Bioinformatics Graduate Student Handbook

Table of Content

• Overview of the Bioinformatics Graduate Programs

• Doctor of Philosophy (Ph.D.) in Bioinformatics
  1. Curriculum Requirements
     
  2. Typical Programs of Study
     
  3. Advisory Committee
     
  4. Comprehensive Examination
     
  5. Admission to Candidacy
     
  6. Dissertation Planning and Prospectus
     
  7. Dissertation Approval and Defense
     

• Master of Science (M.S.) in Bioinformatics
  1. Curriculum Requirements
  2. Advisory Committee
  3. Master's Thesis
  4. Non-Thesis Option
  5. Graduation Requirements
  6. Thesis Defense

• Graduate Certificate in Bioinformatics
  1. Curriculum Requirements
  2. How to Apply for a Certificate

• Course Lists
  1. Core Courses for the Ph.D. program
     
  2. Core Courses for the M.S. program
     
  3. Elective Courses for the Ph.D. and M.S program
     
  4. Foundations for the Certificate program
     
  5. Core Course for the Certificate program
     

• Graduate School Requirements
  

Overview of the Bioinformatics Graduate Programs

With the advent of multiple genome sequences, biological research has become much more quantitative, using tools from physical, mathematical, and computational sciences to generate and analyze large-scale datasets in an attempt to understand the behavior of biological systems. The highly interdisciplinary field of bioinformatics has developed around these new approaches.

The mission of the Institute of Bioinformatics is to educate and train graduate students in bioinformatics research and its applications to attain mastery and leadership in this new interdisciplinary field. The institute offers Ph.D. and M.S. degrees in Bioinformatics, and it also offers Graduate Certificate in Bioinformatics to students already enrolled at UGA. Students matriculating in the graduate programs in bioinformatics will be directed and mentored by faculty members from multiple departments and disciplines.

The bioinformatics graduate program consists of faculty members whose research interests cover a wide spectrum of bioinformatics research in the areas of microbial, fungal, plant, and animal genomics, structural genomics, biomedical (e.g., cancer) genomics, glycogenomics, proteomics, transcriptomics, and pharmacological informatics, using computational, statistical, and experimental technologies. Students should refer to the detailed research descriptions of the faculty members in the IOB.

While in the bioinformatics Ph.D or M.S. program, students will fulfill all the requirements of the Graduate School for a graduate degree. Student progress in the program will be monitored by the Graduate Coordinator and the IOB Graduate Affairs Committee. Upon arrival at the university, students will be assigned a curriculum advisor for guidance and mentoring. Because this program is interdisciplinary, students will be advised to take prerequisite courses in areas where the student does not have the necessary background. Students will select their major professor and establish an advisory committee by the end of their first year in the program.

The advisory committee will meet with the students no less than once a year and will be responsible for mentoring the student's research and training, approving the student's program of study, administering the written and oral comprehensive examination, approving the subject for the dissertation, approving the completed dissertation, and approving the student's defense of his or her research.

Ph.D. students will take their comprehensive examinations at the beginning of their third year under the supervision of the major professor under the Graduate School guidelines. Successful candidates for the PhD degrees then typically concentrate on their research projects, and, after completing their research, they write a dissertation and defend it at a final oral examination.

M.S. students with the thesis option are required to take an oral examination conducted by the advisor committee and to defend his/her thesis and have it approved by the committee. For the non-thesis option, the student will prepare a technical report in a research project in bioinformatics under the direction of a designated member of the IOB faculty. The technical report must be approved by a committee including the project director.

All students will receive training and experience in written and oral communication skills and training in the responsible conduct of research.

Return to Table of Content

Doctor of Philosophy (Ph.D.) in Bioinformatics

1. Curriculum Requirements

   Because of its interdisciplinary nature, the bioinformatics graduate program admits students from diverse backgrounds and leads to multiple career paths, depending upon the background and interests of the students. Thus, this curriculum ensures flexible training of a diverse student body while maintaining the rigor of the program. In particular, for all students, the program requires a core of eight courses listed in the Core Courses for the Ph.D. Program section. These eight courses ensure that all students obtain advanced knowledge of biochemistry and molecular biology, genetics, bioinformatics, computer science and statistics. Students must complete any prerequisites for these core courses.

