearing at the Semester Examination will be allowed to appear at the respective Examinations. However students who have not put in the minimum percentage of attendance in any Semester will be allowed to take re-admission in that Semester (except in I Semester where re-admission is not permitted).

(C) DECLARATION OF RESULTS after II Semester (based on results of I & II Semester Examinations)

After declaration of results of First and Second Semesters a candidate can be put in the following two categories:

(1) Passed: A candidate who has passed in all courses of Examinations of I and II Semester.(2) Failed: A candidate who has failed or failed to appear at any of the examinations of

First and Second Semester taken together.(D) PROMOTION TO THIRD SEMESTER

(i) A candidate who comes under the category “Passed” is eligible to be promoted to Third semester Class, if otherwise eligible.

(ii) “Failed” candidates will not be promoted to III Semester unless they pass the failed courses in the supplementary examination, which will usually be held two weeks before the succeeding odd semester. The students failing at any of the courses even after supplementary examination will be allowed to repeat the semester(s) by taking Re-admission in the subsequent academic session to the appropriate semester(s) in which he/she has failed.

(E) PROMOTION TO FOURTH SEMESTERAll students who have put in minimum percentage of attendance in III Semester and filled in the examination form in time will be promoted to IV Semester.

(F) DECLARATION OF RESULTS AFTER IV SEMESTER (based on results of I, II, III & IV Semester Examinations)

After declaration of results of Third and Fourth Semesters a candidate can be put in the following two categories:

(I) Passed: A candidate who has passed in all courses of Examination of I, II, III & IV Semesters.

(II) Failed: All the students who have not PASSED will be categorized as “FAILED”.Such failed students may clear their failed courses in subsequent examinations as ex-students. There will be a provision of Supplementary Examination for Third and Fourth Semesters after declaration of result of Fourth Semester. Students failing in courses of Third and Fourth Semesters may appear in this Supplementary Examination or subsequent main examinations.

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(G) DECLARATION OF DIVISION

(a) A candidate who has passed in all the courses of I, II, III and IV Semesters taken together will be declared as "Passed". Such passed candidates may be awarded with the Division according to the following criterion:

(i) First Division … CGPA 6.5 and above (ii) Second Division … CGPA 4.5 and above but below 6.5

(H) Further Clarifications

(i) A student has to clear the whole course in NOT MORE THAN THREE YEARS from the latest admission in First Semester of the Course. Even after that if a student fails, he/she has to leave the course.

(ii) A student who is promoted to a higher class or re-admitted due to shortage of attendance shall be required to study the same syllabus as being taught in that year. But if there is any common paper which has been already studied by him/her in I, II, III or IV Semester, he/she may be taught some other paper not studied by him (preferably a paper which is in the new syllabus) with the permission of the Dean.

M.Sc. (TECH.) GEOPHYSICS/MCA 3-YEAR (SIX SEMESTER) COURSES

(I) The promotion rules from First to Second Semester, Second to Third Semester and Third to Fourth Semester will be the same as in the case of Two Year (Four Semester) Course of M.Sc. However promotion from IV to V Semester will be decided on the basis of following rule:

(i) DECLARATION OF RESULTS AFTER IV SEMESTER (based on results of I, II, III and IV Semester Examination).

After declaration of results of Third and Fourth Semesters a candidate can be put in the following two categories:

(a) Passed : A candidate who has passed in all Courses of III & IV Semesters. (b) Failed: A candidate who has failed or failed to appear at any of the courses of III or IV

Semesters.

Candidates will not be promoted to V semester unless they pass the failed courses in the supplementary examination, which will usually be held two weeks before the succeeding odd semester. The student failing at any of the courses even after supplementary examination will be allowed to repeat the semester(s) by taking Re-admission in the subsequent academic session to the appropriate semester(s) in which he/she has failed.

(ii) PROMOTION TO FIFTH SEMESTER

(a) A candidate who comes under the category "Passed" is eligible to be Promoted to Fifth Semester Class, if otherwise eligible.

(iii) PROMOTION TO SIXTH SEMESTER

All students who have put minimum percentage of attendance in V Semester and filled in the examination from in time will be promoted to VI Semester.

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(iv) DECLARATION OF RESULTS after VI Semester (based on results of I, II, III, IV, V & VI Semesters Examinations)

After declaration of results of Fifth and Sixth Semesters a candidate can be put in the following two categories:

(i) Passed: A candidate who has passed in all courses of Examinations of I, II, III, IV, V & VI Semesters..

(ii) Failed: All the students who have not PASSED will be categorized as "FAILED"

Such failed students may clear their failed courses in subsequent examinations as ex-students. There will be a provision of Supplementary Examinations for Fifth and Sixth Semesters after declaration of result of Sixth Semester. Students failing in courses of Fifth and Sixth Semesters may appear in this Supplementary Examination or subsequent main examination(s).

(v) DECLARATION OF DIVISION

(a) A candidate who has passed in all the courses of I, II, III, IV, V and VI Semesters taken together will be declared as "Passed". Such passed candidates may be awarded with the Division according to the following criterion:

(i) First Division … CGPA 6.5 and above(ii) Second Division … CGPA 4.5 and above but below 6.5

(vi) Further Clarification

(a) A student has to clear the whole course in NOT MORE THAN FOUR YEARS from the latest admission to the First Semester of the Course. Even after that if a student fails, he/she has to leave the course.

