POSTGRADUATES PROGRAM BRIEFING

Institute of Systems Biology (INBIOSIS)

IntegratingGenomics, Proteomics,

Transcriptomics, Metabolomicsand Bioinformatics

to reveal the Biology of Plants and Microbes

ASSOC. PROF DR ROOHAIDA OTHMAN

GRADUATE PROGRAMME CHAIRPERSON

Establishment – 24 MARCH 2005

to consolidate and strengthen the university’s reputation in providing modern biotechnology research programs through its centers;

Centre for Gene Analysis and Technology (CGAT)

Centre for Plant Biotechnology (CPB)

Centre for Bioinformatics Research (CBR)

An outstanding institute pursuing innovative research in systems

biology benefiting mankind

VISION

MISSION

Unraveling biological processes and networks leading towards exciting

discoveries

Head of Quality Assurance

Head of Centre for Bioinformatics

Research (CBR)

Head of Centrefor Plant

Biotechnology (CPB)

Head of Centre for Gene Analysis and Technology (CGAT)

Vice Chancellor

INBIOSIS ORGANISATION CHART

Scientific Advisory Committee

Director

Finance and Expenditure Committee

Postgraduate ProgrammeCommittee

Research Committee

Institute Management Committee

Research Fellows

Administrative and Technical Staff

Prof. Dr. Ismanizan Ismail• Plant Cell Biotechnology, Plant Gene Regulation

Prof. Dr. Ismanizan Ismail• Plant Cell Biotechnology, Plant Gene Regulation

Prof. Dr. Normah Mohd. Noor• Plant Tissue Culture, Cryopreservation, Seed Science

Prof. Dr. Normah Mohd. Noor• Plant Tissue Culture, Cryopreservation, Seed Science

Emeritus Prof. Dato’ Dr. Ikram Mohd. Said• Organic Synthesis, Natural Products Chemistry,

Phytochemistry

Emeritus Prof. Dato’ Dr. Ikram Mohd. Said• Organic Synthesis, Natural Products Chemistry,

Phytochemistry

Prof. Dr. Zamri Zainal• Plant Molecular Biology, Plant Biotechnology

Prof. Dr. Zamri Zainal• Plant Molecular Biology, Plant Biotechnology

Prof. Dr. Muhamad Mukram Mohamed Mackeen• Chemical Biology, Biophysical Chemistry

Prof. Dr. Muhamad Mukram Mohamed Mackeen• Chemical Biology, Biophysical Chemistry

Assoc. Prof. Dr. Roohaida Othman• Plant Functional Genomics, Plant Molecular Biology

Assoc. Prof. Dr. Roohaida Othman• Plant Functional Genomics, Plant Molecular Biology

Assoc. Prof. Dr. Zeti Azura Mohamed Hussein• Structural Bioinformatics, Computational Systems

Biology

Assoc. Prof. Dr. Zeti Azura Mohamed Hussein• Structural Bioinformatics, Computational Systems

