College of Science
Faculty Advisor Handbook
This handbook describes policies and procedures for the faculty advisors of M.S. and Ph.D. Bioinformatics students in the College of Science (COS) at George Mason University. Advisors of an academic program are responsible for the student's program of study as well as providing information about specific courses and degree requirements. Progress within the M.S. or Ph.D. Bioinformatics program is the shared responsibility of the student and the advisor. The graduate student is responsible for compliance with the policies and procedures as provided in the Bioinformatics Student Handbook.
∑ Bioinformatics, Ph.D.
∑ Certificate in Bioinformatics
There are several different types of admission status used in the Bioinformatics programs, as explained below:
1. Ph.D. Degree Status - Full admission as a degree-seeking student in the doctoral program. The student may be enrolled either full-time or part-time.
2. Provisional Ph.D. Status - Provisional admission* into the doctoral program. The student may be enrolled either full-time or part-time.
3. M.S. Degree Status - Full admission as a degree-seeking student into the masters program. The student may be enrolled either full-time or part-time.
4. Provisional M.S. Status Ė Provisional admission* into the masters program. The student may be enrolled either full-time or part-time.
5. Certifticate in Bioinformatics - Students may not enroll initially in any COS non degree, M.S., or Ph.D. program, then later transfer into this certificate program. The Certificate in Bioinformatics charges students a differential tuition rate of $100 per credit hour, which is added to the standard GMU graduate tuition rate (regardless of in or out of state status).
6. Non-Degree Status - Non-degree students are not admitted into the Bioinformatics program, but may take up to 12 credit hours of coursework which may be applied to a degree program at a later date if approved. Students who later choose to seek admission to a degree program must reapply for admission using the regular graduate application.
*Note: Provisional admission into the Bioinformatics degree programs may be offered to students who have a GPA below 3.0 or who may require additional preparation in either Biology, Mathematics, or Computer Science. In such cases, the admissions letter will indicate courses that the student must take (usually before enrollment or during the first year in the Ph.D. or M.S. program). Upon successful completion of the indicated courses with a minimum average GPA of 3.0, the student will be notified by letter that he/she has advanced from provisional status to degree status. This change in status will also be documented in the studentís file. All credits of graduate level work earned during provisional status will be applied toward the degree program unless otherwise stated.
The following requirements are applicable to the Master's Degree:
1. Only graduate courses may apply
toward the degree.
2. The majority of the credits applied to the degree must be earned at George Mason University.
3. A minimum of 19 credits have to be taken in degree status (after admission to the degree program).
4. A maximum of 6 credits of master's thesis research (BINF 799) or master's project (BINF 798) may be applied to the degree.
5. A candidate must have a minimum GPA of 3.0 in course work presented on the degree application, which may include no more than 6 credits of C. (The GPA calculation excludes all transfer courses and George Mason Extended Studies not formally approved for the degree).
6. A student has six years from the time of first enrollment as a degree-seeking student to complete their degree.
7. Candidates must successfully complete 31 credit hours as follows:
- 12 credit hours of bioinformatics core courses: BINF 630, 631, 634 and 734
- 3 credit hours of advanced bioinformatics courses numbered BINF 730 and above
- 9-12 credit hours of electives in bioinformatics and computational biology, biology and biotechnology, or computational sciences, as approved by the advisor
- 1 credit hour of bioinformatics colloquium, BINF 704
- Research component: 3 credit hours of BINF 798 (Research Project) or 6 credit hours of BINF 799 (Masters Thesis); exercise of the thesis option results in a corresponding reduction in the electives requirement
The following requirements are applicable
to the Doctoral Degree:
1. Only graduate courses may apply
toward the degree.
2. The majority of the credits applied to the degree must be earned at the George Mason University.
3. More than half of all credits have to be taken in degree status (after admission to the degree program).
4. A candidate must pass a written (comprehensive) candidacy exam.
5. A candidate must complete a minimum and maximum of 24 credits of BINF 998 (doctoral proposal) and BINF 999 (doctoral dissertation) to be applied to the degree.
6. A candidate must pass a final, public defense of the doctoral dissertation.
7. A candidate must have a minimum GPA of 3.0 in course work presented on the degree application, which may include no more than 6 credits of C. (The GPA calculation excludes all transfer courses and George Mason Extended Studies not formally approved for the degree).