(b) A student who is promoted to a higher class or re-admitted due to shortage of attendance shall be required to study the same syllabus as being taught in that year. But if there is any common paper which has been already studied by him/her in I, II, III, IV, V or VI Semester, he/she may be taught some other paper not studied by him (preferably a paper which is in the new syllabus) with the permission of the Dean.

A candidate shall be admitted to the III Semester only when he or she clears both the I and II Semesters. The time limit for clearing the I and II semester for all the courses shall be two years.

Syllabus

The syllabi for the core and major and minor electives shall be framed by each Department. Each Department shall suggest topics for Minor Electives that can be offered by the students of other Departments.

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8. DECLARATION OF RESULTS

Ranking shall be given to those candidates only who pass the main examination in one attempt. Notwithstanding any provisions in the Ordinances to the contrary, in the case of an examinee:

(a) Who having been duly admitted to a regular examination of the University is/was unable to take that examination in full or in some paper(s) due to some disruption of examination, and

(b) Who took the next following examination of that course in the papers missed by him/her in the regular examination.

The marks obtained by him/her at the Examination will be considered as the basis for the University ranking, scholarship and other distinctions.

In order to get the benefit of this provision, the student should claim that he/she is eligible for this benefit and get a decision in writing after proving his/her eligibility therefore.

DEFINITIONS

1) A "Regular Student" is one who has pursued a regular course of Study and obtained prescribed attendance mentioned hereafter and is eligible to appear in the examination for the aforesaid course.

2) "Ex-student" means one who has studied in the Faculty for at least one semester preceding the date of the examination and has filled up the examination form, but has failed or failed to appear in the examination, though otherwise eligible.

Academic calendar for the odd and even semesters shall be announced at the beginning of every academic year.

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M.Sc. IN BIOINFORMATICSSYLLABUS BASED ON THE SEMESTER SYSTEM

Women candidates who have passed (a) 10+2 with Science (b) Bachelor's degree under 10+2+3 pattern in Science / Engineering/Technology/ Agriculture/ Medicine/ Veterinary Science/ Pharmaceutics with atleast 50% marks in the aggregate from recognized university will be eligible for admission to M.Sc. course in Bioinformatics. The selection will be through all India entrance examination. The course will be of two years duration and shall be completed in FOUR semesters. 90 credits will qualify a student for the M.Sc. Bioinformatics degree.

Outline of courses in different semesters

Semester 1Theory CreditsMBIF 101: Introduction to Programming Languages and Programming Through C 4 MBIF 102: Cell Biology and Genetics 4 MBIF 103: Essential Mathematics and Statistics I 4 MBIF 104: Introduction to Bioinformatics 4Practical1. Based on MBIF 101 & 103 32. Based on MBIF 102 & 104 3

Semester 2TheoryMBIF 201: Data Structures and Algorithms 4MBIF 202 Microbiology and Biotechnology 4MBIF 203: Essential Mathematics and Statistics II 4MBIF 204: Basic Biochemistry and Immunology 4MBIF 205: Comprehensive Viva based on MBIF 101 to 204 1Practical1. Based on MBIF 201 & 203 32. Based on MBIF 202 & 204 3

Semester 3TheoryMBIF 301: DBMS with reference to Biological Data 4MBIF 302: Biodiversity and Ecological Informatics 4MBIF 303: Genoinformatics 4 MBIF 304: Prediction of Protein Structure and Modeling 4Practical1. Based on MBIF 301& 302 32. Based on MBIF 303 & 304 3

Semester 4TheoryMBIF 401: Tools and Techniques (One of the electives given below*) 4 MBIF 402: Applications of Bioinformatics 3MBIF 403: Molecular Biology Techniques 4MBIF 404: Seminar 1 MBIF 405: Comprehensive Viva based on MBIF 301 to 403 1MBIF 406: Project Work 6PracticalBased on MBIF 401 to 403 4* Electives MBIF 401 A Simulation and Modeling for Biologists MBIF 401 B Soft Computing TechniquesMBIF 401 C Biophysics: Experimental Techniques

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SEMESTER- 1Credits: 4

MBIF 101: INTRODUCTION TO PROGRAMMING LANGUAGES AND PROGRAMMING THROUGH C

Introduction to programming Languages and Paradigms, Syntactic Structure, Semantics, Data Representation, Data Abstraction, Procedure activation, Structured Programming, Block Structuring

Procedural Languages, Object-oriented Programming, Functional Programming, Logic Programming

Introduction to Programming Language C, Data Type, Operators and Expressions in C, Control and Repetitive Statements: IF-THEN-ELSE, SWITCH, WHILE, FOR, DO; Break and Continue Statements, Input and Output functions, Function and Program Structure in C, Parameter passing, Pointers, Arrays, Structures, C-Library

Perl

Suggested Readings

1. Sethi, R.,1996, Programming Languages, Addison-Wesley. 2. Appleby, D. and Vandkopple, J.J., 1991, Programming Languages, Tata McGraw-Hill. 3. Kernighan, B.W. and Ritchie, D.M., The C Programming Language, PHI. 4. Hutchinson, R.C. and Just, R.B., Programming using the C Language, McGraw-Hill. 5. Gottfried, B.S., Schaum’s Outline of Theory and Problems of Programming with C, McGraw-Hill. 6. Schildt, H., C Made Easy, Osborne McGraw-Hill.7. Tisdall, J.D. 2001 Beginning Perl for Bioinformatics. O’Reilly & Associates.