Biology

Assoc. Prof. Dr. Choong Chee Yen• Plant Molecular Systematic, Plant Genomics

Assoc. Prof. Dr. Choong Chee Yen• Plant Molecular Systematic, Plant Genomics

Assoc. Prof. Dr. Mohd. Firdaus Mohd Raih

• Computational structural biology, RNA bioinformatics, Bacterial genomics

Assoc. Prof. Dr. Mohd. Firdaus Mohd Raih

• Computational structural biology, RNA bioinformatics, Bacterial genomics

Dr. Syarul Nataqain Baharum• Molecular Biology, Enzyme Technology, Metabolite

Profiling

Dr. Syarul Nataqain Baharum• Molecular Biology, Enzyme Technology, Metabolite

Profiling

Dr. Maizom Hassan• Applied Enzymology, Applied Microbiology, Biochemistry

Dr. Maizom Hassan• Applied Enzymology, Applied Microbiology, Biochemistry

Dr. Ng Chyan Leong• Structural Biology, Molecular Biology

Dr. Ng Chyan Leong• Structural Biology, Molecular Biology

Dr. Goh Hoe Han• Plant Developmental & Molecular, Systems Biology

Dr. Goh Hoe Han• Plant Developmental & Molecular, Systems Biology

Dr. Sureshkumar Sampathrajan• Bioinformatics

Dr. Sureshkumar Sampathrajan• Bioinformatics

Dr. Kamalrul Azlan Azizan• Fluxomics, Metabolomics, Chemical Engineering

Dr. Kamalrul Azlan Azizan• Fluxomics, Metabolomics, Chemical Engineering

Dr. Wan Mohd Aizat Wan Kamaruddin• Plant Biotechnology

Dr. Wan Mohd Aizat Wan Kamaruddin• Plant Biotechnology

Human capacityPost Number of Staff

Research Fellow 17

Associate research fellow‐Assoc. Prof. Dr. Masturah Markom (Engineering Faculty, UKM)‐Assoc. Prof. Dr. Noraziah Mohamad Zin (FSK, UKM)‐Assoc. Prof. Dr. Mohd. Shahir Shamsir (UTM)‐Prof. Dr. I.Sahidin (University of Haluoleo, Indonesia)‐Dr. Siti Azma Jusoh (UiTM)

5

Research officers  2

Science officers  4

Engineer 1

Assistant Science Officers  3

Technician/Lab Assistant 2

General worker  1

Administration 4

TOTAL 39

Microbial & Plant Genome InformationMicrobial & Plant 

Genome Information

Modeling of Secondary Metabolite Biosynthetic Pathway 

Modeling of Secondary Metabolite Biosynthetic Pathway 

Metabolite ProfilingMetabolite Profiling TranscriptomicsTranscriptomics

Gene Cloning &Functional AnalysisGene Cloning &

Functional Analysis

Holistic Understanding on Secondary MetaboliteBiosynthetic Pathway

ProteomicsProteomics

Kitano et al .Science. 2002. 295:1662

Graduate ProgrammesMasters in Systems Biology

Computational Biology

In silico Biology

Biomolecular Sciences

Proteome Sciences

PhD in Systems Biology

Educational Goals

• To bring together highly qualified independent researchers to investigate highly complex biological processes and networks in the best way possible – in interdependent interdisciplinary teams.

• To serve as a supportive venue for researchers in interdisciplinary teams as they learn how to talk across disciplinary borders, languages and traditions.

Programme Offered

NO NAME OF PROGRAMMES

TYPE OF REGISTRATION OFFER TO

Full Time (Code = FT) Local Student (Code = L)

Part Time (Code = PT)Foreign Student

(Code = F)

1 Doctor of Philosophy (Systems Biology)FT L & FPT L

2 Masters in Systems Biology (Computational Biology)FT L & F

PT L

3 Masters in Systems Biology (In Silico Biology)FT L & FPT L

4 Masters in Systems Biology (Biomolecular Sciences)FT L & F

PT L

5 Masters in Systems Biology (Proteome Science)FT L & FPT L

Duration of Study

Programmes Full time

Masters in Systems Biology

Min: 2 semestersMax: 6 semesters

Doctor of Philosophy

Min : 6 semestersMax: 12 semesters

Program Structure:MASTERS IN SYSTEMS BIOLOGY

a. Research and preparation of a thesis

b. RARA6014 Research Methodology Course (4  credit hours) and  other relevant courses (2 credit hours)

c. General Seminar (10 hours)Candidates must attend seminars, workshops and training sessions that are related to systems biology as identified by the institute.

d. Specific Seminar (5 hours)Candidates must attend seminars, workshops and training sessions that are related to their field as proposed by the supervisor and Masters Committee.

e. Research Seminar (8 hours)Candidates must give a presentation on the research done as below:• Presentation of paper proposal in Semester 1• Presentation of research progress in each Semester (2,3)• Presentation of research findings in the middle or end of Semester 4(as preparation for oral examination)

f. Publish at least one article in a journal in ISI/Scopus(accepted for publication) before completion of  studies.

MASTERS IN SYSTEMS BIOLOGYg. Candidates with no related background field (for example, those with computer 

sciences  background who are interested to do research on biological systems) are required to attend courses proposed by the Graduate Committee, while biologists will be required to take courses related to other than Biological Sciences, as proposed by the Graduate Committee.

Program Structure:

Program Structure:DOCTOR OF PHILOSOPHY

a. Research and preparation of a thesis

b. RARA6014 Research Methodology Course (4  credit hours) and  other relevant courses (4 credit hours)

c. General Seminar (25 hours)candidates must attend seminars, workshops and training sessions that are related to systems biology as identified by the institute.

d. Specific Seminar (20 hours)Candidates must attend seminars, workshops and training sessions that are related to their field as proposed by the supervisor and Doctor of Philosophy Committee.

e. Research Seminar (15 hours)Candidates must give a presentation on the research done as below:• Presentation of paper proposal in Semester 1• Presentation of research progress in each Semester (2,3,4 and 5)• Presentation of research findings in the middle or end of Semester 6(as preparation for oral examination)

f. Publish at least two articles  in a journals in ISI/Scopus (accepted for publication) and present research results at related conferences before  completion of studies.