   Students will then augment this core with at least four elective courses from the courses listed in the Elective Courses section. The goals of these electives are to provide the foundation or background for interdisciplinary training as well as advanced specialization. For many students, two of the elective courses will be used for foundation and two of the elective courses will be used to develop an area of specialization. For students with an exceptionally strong foundation, the electives will be used entirely to develop one or more areas of advanced specialization.

   The core contains more than 16 hours of 8000- and 9000-level courses in addition to research, dissertation writing, and directed study and fulfills these requirements of the Graduate School. For a student who bypasses the master's degree, there is an additional requirement of 4 semester hours of University of Georgia courses open only to graduate students in addition to 16 semester hours of 8000- and 9000-level courses. This requirement will be met with one or more elective courses at the 8000- or 9000-level.

   Each student should take electives that form a coherent specialization and must include at least one 8000-level course. The student's selection of electives must be approved by the thesis committee. Students who do not need the foundation courses should take their electives in no more than two areas of specialization.

   Foundation courses are intended for students who are lacking previous coursework in key areas of bioinformatics. These may only be counted as electives by students who do not have prior background in the subject. For example, a student with an undergraduate degree in biology may not count BIOL 6000 as an elective. Foundation courses may not be used to fulfill the elective requirement without approval from the IOB Graduate Coordinator. The Graduate Coordinator will determine whether a foundation course is appropriate as an elective based on the student's backrground prior to entering the IOB program.

   Return to Table of Content

2. Typical Programs of Study

   Students will be required to take twelve courses, including a core of eight courses and four electives. For many students, two of these electives will be foundation or background courses to augment their interdisciplinary training. The remaining electives will be used to develop an area of strength or specialization. Two examples of typical programs of study are given below. The program entitled Bioinformatics Applications is designed for students with background and strengths in the biological sciences. The program entitled Bioinformatics Methods Development is designed for students with background and strengths in the computer science, mathematics, and statistics.

   (1) Bioinformatics Applications

   Year 1		Year 2
   Fall	Spring	Fall	Spring
   BCMB(BINF) 8210	BCMB(BINF) 8211	ELECTIVE	MICRO/BCMB 8270L or Bioinformatics Project
   CSCI 7010	STAT 6310	STAT 6630	STAT 6640
   BCMB 8010	GENE 8930	CSCI 6490	elective
   BINF 6001 Professors on Parade	BINF 6001 Professors on Parade	BINF 6001 Professors on Parade	BINF 6001 Professors on Parade

   (2) Bioinformatics Method Development

   Year 1		Year 2
   Fall	Spring	Fall	Spring
   BCMB(BINF) 8210	BCMB(BINF) 8211	ELECTIVE	MICRO/BCMB8270L or Bioinformatics Project
   STAT 6630	STAT 6640	CSCI 6490	ELECTIVE
   BINF 6040 or BCMB 6000	ELECTIVE	BCMB 8010	GENE 8930
   BINF 6001 Professors on Parade	BINF 6001 Professors on Parade	BINF 6001 Professors on Parade	BINF 6001 Professors on Parade

   In addition to the courses students will complete at least 30 credit hours of dissertation research and 6 hours of dissertation writing during their program. The expected time to completion of the degree is four years.

   Return to Table of Content

3. Advisory Committee

   Upon arrival at the university, students will be assigned a curriculum advisor for guidance and mentoring. Because this program is interdisciplinary, students will be advised to take prerequisite courses in areas where the student does not have the necessary background.

   By the end of their first year in the program, students will select their major professor and establish an advisory committee. The major professor must be a full member of the Institute of Bioinformatics and the Graduate Faculty. The advisory committee must consist of the major professor and at least three other faculty members. At least two members of the advisory committee must be full or associate members of the IOB. The advisory committee will also be composed of representatives of both the biological and the quantitative sciences. At least one member of the advisory committee will represent the student's focused area of study e.g. computer science, plant biology, microbiology, etc., from outside the institute. This member of the committee will provide input from outside bioinformatics and ensure that the program of study is consistent with the practices of the most related outside discipline.