16

Credits: 4

MBIF 102: CELL BIOLOGY AND GENETICS

Cell Biology

Cell concept, structural organization of plant and animal cells, cell membrane and cell wall Cell cycle: Cell division and regulation, Apoptosis Genetic code: A brief account Nucleic acids: Structure and properties of different forms of DNA and RNA; DNA replication Basic concepts of signal transduction Gene expression and regulation in procaryotes (lac operon)

Genetics

Mendel’s laws of inheritance and their chromosomal basis, extrachromosomal inheritenc Organization and packaging of genetic material of prokaryotes and eukaryotes, C-Value paradox, repetitive DNA, structure of chromatin - euchromatin and heterochromatin, chromosome organization and banding patterns, structure of gene - intron, exon and their relationships, overlapping gene . Molecular mechanism of general recombination, homologous and site-specific recombination, gene conversion Types of mutation, mutagens, molecular mechanisms of mutation, site-directed mutagenesis, detection and isolation of mutants, transposons in mutation, repair mechanisms

Suggested Readings

1. Alberts et. al. 2002, Molecular Biology of the Cell. Garland. 2. Lewin 2004, Genes VIII. Pearson. 3. Lodish et. al. 2004, Molecular Cell Biology. Freeman. 4. Karp 2002, Cell and Molecular Biology. John Wiley. 5. Pollard & Earnshaw 2002, Cell Biology. Saunders.6. Tobin & Morcel 1997, Asking about Cells. Saunders. 7. Watson et. al. 2004, Molecular Biology of the Gene. Pearson. 8. Atherly et. al. 1999, The Science of Genetics. Saunders. 9. Griffiths et. al. 2004, An Introduction to Genetic Analysis. 10. Hartl & Jones 1998, Genetics - Principles & Analysis. Jones & Bartlett. 11. Snustad et. al. 1998, Principles of Genetics. Wiley & Sons. 12. Strickberger 1985, Genetics. Macmillan. 13. Russell 2002, Genetics. Benjamin.

17

Credits: 4

MBIF 103: ESSENTIAL MATHEMATICS & STATISTICS I

Mathematics

Vectors and Matrices Basic Calculus: Differentiation and Integration

Statistics

Numerical Description of Data: Mean, Median, Mode, Quantiles, Standard Deviation, Variance, Coefficient of Variation

Simple Linear Regression and Correlation: Linear Regression Model, Least Squares Method Estimating Model Parameters, Residual Sum of Squares Probability Theory: Sample Space and Events, Axioms of Probability, Conditional Probability,

Independent Events, Bayes’ Formula Random Variables: Discrete and Continuous, Expected Value, Variance Discrete and Continuous Distributions, Chi-Square, Student’s t, Snedecor’s F and Z

Distributions Estimation Theory: Unbiased Estimator; Confidence Interval: Population Mean, Population

Variance Limit Theorems: Central Limit Theorem, Strong Law of Large Number, Weak Law of Large

Number

Suggested Readings

1. Ewens, W.J. and Grant, 2001 Statistical Methods in Bioinformatics: An Introduction. Springer-Verlag.

2. Devore, J.L., 2002 Probability and Statistics, 5th edition, Thomson Asia. 3. Hoel, Port and Stone, Introduction to Statistics. 4. Miller & Freund: Probability and Statistics for Engineers, 7th Edition. 5. Chung, Kai Lai, Elementry Probability Theory with Statistical Processes (Student Edition) Springer

International6. Feller, W., An Introduction to Probability :Theory and its Applications, Wiley Eastern Limited. 7. Larson, H.J., Introduction to Probability Theory and Statistical Inference, John Wiley & Sons. 8. Warren J.J., Ewens Warren, Ewens Gregory Grant, Statistical Methods in Bioinformatics: An

Introduction, Springer-Verlag. 9. Gupta, S.C. and Kapoor, V.K.: Fundamentals of Mathematical Statistics, Sultan Chand & Sons. 10. Goon, A.M., Gupta, M.K. and Dasgupta B.: Fundamental of Statistics - Vol. 1, The World Press

Pvt. Ltd. 11. Ayers, F. , Matrices and Vectors, Schaum 12. Prasad, G.: Differential Calculus, 2003 Poothisala Publication .13. Prasad, G.: Integral Calculus, 2003 Poothisala Publication.14. Boas, Mathematical methods in the Physical Sciences, Wiley Publication.

Credits: 4

18

MBIF 104: INTRODUCTION TO BIOINFORMATICS

Introduction to Bioinformatics: Definition and History of Bioinformatics, Internet and Bioinformatics, Introduction to Data Mining, Applications of Data Mining to Bioinformatics Problems and Applications of Bioinformatics

Bioinformatics Softwares: Clustal V, Clustal W 1.7, RasMol, Oligo, Molscript, Treeview, Alscript, Genetic Analysis Software, Phylip

Biocomputing: Introduction to String Matching Algorithms, Database Search Techniques, Sequence Comparison and Alignment Techniques, Use of Biochemical Scoring Matrices, Introduction to Graph Matching Algorithms, Automated Genome Comparison and its Implication, Automated Gene Prediction, Automated Identification of Bacterial Operons and Pathways; Introduction to Signaling Pathways and Pathway Regulation. Gene Arrays, Analysis of Gene Arrays

Systems Biology-an introduction Markov chains and applications: Machine Learning Methods,Hidden Markov

models,Applications of HMM in gene identification and Profiles HMMs, Neural Networks and Support Vector machines