KAEDAH PENILAIAN/EVALUATION METHOD

Research Methodology Course (RARA6014)

Bil. 

Perkara /Item Peratusan (%) 

1.  Kehadiran

Attendance

20

2.  Pembentangan Akhir

Final Presentation

40

3. Cadangan Penyelidikan

Research Proposal

40

Jumlah/Total 100% 

KAEDAH PENILAIAN/EVALUATION METHOD

Bil.  Perkara /Item Peratusan (%) 

1. Kehadiran/keterlibatan

Attendance/involvement

10

2.Pembentangan (2)

Presentation (2)

50

3. Tugasan (2)

Assignment (2)

40

Jumlah/Total 100% 

Concepts and Applications of Systems Biology (RBRB6012)

Monitoring Method for  Postgraduate Program

• Presentation of research proposal in Semester 1• Presentation of research progress every semester until thesis submission

• Presentation of research findings after thesis submission (as preparation for oral examination)

• Seminar registration form – total hours of seminar attended

• Student Information sistem (SMP) – total credit hours achieved

Postgraduate StudentsNO NAME OF PROGRAMMES NO. OF STUDENTS

1Doctor of Philosophy

(Systems Biology) 9

2Masters in Systems Biology

(Biomolecular Sciences) 29

3Masters in Systems Biology

(Proteome Science) 5

Total = 43

Facilities• Platform: METABOLOMICS

• Gas Chromatography-Mass Spectrometry (GC-MS)

• High Performance Liquid Chromatography (HPLC)

• Fourier Transform Infrared Spectrometry (FTIR)

• Radial Chromatography

• Hydro Distillation System

• Liquid Chromatography (UHPLC)-Quadrupole Time of Flight-Mass Spectrometry

(LC-QTOF-MS)

Facilities• Platform: GENOMICS and TRANSCRIPTOMICS

• Molecular Imaging

• UV Vis NanoDrop

• DNA Analyzer & Infrared Imaging System

• Thermal Cycler Real Time PCR

• Hybridization Oven

• Microarray Scanner

Facilities• Platform: PROTEOMICS

• FPLC Akta Purifier

• 2D Gel Electrophoresis Apparatus

• Molecular Imager Calibrated Densitometer

• UV Vis Spectrophotometer

• High Speed Centrifuge

• Isoelectric Focusing System (IEF)

Facilities• Platform: TRANSGENIC/TISSUE CULTURE

• Tissue Culture Facilities

• Conviron - Growth Chamber

• Fluorescent Microscope

• Stereomicroscope

• Shade and green house

• Experimental Plot

• Transgenic Glass House

• Platform: COMPUTATIONAL BIOLOGY• Databases

• Bioinformatic Analysis Tools

• Servers – Xserve and Windows-based server

Facilities

PC2 Greenhouse (RTPC2)

Research Plots

Publication

0

10

20

30

40

50

60

2010 20112012

20132014

54 55

33

42

31

58

31

22

32 34

No.

of p

ublic

atio

ns

Year

Publication 2010-2014

Journals

Proceedings

Technology

International Conference• Organized Asian Regional

Conference on Systems Biology (ARCSB) in year 2010 & 2013

• New Collaboration since 2010• MOA

• National Academy of Agricultural Science, Rural Development Administration, Korea

• MOU• University of Tsukuba, Japan

• National Academy of Agricultural Science, Rural Development Administration, Korea

• LOI• Auckland University of Technology, NZ

• University of Haluoleo, Indonesia

Collaborative research

Collaborative LaboratoryCollaborative Laboratory Launched on 21 July 2011

Collaboration - International

Collaboration - National

What we can offer

• New knowledge and information for tropical plants and microbes

• Dynamic infrastructure and environment to cater multidisciplinary basic research on tropical biology resources

• Technology platform for systems biology research

aimsto develop and establish

systems biology research in Malaysia

Definition of hours1. Workshop/training :

1 day = 4 contact hours = 2 hours

2. Seminar1 contact hour = 0.5 hour2 contact hours = 1 hour

3. Attachment1 month = 20 working days1 day      = 8 contact hours = 0.4 hour20 working day = 8 hours

Borang Daftar Kursus : Diisi setiap akhir semester

Graduate Studies Act, 1984

1. Thesis :1.1 A candidate is not permitted to re‐submit any thesis which haspreviously been presented to UKM, or any other university, but mayinclude parts of his/her previous work provided they are clearlyreferenced.