   The advisory committee will meet with the students no less than once a year and will be responsible for mentoring the students research and training, approving the students program of study, administering the written and oral comprehensive examination, approving the subject for the dissertation, approving the completed dissertation, and approving the students defense of his or her research. Students will take their comprehensive examinations at the beginning of their third year supervised by the major professor under the Graduate School guidelines.

   Return to Table of Content

4. Comprehensive Examination

   The student must pass the Ph.D. comprehensive examination that covers the student's major research areas of study. The examination consists of two parts: a written part and an oral part. Students have at most two attempts to pass the written part. The oral part may not be attempted unless the written part has been passed. The exams are administered by the student's advisory committee.

   For the written comprehensive examination, typically, each member of the advisory committee will prepare a multi-part question relevant to the student's area of advanced study. These questions will be given to the student in the form of a take-home examination.

   The oral comprehensive examination typically consists of follow-up questions to the written comprehensive examination. This exam must be announced to the Institute of Bioinformatics and the Graduate School at least two weeks ahead of time. This exam requires that all members of the advisory committee be present and is open to all members of the IOB faculty. After the exam, the committee will cast votes of pass or fail on both the oral and written exams. Passage of each exam requires all but one of committee members to vote for approval. These results are recorded on the Report of the Written and Oral Comprehensive Examination form. This form must be obtained from the graduate school.

   Return to Table of Content

5. Admission to Candidacy

   The student should initiate an application for admission to candidacy once all requirements, except the dissertation prospectus and the dissertation, have been completed. The Application for Admission to Candidacy for Doctoral Degrees form must be filed with the Graduate School at least two semesters before graduation.

   Return to Table of Content

6. Dissertation Planning and Prospectus

   Dissertation planning will involve exploratory research leading to the preparation of a dissertation prospectus. BINF 9000 Doctoral Research course may be taken at this time. The prospectus must be presented to the advisory committee for approval. The prospectus must be presented to the advisory committee. This presentation should be open to both faculty and graduate students within the institute. The prospectus must be approved by all but one members of the advisory committee and so indicated by a letter from the major professor to the Graduate Coordinator. This letter must contain signatures from the entire committee. Students must be enrolled for at least one semester after passing the prospectus.

   Return to Table of Content

7. Dissertation Approval and Defense

   The student's dissertation must represent originality in research, independent thinking, scholarly ability, and technical mastery of a field of study in bioinformatics. The dissertation must also demonstrate competent style and organization (see Graduate School for guidelines for theses and dissertations). While working on his/her dissertation, the student must enroll for a minimum of 6 hours of BINF 9300 Doctoral Dissertation course spanned at least 2 semesters. Students may not register for this course until they have been admitted to candidacy. Once the student's major professor approves the final version of the dissertation, it will be distributed to the other members of the advisory committee, and a dissertation defense scheduled no sooner than three weeks after the distribution. This exam requires that all members of the advisory committee be present and is open to faculty members and graduate students. All but one of the members of the advisory committee must approve the student's dissertation and defense. These results are recorded on the Approval Form for Doctoral Dissertation and Final Oral Examination.

   Return to Table of Content

1. Curriculum Requirements

   Because of its interdisciplinary nature, the bioinformatics M.S. degree program admits students from diverse backgrounds and leads to multiple careers paths, depending upon the background and interests of the students. Thus, the curriculum ensure to provide flexible training of a diverse student body while maintaining the rigor of the program.

   The M.S. program offer thesis and non-thesis options. Both options require the M.S. student to take the five courses or 17 hours of core courses listed Core Courses for the M.S. Program section. Students must complete all prerequisites for the core courses. Students will also be required to complete or possess an equivalency for up to four or 13 hours of elective courses listed in the Elective Courses section. Students with a largely biology background will be required to take appropriate foundation courses to strengthen their quantitative and computational skills, while students with largely quantitative science background will be required to take appropriate foundation courses to strengthen their knowledge of biology. Students with a strong background in both the biological and quantitative science who already possess equivalent course work for all the foundation courses will develop a second area of specialization with electives.