Suggested Readings

1. Claverie, J.M. and Notredame C. 2003 Bioinformatics for Dummies. Wiley Editor. 2. Letovsky, S.I. 1999 Bioinformatics. Kluwer Academic Publishers. 3. Baldi, P. and Brunak, S. 1998 Bioinformatics. The MIT Press. 4. Setubal, J. and Meidanis, J. 1996 Introduction to Computational Molecular Biology. PWS

Publishing Co., Boston. 5. Lesk, A.M. 2002 Introduction to Bioinformatics. Oxford University Press. 6. Rastogi, S.C., Mendiratta, N. and Rastogi, P. 2004 Bioinformatics: Concepts, Skills &

Applications. CBS Publishers & Distributors, New Delhi. 7. Vyas, S.P. and Kohli, D.V., Methods in Biotechnology and Bioengineering. 8. Singer, M. and Barg, P. Exploring Genetic Mechanism. 9. Fogel, G.B. and Corne, D.W., Evolutionary Computation in Bioinformatics.10. Genetic Library Construction and Screening: Advanced Techniques and Applications:

Lab Manual 11. Patterson, B.K., Techniques in Quantification and Localization of Gene Expression.12. Mont, D.W., Bioinformatics: Sequence and Genome Analysis.13. Evens, W.J. and Grant, G.R., Statistical Methods in Bioinformatics: An Introduction.14. Liu, B.H., Statistical Genomics: Linkage Mapping and QTL Analysis15. Bowtell, D. and Sambrook, J. DNA Microarrays. 16. Pierre Baldi and Soren Brunak, Bioinformatics: The Machine Learning Approach. 17. Jae K. Lee, Statistical Bioinformatics, John Wiley & Sons Inc.

19

SEMESTER- 2Credits: 4

MBIF 201: DATA STRUCTURES AND ALGORITHMS

Data Structures

Basic Data Structures: Arrays, Linked Lists, Stack, Queue, Dequeue, Tree, Heap, Hash Table and Collision resolution. Basic algorithms for Creation, Manipulation of Data Structures

Internal Sorting Algorithms: Bubble, Heap, Quick Sort. Tape sorting and Merging

Algorithms

Simple Algorithms, Analyzing Algorithms, Asymptotic Notation Design Methods: General Consideration, Algorithm Design Paradigms and Representative

Problems: Divide and Conquer (Binary search, Merge Sort), Greedy Method (Minimal Spanning Tree), Dynamic Programming (Chained Matrix Multiplication), Longest common subsequence, Backtracking (8-queens problem), Branch and Bound (0/1 Knapsack Problem)

String Matching Problem, Brute Force Method, KMP Algorithm, Boyer-Moore Algorithm, Approximate String matching

Intractable Problems: Basic Concepts, Nondeterministic Algorithms, NP Completeness (Brief introduction only- no proof)

Suggested Readings

1. Lipshutz, Data Structure, McGrawa Hill. 2. Standish, Data Structure, Addison-Wesley.3. Salzberg, B., 1988, File Structures, Prentice-Hall. 4. Tharp, A.L., 1988, File Organization and Processing, John Wiley and Sons. 5 Aho, A., Hopcroft, J. and Ullman, J., The Design and Analysis of Computer Algorithms, Addison

Wesley. 6. Horowitz, E. and Sahani, S., Fundamentals of Computer Algorithms. Galgotia, New Delhi. 7. Goodman S.E. and Hedetniemi, S.T., Introduction to the Design and Analysis of Algorithms.

McGraw Hill. 8. Brassard, G. and Bratley, P., Algorithmics, PHI. 9. Basu, S.K., 2005 Design Methods and Analysis of Algorithms, Prentice Hall of India (Pvt) Ltd,

New Delhi.

20

Credits: 4

MBIF 202: MICROBIOLOGY AND BIOTECHNOLOGY

Microbiology

Major groups of micro-organisms: General characteristics of Archaea, Eubacteria, Mycoplasma, Rickettsiae and Chlamydias Bacterial classification ; construction of phylogenetic tree General structure of prokaryotic cell Growth kinetics in batch cultures General characteristics and classification of plant and animal viruses; Structure and replication of Bacteriophage (T2, and ), Viroids & Prions Organization of viral and bacterial genomes; Plasmids Genetic recombination in bacteria: Conjugation, Transformation and Transduction; Construction of genetic maps in bacteria

Biotechnology

Plant and animal cell and tissue culture: General introduction, concept of cellular differentiation and totipotency Cloning vectors Enzymes used in DNA technology Gene transfer in plant and animal systems Application of PCR in cloning, Role of molecular markers and nucleic acid probes in gene analysis, selection and expression Techniques of DNA sequencing, chemical synthesis of oligonucleotides Applications of recombinant DNA Technology: Crop and live-stock improvement; Molecular

genetic analysis of human diseases; Gene therapy- somatic and germline gene therapy; DNA drugs and vaccines

Suggested Readings

1. Prescott, L.M., Harley, J.P. and Klein, D.A. Microbiology. 5th Ed. 2002 WmC Brown Publishers, McGraw.

2. Madigan, M.T., Martinko, J.M. and Parker, J. Brocks. Biology of Micro-organism. 10th Ed. 2003, Prentice Hall.

3. Snyder, L and Champress, W.. Molecular Genetics of Bacteria .2nd Ed. 2003. ASM, Washington. 4. J.G. Black. Microbiology Principles and Explorations. 5th Ed. 2002. John Wiley and Sons. 5. Stanier, R.Y., Ingrahm, J.L. Wheelis, M.L. and Painter, P.R. General Microbiology 5th Ed. 1987,