1.2 If agreed upon by the supervisor or Graduate Committee, acandidate may publish papers based on his/her work done during theperiod of candidature, provided they contain due acknowledgement tothe University

1.3 The Doctor of Philosophy thesis shall not exceed 100,000words. The Master’s thesis (without coursework) shall not exceed60,000 words. The Master’s thesis with coursework shall not exceed30,000 words. The prescribed total number of words does not includefootnotes, quotations, appendices, summaries, schedule, charts etc.

Graduate Studies Act, 1984

1. Thesis :1.4 Permission to exceed the number of prescribed words in the thesis may be obtained by writing to the Dean CGS at least three months before submission of the thesis for examination.

1.5 The thesis shall be written in Bahasa Malaysia, to be preceded by an abstract, and the translation the abstract in English or Arabic. Under certain circumstance, a thesis may be written in English or Arabic with the translated abstract in Bahasa Malaysia, and a longer abstract, also in Bahasa Malaysia, not exceeding 1000 words. Any request to write a thesis in any other language (English or Arabic only) shall be made to the Dean CGS for consideration and approval.

1.6 Regulations on preparation of the thesis are stipulated in the Panduan Menulis Tesis Gaya UKM (The UKM Style Guide)

Graduate Studies Act, 1984

1. Thesis :1.7 A candidate who submits his/her thesis shall:

1.7.1 notify the Dean, CGS, in writing three months prior  to submitting his/her thesis for examination;

1.7.2 obtain prior written approval from the supervisor.

1.8 A candidate shall submit five copies of his/her thesis which has been approved by the Senate to CGS at the end of his/her study programme.

1.9 The thesis may be published only with permission from the University. 

1.10 A candidate who fails the degree of Doctor of Philosophy may be considered for the Master of Philosophy degree if the Board of Graduate Examiners is of the opinion that the thesis submitted does not meet the standard required for the degree of Doctor of Philosophy. 

Research Methodology Course (RARA6014)

1. Tajuk KursusCourse Title

Kaedah PenyelidikanResearch Methodology

2. Kod KursusCourse Code

RARA6014

3. Jam KreditCredit Hours

4

4. Jam PertemuanContact Hours

34

5. Kursus PrasyaratPre Requisties

Tiada/ None

COURSE DETAILS :

Research Methodology Course (RARA6014)

HASIL PEMBELAJARAN KURSUSCOURSE OUTCOMES (CO)Pada akhir kursus ini, pelajar berkebolehan untuk :

CO1:  Merancang sesebuah penyelidikanAble to plan a scientific research 

CO2:  Menyampaikan hasil penyelidikan melalui pembentangan dan penerbitan secara berkesanAble to deliver effectively, in written and orally the research findings to target group 

CO3:  Memahami falsafah dan etika dalam menjalankan penyelidikanKnowledgeable in the philosophy and ethic in conducting research 

CO4:  Memahami peranan penyelidik dan kepentingan penyelidikanKnowledgeable in the role of researcher and the important of research 

CO5:  Menyediakan disertasi sesuai dengan format yang ditetapkanCapable of preparing a dissertation according to required format

CO6:  Memahami tentang aspek perundangan dan pengkomersilan hasil penyelidikan.Understand of the legal and commercial aspects of research findings 

KAEDAH PENILAIAN/EVALUATION METHOD

Research Methodology Course (RARA6014)

Bil. 