   In addition, 6 hours of BINF 7000 Master Research course and 3 hours of BINF 7300 Master's Thesis course work are required for students with the thesis option. In the absence of a thesis, students will take 9 hours of 8000-level courses in an area of specialization to be approved by their committee as well as prepare a final technical report on a topic assigned by the students advisor.

   Return to Table of Content

2. Advisory Committee

   Upon arrival at the university, students will be assigned a curriculum advisor for guidance and mentoring. Because this program is interdisciplinary, students will be advised to take prerequisite courses in areas where the student does not have the necessary background. Students will select their major professor and establish an advisory committee by the end of their first year in the program. The major professor must be a full member of the IOB and the Graduate Faculty. The advisory committee must consist of the major professor and at least two other faculty members. At least two members of the advisory committee must be full or associate members of the IOB. The advisory committee will also be composed of representatives of both the biological and the quantitative sciences.

   For the non-thesis option, the student will prepare a technical report in a research project in bioinformatics under the direction of a designated full member of the IOB faculty. The technical report must be approved by a committee of at least three full members of the IOB, including the project director. This committee will be appointed by the Graduate Coordinator.

   Return to Table of Content

3. Master's Thesis

   For the thesis option, the students are required to take an oral examination conducted by the advisory committee and to have his/her thesis approved by the committee.

   The thesis is a report of the student's investigations under the supervision of his/her major professor and requires the approval of the major professor and the advisory committee. The thesis must demonstrate competent style and organization, and communicate technical knowledge. The thesis often includes original research in bioinformatics. It must demonstrate mastery of a particular area of bioinformatics. The student's advisory committee assures that the quality of the thesis meets the standards of the IOB and the Graduate School. The candidate must register for BINF 7300 Master's Thesis for at least 3 hours of credit while working on the thesis.

   Return to Table of Content

4. The Non-Thesis Option

   For the non-thesis option, the student will prepare a technical report in a research project in bioinformatics under the direction of a designated full member of the IOB faculty. The technical report must be approved by a committee of at least three full members of the IOB, including the project director. This committee will be appointed by the Graduate Coordinator.

   Return to Table of Content

5. Graduation Requirements

   Before the end of the second semester in residence, a student must submit to the Graduate School, through the graduate coordinator, the following forms: (i) a Program of Study Form and (ii) an Advisory Committee Form. The Program of Study Form indicates how and when degree requirements will be met and must be formulated in consultation with the student's major professor. An Application for Graduation Form must also be submitted directly to the Graduate School.

   Return to Table of Content

6. Thesis Defense

   After all course work has been completed and the thesis has been approved by the student's major professor, the thesis is submitted to the other members of the advisory committee at least two weeks before the thesis defense date. The thesis defense is an oral examination conducted by the student's advisory committee, and constitutes the second part of the master's final examination. All members of the advisory committee must be present at the defense. The advisory committee members including the major professor must vote on whether the student passed the defense and record their votes on the Approval Form for Master's Thesis, Defense, and Final Examination. To pass the exam, at least two of the three votes must be passing.

   Return to Table of Content

Graduate Certificate in Bioinformatics

1. Curriculum Requirements

   Students seeking a Certificate must be currently enrolled and in good standing in a graduate program at the University of Georgia, Athens.

   The certificate can be achieved by taking: (1) one foundation course with at least 3 credit hours in an area in which the student has the least training and (2) any four of the core courses totaling at least 10 credit hours (see Foundation Courses and Core Courses for the certificate program). Hence, the entire requirements for the certificate are 13 - 17 hours, depending upon the specific courses taken.

   Exceptional students who already have a sufficient knowledge in the areas covered by the background courses may be exempted from taking them. Students must maintain an overall average of a B on courses taken for the Certificate.

   Return to Table of Content

2. How to Apply for a Certificate

   Before you apply, please notify the Graduate Coordinator of the Institute of Bioinformatics one month before the end of the semester in which you intend to apply for the Certficate.