Macmillan. 6. Tortora, C.J., Funke, B.A. and Case, C.L. Mircrobiology An Introduction. 8th Ed. 2004. Pearson

Education. 7. Streips & Yasbin 2002 Modern Microbial Genetics. Wiley. 8. Turn & Trumpy 2004 Fundamental of Bacterial Genetics. Blackwell. 9. Vold et. al. 1991 Essentials of Medical Microbiology. Lippincott & Co. 10. Jackson, J.F. and Linskens 2003 Genetic Transformation of Plants. Springer. 11. Butler 2004 Animal Cell Culture and Technology. 12. Bhojwani, S.S. and Rajdan, M.K. 2004 Plant Tissue Culture. Elswea

21

Credits: 4

MBIF 203: ESSENTIAL MATHEMATICS AND STATISTICS II

Mathematics

Numerical Computation: Errors in Computer Arithmetic, Normalization Polynomial Interpolation, Solution of Non-linear Equations, Errors, Convergence of Solutions, Iterative Methods for System of Linear Equations, Matrix Inversion, Numerical Differentiation and Integration

Discrete Structures: Formal grammars, Chomsky Hierarchy, Permutation, Combination, Recurrence Relations, Principle of Inclusion and Exclusion; Basic Concepts of Graphs and Trees, Adjacency and Incidence Matrices, Spanning Tree, Transitive Closure, Shortest Path, Plannar Graphs, Graph Colouring, Applications of Graph, Theoretic concepts to Biology

Statistics

Maximum Likelihood Estimation: Discrete and Continuous Distributions, Likelihood Function; Log-Likelihood Functions (Use of Package Recommended)

Tests of Hypothesis: Formulation of Hypothesis - Simple and Composite, Type I and Type II Errors, Power of a Test, Significance of Test, p-value; Applications of t, 2, F and Z Distributions; Non-parametric tests

Multivariate Analysis: Principle Component Analysis, Cluster Analysis, Analysis of Variance

Suggested Readings

1. K. Rosen, 2001 Application of Discrete Mathematics, 5th Edition, New York, McGraw Hill.2. S. Wiitala, 1987 Discrete Mathematics, A Unified Approach, McGraw Hill. 3. C.L. Liu, 2000 Elements of Discrete Mathematics, McGraw Hill Book Co. 4. Jain, Iyenger & Jain, 2003 Numerical Methods for Scientific & Engineering Computation 4th

Edition. Wiley Eastern Limited. 5. S.S. Sastry, 2003 Introductory Methods of Numerical Analysis 3rd Edition. Prentice Hall. 6. Pierre Baldi and Soren Brunak, Bioinformatics: The Machine Learning Approach. 7. Jae K. Lee, Statistical Bioinformatics, John Wiley & Sons Inc. 8. Goon, A.M., Gupta, M.K. and Dasgupta, B., Fundamental of Statistics – Vol. I & II, The World

Press Pvt. Ltd. 9. Medhi, J., Stochastic Process, Wiley Eastern Ltd. 10. Gupta, S.C. & Kapoor V.K., Fundamentals of Mathematical Statistics, Sultan Chand & Sons. 11. Anderson, T.W., An Introduction to Multivariate Statistical Analysis, John Wiley & Sons.

Credits: 4

22

MBIF 204: BASIC BIOCHEMISTRY AND IMMUNOLOGY

Biochemistry

Bioenergetics: Laws of Thermodynamics and its Applications; Concept of free energy; High energy compounds; ATP as the main source of free energy in biological systems Amino Acids, Peptides and Proteins: Structure of Proteins: Primary, Secondary, Tertiary and

Quaternary; Protein Folding; Structure-Conformation Function relationship Enzymes: Classification, nomenclature, mechanism of action, binding of substrate, lowering of

activation energy, factors controlling enzyme activity, allosteric enzymes, isoenzymes Carbohydrates and Lipids: Basic Structure and functions

Immunology

General properties of immune responses: Innate and adaptive immunity; Cells and tissues of immune system - macrophages, B and T lymphocytes, dendritic cells, eosinophils, basophils, mast cells, haematopoiesis; Humoral and cell-mediated immunity; Clonal selection and expansion; Cytokines and their function

Antibodies and Antigen: Molecular structure of antibodies and their interaction with antigens; Complement system and its activation; Hybridoma technology

Disorders of Human Immune System: Self tolerance and autoimmunity; Acquired immunodeficiencies; Hypersensitivity

Suggested Readings1. Murray et. al., 2003 Harpers Illustrated Biochemistry. Prentice Hall Int. 2. Nelson, D.L. & Cox, M.M., 2004 Lehninger’s Principles of Biochemistry 4th Edition. Macmillan

UK, Worth Publishers, USA. 3. Berg, J.M., Tymoczko, J.L., Stryer, L., 2002 Biochemistry 5th Edition. W.H. Freeman & Co. New

York. 4. Zubay, Geoffrey L., 1998 Biochemistry 4th Edition. Wm C. Brown Publishers, USA. 5. Lodish, H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.P., Zipurskey, S.L.,