Perkara /Item Peratusan (%) 

1.  Kehadiran

Attendance

20

2.  Pembentangan Akhir

Final Presentation

40

3. Cadangan Penyelidikan

Research Proposal

40

Jumlah/Total 100% 

Gred Markah RARA6014

GRED MARKAH STATUS

A 70 LULUS

A‐ 65 LULUS

B+ 60 LULUS

B 55 LULUS

B‐ 50 GAGAL

C+ 45 GAGAL

C 40 GAGAL

D 35 GAGAL

E 30 GAGAL

1. Tajuk KursusCourse Title

Konsep dan Aplikasi Biologi SistemConcepts and Applications of Systems Biology

2. Kod KursusCourse Code

RBRB6012

3. Jam KreditCredit Hours

2

4. Jam PertemuanContact Hours

52

5. Kursus PrasyaratPrerequisites

Tiada/ None

COURSE DETAILS 

Concepts and Applications of Systems Biology (RBRB6012)

• HPP1: Graduan berkeupayaan menghuraikan definisi biologi sistem dalam konteks keseluruhan dan khusus • Can define systems biology in general and specific contexts• HPP2: Graduan berkebolehan menemui ilmu baru bermakna secara merdeka yang berupa hubung kait di antara 

disiplin bidang penyelidikan berbeza• Can discover new meaningful knowledge independently to relate multidisciplinary research• HPP3: Graduan berkebolehan menggunakan kaedah kesarjanaan yang diterima dalam bidang ilmu berkenaan 

untuk mendapatkan data atau maklumat yang sah dari sumber primer serta mengolah data atau maklumat itu untuk mendapatkan ilmu baru

• Can apply scientific method in the acquisition of data or information from primary sources and capable of analyse these information to generate new knowledge 

• HPP4: Graduan berkebolehan mempelajari dan memperoleh ilmu secara merdeka, kreaktif dan inovatif• Capable of learning and acquiring knowledge independently in a creative and innovative manner• HPP5: Graduan berkebolehan mendemonstrasi dan memahami kaedah analisis secara kritikal • Can demonstrate and understand critically analytical methods • HPP6: Graduan berkeupayaan mengintepretasi jurnal tersohor dalam bidang biologi sistem dan dapat menilai 

penemuan sesuatu penyelidikan.• Can interpret renowned journal articles in systems biology and evaluate the research findings• HPP7: Graduan berkebolehan untuk membentangkan topik‐topik berkaitan biologi sistem dengan jelas dan yakin• Capable of presenting topics in systems biology clearly and confidently• HPP8: Graduan berkebolehan membangun dan mengekalkan rangkaian kerjasama dengan penyelia dan rakan‐

rakan penyelidik lain • Can develop and maintain research network with supervisor and peers

RBRB6012Hasil pembelajaran/learning outcomes

KAEDAH PENILAIAN/EVALUATION METHOD

Bil.  Perkara /Item Peratusan (%) 

1. Kehadiran/keterlibatan

Attendance/involvement

10

2.Pembentangan (2)

Presentation (2)

50

3. Tugasan (2)

Assignment (2)

40

Jumlah/Total 100% 

Concepts and Applications of Systems Biology (RBRB6012)

Gred Markah RBRB6012

GRED MARKAH STATUS

A 70 LULUS

A‐ 65 LULUS

B+ 60 LULUS

B 55 LULUS

B‐ 50 GAGAL

C+ 45 GAGAL

C 40 GAGAL

D 35 GAGAL

E 30 GAGAL

THESIS SUBMISSION AND VIVA

Appointment of Examiners by Supervisor

• Masters : Semester 3                                                               (Internal examiner: 1;  External examiner : 1)

• PhD       : Semester 5                                                                (Internal examiner: 1;  External examiner : 2)

Notication to submit thesis by 

student

• 3 months prior to submission of thesis (yellow form)

• Notice of less than 3 months will be subjected to a fine

• Reminder will be sent 1 month before the due date 

Thesis Submission for Examination 

by student

• Thesis  submitted 3 months after notice – 7 copies (blue form)

• Payment for thesis submission (green form) –send to Unit Kewangan Pelajar, JabatanBendahari

Dispatch of thesis to Examiners by Postgraduate Secretariat

• Within 7 working days• Viva date set 9 weeks from date of thesis dispatch to examiners

Thesis examination by Examiners

• Maximum 7 weeks

Setting viva date by Postgraduate Secretariat

• Two (2) weeks upon receiving thesis examination report from Examiners

Viva organised by Secretariat

• Postgraduate Committee and Viva Examination Meeting

• Members: Chairperson (Professor/Assoc. Prof.) ,  Director/representative,  Representative of INBIOSIS, External and Internal Examiners

Thesis submission after correction by 

student

• Thesis that has been corrected must be submitted according to the date set in the the viva  (pink form)

Graduation• Viva voce minit passed by SENAT, UKM

Thank you