   To apply for the Certificate, send a letter to the Graduate Coordinator of the Institute of Bioinformatics that includes: your name, your student identification number, and the courses completed to fulfill the Certificate requirement. For each course, include only the course prefix and number (e.g., MIBO 8110L) and the semester in which the course was completed. Include a copy of your transcript that shows the grades for the courses used for completion of the Certificate. For courses recently completed whose grades are not included on your transcript, include a brief letter from the instructor stating that you have received a grade of B or higher. This information must be received within three days following the grade role deadline to receive the Certificate within that semester.

   Return to Table of Content

Course Lists

1. Core Courses for the Ph.D. Program

   Every Ph.D student needs to take the following eight core courses and to complete any necessary prerequisites for these courses:

   Ph.D. Core Courses

   Prefix	Number	Title	Credit Hours
   BCMB	8210	Computational Methods for Bioinformatics	4
   BCMB	8211	Advanced Methods for Biological Data Analysis II	4
   GENE	8940	Genome Analysis	2
   BCMB	8010	Advanced Biochemistry & Molecular Biology	4
   GENE	8930	Advanced Molecular Genetics	3
   STAT	6630	Statistical Bioinformatics I	3
   STAT	6640	Statistical Bioinformatics II	3
   CSCI	6490	Algorithms for Computational Biology	4

   Return to Table of Content

2. Core Courses for the M.S. Program

   Every M.S. student needs to take the following five core courses and complete any prerequisites for these courses.

   M.S. Core Courses

   Prefix	Number	Title	Credit Hours
   BCMB	8210	Computational Methods for Bioinformatics	4
   BCMB	8211	Advanced Methods for Biological Data Analysis II	4
   GENE	8940	Genome Analysis	2
   STAT	6630	Statistical Bioinformatics I	3
   CSCI	6490	Algorithms for Computational Biology	4

   Return to Table of Content

3. Elective Courses for the Ph.D. and M.S. programs

   Foundation courses for biologists:

   STAT 6310 Statistical Analysis I (3 hours)
   CSCI 7010 Computer Programming (4 hours)

   Foundation courses for quantitative scientists:

   BCMB 6000 General Biochemistry and Molecular Biology (3 hours)
   BIOL 6040 Essential Biology for the Quantitative Scientists (3 hours)

   Specialization in Applied Probability:

   STAT 6510 Mathematical Statistics I (3 hours)
   STAT 6520 Mathematical Statistics II (3 hours)
   STAT 8700 Applied Stochastic Processes (3 hours)
   STAT 8730 Sequential Analysis (3 hours)

   Specialization in Computer Algorithms:

   CSCI 4470/6470 Algorithms (4 hours)
   CSCI 8470 Advanced Algorithms (4 hours)
   CSCI 8610 Topics in Theoretical Computer Science (4 hours)
   CSCI 4140/6140 Numerical Methods and Computing (4 hours)
   CSCI 8140 Parallel Processing and Computational Science (4 hours)
   CSCI 8150 Advanced Num. Methods and Sci. Comp. (4 hours)

   Specialization in Database and Software Systems:

   CSCI 6350 Global Information Systems (4 hours)
   CSCI 6370 Database Management (4 hours)
   CSCI 6800 Human-Computer Interaction (4 hours)
   CSCI 8350 Semantic Web (4 hours)
   CSCI 8351 Semantic Web Servers and Processes (4 hours)
   CSCI 8370 Advanced Database Systems
   CSCI 8380 Advanced Topics in Information Systems (4 hours)
   CSCI 8820 Computer Vision and Pattern Recognition
   CSCI 8950 Machine Learning (4 hours)

   Specialization in Ecology:

   ECOL(PBIO) 6580 Foundations of Ecology (2 hours)
   ECOL 8310 Population Ecology (4 hours)
   ECOL 8325-8325L Modeling Population Ecology (4 hours)
   ECOL 8580-8580L Theory of Systems Ecology ((4 hours)