Darnell, J., 2004 Molecular Cell Biology 5th Edition, Freeman. 6. Voet, Donald & Voet, J.G.., 2004 Biochemistry 3rd Edition. John Wiley & Sons Inc., USA. 7. Roitt et. al., 2000 Immunology. Mosloy. 8. Roitt et. al., 2003 Essential Immunology. Blackwell. 9. Kuby, 2003 Immunology. Freeman. 10. Benjamin et. al., 2000 Immunology – A Short Course. Wiley-Liss. 11. Barrett, 1988 Text Book of Immunology. Mosloy. 12. Abbas et. al., 2001 Cellular and Molecular Immunology. Saunders. 13. Rodney M.J. Cotterill, Biophysics an Introduction 1st Edition. John Wiley & Sons. 14. Fung, Y.C., Biomechanics: Mechanical Properties of Living Tissues 2nd Edition. Springer.15. Becker Robert & Selden Gary, The Body Electric: Electromagnetism and the Foundation of Life

1st Quill Edition. Perennial Currents. 16. Daune Michel, Molecular Biophysics: Structures in Motion. Oxford University Press. 17. Roy, R.N., A Text Book of Biophysics. 1st Edition. New Central Book Agency. 18. Brijlal and Subramaniam, Heat and Thermodynamics.19. Halliday, Resnick and Walker. Fundamental of Physics 6th Edition. John Wiley & Sons.

23

MBIF 205: COMPREHENSIVE VIVA BASED ON MBIF 101 TO 204 (Credit 1)

PRACTICALS

1. Based on MBIF 101 & 103 (Credits 3)2. Based on MBIF 102 & 104 (Credits 3)3. Based on MBIF 201 & 203 (Credits 3)4. Based on MBIF 202 & 204 (Credits 3)

24

SEMESTER- 3Credits: 4

MBIF 301: DATA BASE MANAGEMENT SYSTEMS WITH REFERENCE TO BIOLOGICAL DATA

DBMS Concepts: Data Abstraction, Database System Architecture, Schemas and Subschemas, Data Independence, Physical Data Organization - Hashed, Index File, B-tree

Data Models: Data Modeling using entity relationship, Hierarchical and Network Model, DBTG Proposals, Data Manipulation Languages

Relational Model: Relational Algebra and Calculus, Storage Organization for Relations, Functional, Multivalued and Project-Join Dependencies, Decomposition. Normal Forms- First, Second, Third, BCNF, Fourth and PJ normal forms

Relational Query Language, Query Processing, Query Optimization- General Strategies of Optimization

Security in DBMS to gain integrity mechanism of roll-back and recovery, validation and data translation of database operation and management

Introduction to Data mining: Classification, Clustering, Data Warehousing, Applications of Data Mining

Data Bases: Nucleic Acid Sequences, Genomes, Protein Sequence and Structures, Bibliographic

Access to Molecular Biology Data Bases: Entrez, Sequence Retrieval System (SRS), Protein Identification Resource (PIR)

Suggested Readings

1. Date, C.J. An Introduction to Database Systems, Vol I & II. Addison Wesley. 2. Ullman, J.D. Principles of Database Systems. Galgotia, New Delhi. 3. Wiederhold, Database Design. McGraw Hill. 4. Miers, Relation Database. Computer Science Press.

25

Credits: 4

MBIF 302: BIODIVERSITY AND ECOLOGICAL INFORMATICS

Biodiversity

Basic Principles of Taxonomy & Phylogeny Modern Taxonomical Methods Molecular Systematics: Molecular data types, generation and analysis An Overview of Green Plant Phylogeny Botanical Library and Systematic Databases Diversity of Life: Genetic, Species, Community and Landscape Diversity Species Diversity: Measurement methodologies, Indices Trends of Species Diversity: Gradients, Biodiversity Hot Spots Biodiversity Informatics: Databases, National, Regional and Global Diversity Information

Systems and Networks Online Biodiversity and Ecosystem based Databases

Ecological Informatics

The ecosystem concept Ecosystem Function: Energy flow- Food chains, Food webs, Energy pyramids, Productivity

and Nutrient cycling Ecosystem Succession: Primary, Secondary, Models of Ecosystem Succession Electronic Catalogues: Environmental Data and Information Management, Digitization of

Biological Collection, Metadata Environmental and Ecological Modeling and Assessment Environmental Geomatics - GIS, RS and other Spatial Information Technologies Monitoring and Analytical Techniques of Environmental Quality

Suggested Readings

1. Recknagel, F. 2002 Ecological Informatics: Understanding Ecology by Biologically- Inspired Computation. Springer, New York.

2. Phillipson, J. 1972 Ecological Energetics, Edward Arnold. 3. Odum, E.P. 1983 Basic Ecology. Saunders International Edition, Japan.4. Atkinson, P.M. and Tate, N.J.(Eds.) 1999 Advances in remote sensing and GIS analysis., Wiley,

New York.5. Gunther,O. 1998 Environmental Information Systems. Berlin, New York, Springer.6. Pankhurst, R.J. 1981 Practical taxonomic computing. Cambridge University Press, Cambridge,

U.K.7. Judd, W.S., Campbell, C.S., Kellogg, E.A.,Stevens, P.F. and Donoghue, M.J.(2002) Plant

Systematics: A Phylogenetic Approach, 2nd Ed., Sinauer Associates, Inc. Publishers, Sunderland, Masssachusetts, U.S.A.