8. A student has six years from the time of first enrollment as a degree-seeking student to become advanced to candidacy. Students have five years from the time of advancement to candidacy to graduation.
9. Candidates must successfully complete 72 credit hours* as follows:
- Fundamental bioscience courses (12 credits): BINF 701, 702, plus 3 credit hours each of BINF 703 (lab rotation) and BINF 704 (colloquium)
- Core bioinformatics courses (13 credits): BINF 690, 705, 730, 731, and either 732 or 740.
- General electives and independent research (23 credits)
- Dissertation research (24 credits): 12 credits of BINF 998, plus 12 credits of BINF 999**
* For those holding a previous master's degree, the 72 required credit hours may be reduced by up to 30 credits, depending on graduate courses completed.
** With the Academic Dean's approval, the combination of 998/999 credit hours may vary from 12 each, as long as there are 24 total.
Graduate students are considered full time if they are enrolled in at least 9 credits per semester, or if they hold a full time assistantship (20 hours a week) and are enrolled in at least 6 credits per semester. Graduate students who are enrolled in dissertation credits (either 998 or 999) are considered full time if they are enrolled in at least 6 credits per semester, regardless of whether they hold an assistantship. Graduate students who have completed the minimum number of credits required by their degree program, including the minimum number of credits of 999 required by their degree program, are considered full time if they are registered for at least 1 credit of 999, and their advisors and department chairs certify each semester that they are working full time on the dissertation. Note that different criteria for full-time status may apply for tuition, verification, and financial aid.
Graduate credit earned prior to admission
to a master's or doctoral program may be eligible to be transferred
into the program and applied to the degree. Transfer of credit
requires the approval of the Bioinformatics Program Director and the
Assistant Dean of Acadmics of the College of
Science. Credit is usually considered for transfer
at the request of the student at the
time of initial registration as a degree-seeking student.
supply official transcripts (plus an official transcript evaluation for
transcripts from outside the U.S.). Credit transfer requests from
who are admitted provisionally are not considered until they have
the conditions of their admission and had the provisional qualifier
from their records.
To be eligible for transfer credit, the
credit must be graduate credit earned at another accredited university,
or earned at George Mason while in a non-degree status. The
credit must have been earned within six years prior to first enrollment
as an admitted student
in the M.S. or Ph.D. degree program, and a minimum grade of B (3.0)
have been earned. The course must be applicable toward a degree
at the institution offering the course. Extension and in service
courses that are not intended by the institution offering the courses
to be applied to a degree program are not eligible for transfer credit
to George Mason. The credits cannot have been previously applied
toward a degree at another institution or
at George Mason.
The student may obtain a Transfer of Graduate Credit form at the Bioinformatics program's Student Coordinator's office. This form should be filled out by the student and given to their academic advisor for review, and then submitted to the Program Director before being sent to the Assistant Dean of Academics. All courses requested for transfer must have a description attached. The student must supply the course description from the previous institution in either a URL or course catalog format. COS will allow up to 12 credit hours from another institution, or from GMU (if they have not been applied towards another degree) to be transferred into the M.S. Bioinformatics, and up to 24 credit hours from another institution, or from GMU (if they have not been applied towards another degree) to be transferred into the Ph.D. Bioinformatics program. Up to 12 non-degree credit hours from GMU will be allowed by COS to be transferred into both the M.S. and the Ph.D. programs.
Reduction of credit is limited to a maximum of 30 credits in the Ph.D. Bioinformatics program. There are no reductions of credits hours available for students in the M.S. program. Students requesting a reduction of credit must supply official transcripts (plus an official transcript evaluation for transcripts from outside the U.S.) Reduction of credit requires the approval of the Bioinformatics Program Director and the Assistant Dean of Acadmics of the College of Science, who will determine the number of credits to be reduced and whether the credits are applicable to the degree program.
The student may obtain a Reduction of
Credit Hours form at the Bioinformatics program's Student
Coordinator's office. This form should be
filled out by the student and given to their academic advisor for
review, and then submitted to the Program Director before being sent to
the Assistant Dean of Academics.