   Specialization in Genomics and Proteomics

   PBIO(BIOL) 4550/6550 Bioinformatics Applications (3 hours)
   BCMB 8140 Genomics and Bioinformatics (3 hours)
   BCMB 8300 Advanced Proteomics (3 hours)
   MIBO(BCMB) 8270-8270L Composition, Organization, and Evolution of Genomes (3 hours)
   PBIO 6510 Genome Evolution Across the Tree of Life (3 hours)

   Specialization in Microbiological Processes:

   MIBO 6090 Prokaryotic Biology (3 hours)
   MIBO 8110L Electronic Exploration of Prokaryotic Biology (3 hours)
   MIBO 8600 Fundamental Processes of Prokaryotic Cell Biology (3 hours)
   MIBO 8610 Prokaryotic Physiology and Diversity (3 hours)

   Specialization in Microbiological Interactions:

   MIBO 6220 Bacterial Pathogenesis (3 hours)
   MIBO 6300 Environmental Microbiology and Biotechnology (3 hours)
   MIBO 6500 Bacterial Symbioses (3 hours)
   MIBO 8610 Prokaryotic Physiology and Diversity (3 hours)

   Specialization in Plant Genomics:

   PBIO 6510 Genome Evolution Across the Tree of Life (3 hours)
   PBIO 6720-6720L Plant Variation and Evolution (4 hours)
   PBIO 8100 Plant Genetics (4 hours)
   PBIO 8111 Plant Development (4 hours)
   GENE 8940 Genome Analysis (2 hours)
   GENE 8950 Molecular Evolution (3 hours)
   

   Specialization in Statistical Genetics:

   STAT 6320 Statistical Analysis II (3 hours)
   STAT 6810 Probability Distributions (3 hours)
   STAT 6820 Statistical Inference (3 hours)
   STAT 8090 Statistical Analysis of Genetic Data (3 hours)

   Specialization in Toxicology:

   PHRM 6910 Introduction to Toxicology (3 hours)
   BIOS 8100 Case Studies in Nonlinear Biostatistics (3 hours)
   EHSC 8510 Environmental Risk Assessment and Communication (3 hours)
   EHSC 8220-8220L PBPK Models (4 hours)
   
   

   Return to Table of Content

4. Foundation Courses for the Certificate Program

   This program will bring together students from widely different fields; hence, we have prepared a list of background courses, so that students will learn the necessary concepts and vocabulary of the various fields that intersect to form Bioinformatics. For example, students from Computer Science, Mathematics, or Statistics will be expected to take their background course in biology. Similarly, a student from Biology will be expected to take their background course in Computer Science or Statistics. An exception may be granted for an unusual student who already has a background in both of these areas. One of the following courses must be taken for the certificate program:
   BCMB 6000 General Biochemistry and Molecular Biology (3 hours)
   Proposed: BIOL/GENE 7200 Genetics (3 hours)
   Proposed: CSCI 7720 Data Structures (4 hours)
   BIOL/PBIO 4500/6500 Gene Technology (3 hours)
   CSCI 6470 Algorithms (4 hours)
   CSCI 7010 Computer Programming (4 hours)
   STAT 6310 Statistical Principles (3 hours)
   

   Return to Table of Content

5. Core Courses for the Certificate Program

   At least four of the following core courses must be taken:
   BCMB 8140 Genomics and Bioinformatics (3 hours)
   BCMB 8210 Computational Methods in Bioinformatics (3 hours)
   BCMB 8211 Advanced Methods for Biological Data Analyses (3 hours)
   MIBO 8110L Electronic Exploration of Prokaryotic Biology (3 hours)
   BIOL/PBIO 6550 Bioinformatics Applications (3 hours)
   CSCI 4490/6490 Algorithms for Computational Biology (4 hours)
   STAT 6630 Statistical Bioinformatics I (3 hours)
   GENE 8940 Genome Analysis (2 hours)
   

   Return to Table of Content

Graduate School Requirements

The Graduate School sets forth additional requirements concerning residence, time limits, programs of study, acceptance of transfer credits, admission to candidacy, minimum GPAs, dissertation, and examinations. The students should refer to the Graduate School Bulletin for details.

Return to Table of Content