8. Nordenstam, B., El Gazaly, G. and Kassas, M. 2000 Plant Systematics for 21st Century. Portland Press Ltd.,London.

Credits: 4

26

MBIF 303: GENOINFORMATICS

Diversity of Genomes: Prokaryotic and Eukaryotic Genomes: Structure, Organization Gene Families Genome Analysis: Introduction, Gene prediction methods, Gene mapping and applications-

Genetic and Physical Mapping, Integrated map ; Sequence assembly and gene expression Completed Genomes: Bacterium, Nematode, Plant and Human Evolution of Genome: Lateral or Horizontal Transfer among Genomes Transcriptome and Proteome- General Account Phylogenetic analysis: Evolutionary Change in Nucleotide Sequences, Rates and Patterns of

Nucleotide Substitution, Models for Nucleotide Substitution and Methods for Phylogenetic analysis: Sequence Alignment, Soft wares (SSearch, BLAST, FASTA, CLUSTAL), Construction of Phylogenetic Tree

Genome Annotation- Introduction

Suggested Readings

1. Wilkins, M.R., Williams, K.L., Appel, R.D., Hochstrasser, D.F. (Editors) 1997 Proteome Research: New Frontiers in Functional Genomics. Springer Verlag Berlin Heidelberg.

2. Baxevanis, A. and Ouellette, F.B.F (Editors) 1998 Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons, New York.

3. Dale and Schartz 2003 From Genes to Genomes. Humana. 4. Hawley and Mori 1999 The Human Genome. Academic. 5. Primrose and Twyman 2003 Principles of Genome Analysis & Genomics. Blackwell. 6. Pasternak 2000 An Introduction to Molecular Human Genetics. Fritzgerald. 7. Sudbery 2002 Human Molecular Genetics. Prentice Hall. 8. Liebler, D. 2002 Introduction to Proteomics: Tools for New Biology. Human Press Totowa. 9. Brown, T.A. 2002 Genome. John Wiley Press, US. 10. Campbell, A.M. & Heyer, L.J. 2002 Discovering Genomics, Proteomics and Bioinformatics.

Benjamin/Cummings. 11. Jerome, P.E. 2002 Mathematics for Genome Analysis. Cambridge. 12. Hall, B.G. 2001 Phylogenetic Tress Made Easy: A How to Manual for Molecular Biologists.

Sinauer Ass., USA. 13. Nei, M. and Kumar, S. 2000 Molecular Evolution and Phylogenetics, Oxford University Press.

27

Credits: 4

MBIF 304: PREDICTION OF PROTEIN STRUCTURE AND MODELING

Protein Secondary Structure Prediction Methods Statistical Methods of Chou and Fasman, Garnier-Osguthorpe-Robson, Stereochemical Method

of Lim and Neural Network Method, etc, Fold Recognition and Threading Methods Profiles, Motifs – Regular Expressions Position Specific Scoring Matrices Repeat Finding and pattern Recognition Classification of Three Dimensional Structures of Proteins Prediction of Structural Classes, Motifs, Folds and Domains, Classification of Three

Dimensional Structures in Brookhaven Protein Data Bank (HSSP, SCOP, FSSP, CATH). Protein Structure Prediction: Structural Alignment Methods, Homology Modeling

Dynamical Programming, Molecular Simulation, Rational Drug design and Docking

Suggested Readings

1. Wilkins, M.R., Williams, K.L., Appel, R.D., Hochstrasser, D.F. (Editors) 1997 Proteome Research: New Frontiers in Functional Genomics. Springer Verlag Berlin Heidelberg.

2. Baxevanis, A.D. and Francis Ouellette, B.F. 2004 Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Second Edition, Wiley.

3. Graur, D. and Li, W-H. 2000 Fundamentals of Molecular Evolution. Sinauer Ass., USA. 4. Tisdall, D., 2003 Mastering Perl for Bioinformatics. O’Reilly.

28

SEMESTER- 4

Credits: 4

MBIF 401: TOOLS AND TECHNIQUES (One of the electives given below)

MBIF 401 A: Simulation and Modeling for Biologists

Introduction, general principles; Statistical models in simulation; Queuing models; Random numbers, Random-variate generation; Input modeling, verification and validation of simulation models, output analysis

Biological Models: Population models, Models for Biochemical reaction kinetics, Epidemic models, Vegetation growth models, Bacterial growth model

Introduction to Simulation software

Suggested Readings

1. Payer, T.A., Introduction to Simulation, McGraw Hill. 2. Gordon, G., System Simulation, Prentice Hall. 3. Reitman, J., Computer Simulation Application, Wiley. 4. Spriet, W.A., Computer Aided Modeling and Simulation, Academic Press. 5. Barnes, B., Modeling and Performance Measurement of Computer Systems. 6. Manuals for SIMULA/SIMSCRPIT.7. Deo, N., System Simulation with Digital Computer, PHI. 8. Law, A.M. and Kelton, W.D., 1991 Simulation Modeling and Analysis, McGraw Hill. 9. Banks, J., Carson, J.S. II, Nelson, B.L. and Nicol, 2002 Discrete-Event System Simulation, PHI.

29

MBIF 401 B: Soft Computing Techniques

Introduction to Genetic Algorithm, Genetic Operators and Parameters, Genetic Algorithms in Problem Solving, Theoretical Foundations of Genetic Algorithms, Implementation issues

Neural Model and Network Architectures, Perceptron Learning, Supervised Hebbian Learning, Backpropagation, Associative Learning, Competitive Networks, Hopfield Network, Computing with Neural Nets and Applications of Neural Network

Introduction to Fuzzy Sets, Operations on Fuzzy sets, Fuzzy Relations, Fuzzy Measures, Applications of Fuzzy Set Theory to different branches of Science and Engineering

Suggested Readings

1. Mitchell, M., 1998 An Introduction to Genetic Algorithms, Prentice-Hall. 2. Goldberg, D.E., 1989 Genetic Algorithms in Search, Optimization, and Machine Learning,