Students in the Bioinformatics programs
may have a course waived or substituted
with approval from their advisor, the Program Director, and the
Assistant Dean of Academics. Subsitutions may be requested for
required courses within a program, and are only allowable if one GMU
course is substituted for another. All courses being used as
substitutes for program requirements must appear on the student's GMU
internal transcript at the time of the request. A waiver of a
course in the Bioinformatics program may be
allowable if the student has had a similar course at another academic
The student must supply the course description from the previous
institution in either a URL or course catalog format, as well as the
official transcript showing the course completed. The student may
obtain a Subtitution
and Waiver form at the Bioinformatics and Computational Biology
program's Student Coordinator's office.
A student may withdraw from a semester
after the end of the drop period without academic penalty only for
non-academic reasons. The Application for Withdrawal form
can be obtained by
the student in the Bioinformatics and Computational Biology program's
Student Coordinator's office. This form will need to be
accompanied by a doctor's notice if the student is withdrawing
due to a medical condition, and will need to be approved by the
Assistant Dean of Academics. It is advisable that the student
withdraw from all courses during the semester the request is
petitioned. If a student stops attending classes without the
approval, they will receive Fs in all courses.
A graduate student that has passed a course with a grade of B- or better is not permitted to repeat the course for credit. The student must obtain permission from the Program Director to repeat of course in which a grade of C or below has been earned. When a course is repeated, all credits attempted are used in determination of warning, termination or dismissal. The student's transcript will show grades for all courses attempted; and only one grade per course may be presented on the degree application.
Once the Office of the Registrar has
recorded a final grade in a course, it can be changed only in cases of
computational or recording error, or pursuant to a successful appeal of
grade, as described below. Additional work of any type submitted to
improve a grade after the final grade has been assigned and sent to the
Office of the Registrar is never accepted. All changes of final
grades must be initiated, approved, and recorded by the last day of
classes of the next regular semester (The following spring semester for
fall courses, and the following fall semester for spring and summer
The conditions and time limits for changes from the temporary grades IN, IP, AB and SP, to final grades, appear in the university catalog and can be reviewed on this webpage:
During the M.S. or Ph.D. student's first
of enrollment in the program, an advisor folder is prepared and given
the temporary advisor. The advisor should use this folder to maintain
of forms 1-5 (see Doctoral Program Procedures below), or any other
that relate to the academic progress of the student. If a student
to change their advisor while enrolled in the program, the current
must deliver the student's folder, along with all of it's contents, to
new advisor and notify the Bioinformatics program's Student
Coordinator's office of the change.
Graduate course work is
measured in quantity and quality. A graduate student who receives
a grade C, F,
or IN in a graduate level course, will receive an academic warning on
their transcript. Academic termination may result if a
student fails to meet the conditions of their admission in the time
set at admission, or if they accumulate either grades of F in two
or nine credits of unsatifactory grades (C or below) in their graduate
Students who are terminated are on longer eligible to take
courses in the
Bioinformatics program, but may apply to
degree program within GMU.
Academic dismissal may result if a fully admitted graduate student accumulates either grades of F in two courses, or nine credits of unsatisfactory grades (C or below) in graduate courses. A student may also be dismissed for failure to pass doctoral competence examinations, or failure to show satisfactory progress in his or her doctoral dissertation research. The notation of academic dismissal is affixed to the graduate student's official record and they may not take additional course work at the university.
There is a required research component in
the Bioinformatics M.S. degree program.
to satisfy this program requirement, a student has two options: a
or a project. Once the student picks a topic, he/she should meet
with their advisor to discuss the details. Students employed at
organizations may take up to 6 credits for bioinformatics work done on
job under the guidance of a faculty member or advisor. This
project may be applied either as a 3 credit research project (BINF 798)
as a 6 credit master's thesis (BINF 799).
Once the student selects either the thesis
or project option, a brief abstract of the research proposal is sent to
the Program Director for review and final approval on the M.S. Research
Proposal form. If the research proposal is approved, the student
may enroll in 3 credit hours of research (BINF 799 or 798)
at the beginning of the next semester. Once the student has only
hours remaining of thesis research, they may enroll for one credit hour
per semester until graduation. Graduate students must maintain
enrollment while writing and submitting a thesis.
The master's thesis committee is approved
by the Department of Bioinformatics and Computational Biology Chair,
designate a member of the faculty (usually the advisor) as the thesis
committee chair. The committee consist of at least three persons:
two must be faculty members from the Bioinformatics program, and
one may come from outside the
program. The committee is responsible for directing and guiding
the student's research and writing activities, while the student
is responsible for keeping all committee members informed of the scope,
plan, and progress of both the research and the thesis.
The original master's thesis and one copy,
with two original signed cover sheets must be deposited with the
Bioinformatics Program Director, and later
signed by the Assistant Dean of Academics, before being transferred to
the University Libraries. For degree conferral, two copies with
cover sheets signed by the committee, director and dean must be
submitted to the library by 5 p.m. on the last
Friday of classes.
Sample schedule for M.S. student with
At least one elective must be numbered 730 and above.
Fall semester (1st year) - 630, 631, 634
Spring semester (1st year) - 734, (2) electives
Fall semester (2nd year) - (3) electives
Spring semseter (2nd year) - 704, 798
Sample schedule for M.S. student with
At least one elective must be numbered 730 and above.
Fall semester (1st year) - 630, 631, 634
Spring semester (1st year) - 734, (2) electives
Fall semester (2nd year) - 704, (2) electives
Spring semseter (2nd year) - 799 (6 credit hours)
Sample schedule for Ph.D. student:
Fall semester (1st year) - 690, 701, 702
Spring semester (1st year) - 703 (1 credit hour), 704, 705, 730, 740
Fall semester (2nd year) - 731, 732, 703 (2 credit hours), 704
Spring semseter (2nd year) - 704, (2) electives or 998
Fall semester (3rd year) - (2) electives, 998 or 999
Spring semester (3rd year) - (2) electives, 998 or 999
Advisors must be aware of a typical
academic timeline for the doctoral student in the Bioinformatics
program. The timeline below is structured
for a full time student in the program, but can be adjusted for a
student in part time status.
For further explaination on the Ph.D. timeline, and for
when to file Ph.D. forms 1-5, see the Doctoral Program Procedures.
1. During the first semester in the
program the student will take the computational assessment exam.
2. By the end of the second year in the program the student should have completed their written (comprehensive) exam.
3. Within one year after the completion of the written exam, the student should present their proposal defense.
4. Within two years after the proposal defense, the student should present their dissertation defense.
A student has six years from the time of first enrollment as a degree-seeking student to become advanced to candidacy. Students have five years from the time of advancement to candidacy to graduation.
The Bioinformatics Ph.D. program includes several important milestones that are documented in the student's file using program forms that are available online and in the Student Coordinator's office.
The student should meet with the temporary advisor to create a preliminary listing of anticipated coursework, which is documented on Form #1. Credits from a previous graduate program should be listed on this sheet. Credits taken in Extended Studies or in non degree status at GMU should also be listed. These forms are usually completed during the initial meeting with the temporary advisor.
II. Program of Study
1. Once a student has completed over half of his/her required courses, which should be during the 2nd year of full time study, the student is to begin work with his/her temporary advisor to select a general area of scientific investigation and to identify possible dissertation directors. The student begins to communicate with those faculty members and finally selects a faculty member who is willing to become the dissertation director. The committee membership is documented on Form #2.
2. Students are encouraged to sign up for a Lab Rotation, as a means of investigating the area of research they might wish to pursue.
3. The dissertation director has the primary responsibility for leading the technical direction and content of the work of the student. The dissertation director must be a member of the Bioinformatics program faculty or a well qualified scientist external to GMU. The appointment of the dissertation director must be approved by the COS dean.
4. A dissertation committee
formed by the student with the consent of the dissertation director,
the Bioinformatics Program Director, and the
COS dean. The
committee is to consist of a minimum of three members including the
dissertation director and committee chair (who must be a program
faculty and can be the dissertation director). At least two members of the
must be Bioinformatics program faculty
members and at least one must
outside the Department of Bioinformatics and Computational Biology. Non-GMU members may serve on the
with the consent of the Bioinformatics program faculty members on the
committee. The final membership must represent
at least two
areas. Once the committee is formed, the
Form #2 listing the committee members must be completed
and approved by all committee members, the graduate coordinator, and
the COS dean.
5. For students requesting 998 and 999 credit hours, it is required that they meet with their committee members prior to the start of each semester. The student must show satisfactory progress with his or her research in order to obtain a section of 998 or 999 for the upcoming semester. If a committee exists, all members must agree on the student's satisfactory progress, or make a recommendation if the student is failing to do so. The Dissertation Proposal and Research Progress form should be completed by the student and his or her advisor during the progress review meeting. A student's failure to make satisfactory progress in his or her dissertation research for two consecutive semesters may result in termination from the program.