Addison-Wesley. 3. Michalewicz, Z., 1994 Genetic Algorithms+ Data Structures = Evolution Programs, Springer-

Verlag. 4. Sinha, N.K. and Gupta, M.M., 2000 (Eds), Soft Computing & Intelligent Systems: Theory &

Applications, Academic Press. 5. Hagan, M.T., Demuth, H.B. and Beale, M., 1996 Neural Network Design, Thompson Learning. 6. Lau C., (Ed), 1992, Neural Networks, IEEE Press. 7. Freeman, J. and Skapura, D., 1991 Neural Networks: Algorithms, Applications, and Programming

Techniques, Addison-Wesley. 8. Klir, G.J. and Folger, T.A., 1988, Fuzzy Sets, Uncertainty, and Information, PHI. 9. Klir, G.J. and Yuan, B., 1995 Fuzzy Sets and Fuzzy Logic: Theory and Applications, Prentice-

Hall. 10. Zimmerman, H.J., 1991 Fuzzy Set Theory and Its Applications, Kluwer Academic Press.

30

MBIF 401 C: Biophysics: Experimental Techniques

X-rays, their properties, sources of X-radiation, Application of X-rays to biology and medicine.

Basic principles of X-ray diffraction studies. Electron density map and its interpretation. Protein structure determination by X-rays and electron diffraction. NMR techniques for structure determination, elementary idea of UV/visible, IR, Raman

techniques in biological context. Mass spectrometry Microscopy

Suggested Readings

1. Jan Drenth Principles of Protein X-ray Crystallography (Springer Advanced Texts in Chemistry), Springer-Verlag Telos.

2. Lipson, H. and Steeple, H., Interpretation of X-Ray Powder Diffraction Patterns. St. Martin’s Press. 3. Bovey, F,A., Mirau, P.A. and Gutowsky, H.S., Nuclear Magnetic Resonance Spectroscopy (2nd

Edition). Academic Press. 4. Hallet, F.R., Stinson, R.H., Speight, P.A. and Graham, W.G., 2004 Physics for the Biological

Science, Toronto: Nelson Can. 5. Yadav, L.D.S., Organic Spectroscopy (1st Edition). Springer. 6. Hollas, J.M., High Resolution Spectroscopy (2nd Edition). John Wiley & Sons.

31

Credits: 3

MBIF 402: APPLICATIONS OF BIOINFORMATICS

Chemiinformatics in Biology: Conventions for representing molecules; Cheminformatics resources

Bioinformatics in pharmaceutical industries Bioinformatics in immunology Bioinformatics in agriculture Bioinformatics in forestry Geoinformatics Legal ,ethical and commercial ramifications of bioinformatics Biosensing

Suggested Readings

1. Gasteiger, 2003 Chemoinformatics A Text Book.2. Bujnicki, J.M. 2004 Practical Bioinformatics (Series: Nucleic Acids & Molecular Biology Vol.

15). Springer. 3. Hassan, A.S. 2004 Bioinformatics: Principles and Basic Internet. Trafford Publishing. 4. Kohane, I.S., Kho, A. and Buthe, A.J. 2002 Microarrays for an Integrative Genomics. Barnes &

Noble, MIT Press. 5. Lengauer, T. et. al. 2001 Bioinformatics: From Genomes to Drugs. Wiley-VCH.6. Tudor, I.O., Mannhold, R. Kubinyi, H. and Folkers, G. Chemo Informatics in Drug Discovery

(Methods and Principles in Medicinal Chemistry.7. Jensen, F. Introduction to Computational Chemistry. John Wiley & Sons 8. Stan Tsai, C. An Introduction to Computational Biochemistry 1st Edition. John Wiley & Sons., Inc. 9. Vyas, S.P. and Kohli, D.V Methods in Biotechnology and Bioengineering.

32

Credits: 4

MBIF 403 : MOLECULAR BIOLOGY TECHNIQUES

Technique of DNA Analysis: Preparation of DNA and RNA Probes; Principles of hybridizations and hybridization based techniques (Colony, Plaque, Southern and in situ hybridization); Autoradiography; DNA Fingerprinting

Techniques of gene expression: northern and western blotting; Gel retardation; Primer extension; Reporter assay

DNA sequencing, chemical synthesis of nucleotides Polymerase Chain Reaction and its application Tools of proteome analysis Microarray technology

Suggested Readings

1. Surzycki, S. 2000 Basic Techniques in Molecular Biology. Spring Verlag. 2. Celis, J.E., Cell Biology: A Laboratory Handbook 2nd Edition3. Ninfa, A.J. and Ballou, D.P. 1998 Fundamental Laboratory Approaches for Biochemistry and

Biotechnology. 4. Ausubel et. al. 2002 Short Protocols in Molecular Biology. Wiley. 5. Sambrook et. al. 2001 Molecular Cloning. CSHL. 6. Bartlett 2003 PCR Protocols: Methods in Molecular Biology, Vol. 226 2nd Edition. 7. Simpson, R.J. 2004 A Laboratory Mannual Purifying Proteins for Proteomics. Cold Spring Harbor

Laboratory Press, New York.

MBIF 404: SEMINAR

33

(Credit 1)

MBIF 405: COMPREHENSIVE VIVA BASED ON MBIF 301 TO 403 (Credit 1)

MBIF 406: PROJECT WORK (Credits 6)

PRACTICALS

1. Based on MBIF 301 & 302 (Credits 3)2. Based on MBIF 303 & 304 (Credits 3)3. Based on MBIF 401 to 403 (Credits 4)

34