6. The purpose of the dissertation committee is to guide and direct the student to ensure that the student has the capability to conduct first-rate research and that the dissertation work is of publishable quality in the discipline or interdisciplinary fields of computational sciences and informatics. A primary role of the committee is to test the student in accordance with the policies of the School.
7. The chair of the committee is an Bioinformatics program faculty member who is familiar with COS and university policies and procedures regarding the advancement of a student through the entire process leading to the doctorate. The chair is responsible for organizing all meetings of the committee and ensures that the proper process is being followed. The chair is to work closely with the dissertation director to ensure the consistency and the quality of the examinations and the dissertation work.
8. A faculty member may leave the committee at any time. The replacement member must receive the consent of the rest of the dissertation committee members, the graduate coordinator, and the COS dean. A new Form #2 must be completed and submitted for approval.
9. The student develops a program of study to include graduate courses taken prior to admission, extended studies courses, and Bioinformatics coursework. An area of concentration, proposed date of exam, and dissertation title are included on this form. All committe members, the graduate coordinator, and the COS dean must approve the program of study as shown on Form #2.
1. The Candidacy Examination consists of written, oral, and computational parts. All parts are mandatory.
2. It should determine
mastery of fundamental knowledge and familiarity with current research
in topics that contribute directly to the dissertation research area.
3. The computational exam
will be given as an assessment exam during the first semester of
enrollment in the program. Students who do poorly on this entrance exam
required to take BINF 634 and/or BINF 734.
4. The written (comprehensive) exams will be given once a year in January. The exam schedule will be announced through the Student Services Coordinator. Students will be allowed two attempts to successfully pass the exams.
5. The comprehensive exam will be composed of six exam topics; 1) protein structure analysis, 2) research methods, 3) biological sequence analysis, 4) numerical methods for bioinformatics, 5) cellular and biochemical systems modeling, and 6) genomics. Although there is no specific exam named, students should be knowledgeable in the area of molecular, cellular and biochemistry of the cell, since this information is essential for understanding the field of Bioinformatics.
written exams will be administered and taken on campus and completed
without collaboration, in an assigned room. The
format of the written comprehensive exam may change from year to
year. Details of the exam format will be announced to the
students one month prior to the scheduled exam date.
7. Students must show competency on all six parts and a high degree of competency on four of the six parts of the written exams.
8. The computational assessment and the written exams are graded by faculty members of the Bioinformatics program. The student will be informed of their results in a timely manner.
9. The Proposal Defense will be scheduled and administered by the committee, and will include discussion of the student's proposed dissertation research (see Doctoral Dissertation Proposal below).
10. Students are allowed two attempts to successfully pass the Proposal Defense.
1. Students must prepare a
Dissertation Proposal Defense that will consist of a written proposal
and a oral
presentation to the committee. This proposal
should include a statement of the problem, relevant background
preliminary results and a proposed research plan with a time line.
2. The proposal should be given to the student's committee at least two weeks prior to the scheduled proposal defense date. An abstract of the proposal is submitted on Form #3.
3. Proposals should contain sufficient text, illustrations, tables, equations, and bibliography.
4. Proposals should discuss hardware/software issues including computational tools/techniques to be utilized in the research.
5. Proposals should include
clear set of goals, methods, and models, and a discussion of the
expected results and their anticipated significance. The
discussion should also include any limitations on the generality of
6. The student will make a 15-20 minute
presentation of the proposal to his/her Doctoral Dissertation Committee
and other members of the academic community. There will then be a
closed session for discussion of the proposal in which the student will
answer questions about the proposal and background material needed to
successfully complete the proposal.
7. The proposal defense should be done within a
of passing the comprehensive exam.
8. Proposals must be
approved by the dissertation director and the dissertation committee
and will be reviewed by the graduate coordinator and filed in the
1. After successful completion of all portions of the Candidacy Examination and the approval of the Dissertation Proposal, the student is advanced to candidacy. Advancement to candidacy is documented by Form #4.
2. After submission of Forms #2, #3, and #4, the student will now be advanced to candidacy and the COS Administrative Office will notify GMU records office. The studentís record will then convert to doctoral candidate.
3. Once advanced to candidacy, students must be continuously enrolled in a minimum of three credit hours per semester (however, see item 3 below for exceptions).
1. Once a student has a fully approved dissertation committee and has completed most of the required courses or is within a semester or two of taking the Comprehensive Examination, the student may begin to register for BINF 998, Doctoral Dissertation Proposal, to develop a proposal to present to the dissertation committee, or to work on the dissertation.
2. Once a student has reached candidacy by passing the Comprehensive Examination and having the Dissertation Proposal approved by the committee, then the student must be continuously enrolled in BINF 999, Doctoral Dissertation Research, while working on and completing the dissertation.
3. The total number of credits of BINF 998-999 must be 24 for graduation (only 24 can be included in program requirements). Furthermore, the number of 999 hours should be at least 12 credits. Having reached candidacy, the student must enroll in at least 3 hours of 999 each semester until the last three dissertation hours are reached. Once the student has three or fewer hours remaining, the student may register for one credit of 999 and be considered a full-time student. The student must take at least one credit of 999 during the semester of their graduation.
1. A dissertation is a written piece of original thinking and independent performance that demonstrates the doctoral candidate's mastery of the subject matter, methodologies, and conceptual foundations in their chosen field of study.
2. Content should:
a. be relevant and current in the chosen area
b. demonstrate an understanding of research and development issues
c. demonstrate a mastery of computational tools or techniques
d. make a contribution through either new results or new techniques
e. be of publishable quality
3. Note: A pre-defense and defense of
the dissertation must
be scheduled as follows:
Guidelines for the content and general format of the doctoral dissertation may be found at www.gmu.edu/library/specialcollections/dtwebguide.htm. Please contact Robert Vay at (703) 993-2222, Fenwick Library, for step-by-step instructions on preparing the dissertation.
1. Students may access Graduation information on the web at MasonLink. The URL is http://registrar.gmu.edu/gradchek.html. They must complete a Graduation Intent Form. This can be done online.
2. The Application for Graduation must be completed by the student and signed by the Program Director. It is received in the Administrative Office for verification and the COS dean's signature. A copy is made for the student's file and for verification of the program requirements. It is forwarded to the graduation section of the Registrarís office. This form is also available on the web at the same URL as above.
Summer March 31
Fall October 31
Spring March 31
Summer July 15
Fall November 15
Please note that the above dates are approximate and can change each semester.
1. When the
doctoral dissertation thesis is completed, a candidate must arrange
with his/her committee to schedule the final defense. After
verifying a date with members of the committee, contact
the Student Coordinator for the Bioinformatics program to schedule a
2. A mandatory pre-defense of the dissertation must occur at least one month prior to the final defense. All committee members are required to attend.
dissertation must be given to the student's committee for reveiw at
least two weeks before the pre-defense and/or final defense is
4. It is the responsibility of the candidate and his/her committee to correct any errors in thesis content. After review by Robert Vay, firstname.lastname@example.org, Special Collections, Fenwick Library, the candidate must bring a draft to the Johnson Center Library for review by the GMU community. The Bioinformatics student coordinator will prepare a flyer announcing the candidateís dissertation topic and final defense date. This will be distributed to the GMU community and must be posted at least two weeks prior to the public defense.
5. After the final defense, the candidate must obtain all required signatures (in black ink) and submit the following documents to Robert Vay, wing 2C, Fenwick Library:
a. Three original signature sheets (black ink). Please type out the members names next to their signatures on bond paper.
b. Two original copies of complete dissertation on 100% cotton bond paper.
c. One copy for microfilming with $50.00 check and completed application form to UMI Dissertation Services.
d. Completed National Research Council Survey.
e. Please submit a copy of your dissertation and your defense of Doctoral thesis form (Form #5) to the Bioinformatics program office.
6. The candidate is responsible for getting his/her thesis bound for COS archives. We suggest brown or rust color with dissertation title and candidateís name on the spine of the book. Please refer to the COS graduates' theses available for review in the COS office in Fairfax. They may not be removed from room 103.
 To apply previous graduate credits to the program, the Transfer of Graduate Credit form (Ex. D) must be completed. For Extended Studies credit, complete Transfer of GMU Extended Studies form (Ex. E).