Program in Biophysics Graduate Student HandbookDoctoral Degree Requirements«
Return to Table of Contents I. REQUIREMENTS
FOR THE DOCTORAL DEGREE A. GENERAL REQUIREMENTS
The Graduate College recognizes three stages in a Doctoral degree program, each
accounting for a minimum of 32 hours of course work (including 590 and
599 credits for research, where appropriate). The total credit should be a minimum
of 96 hours. Stage I: Course work taken in consultation
with the first year advisor or research advisor, culminating in the successful
passing of the Biophysics Qualifying Exam (BQE). Three lab rotations must be completed
by the end of the first semester, resulting in the selection of a research advisor.
If supported by a training grant, students are given to the end of the first year
to choose an advisor and complete their lab rotations. Stage II:
Research (Biophysics 599), culminating in the successful passing of the Preliminary
Exam. The Prelim must be passed by the end of the 3rd year. Stage
III: Research (Biophysics 599), culminating in the successful passing of the
Doctoral Exam. For the Ph.D. degree, a total of 32 hours of credit
in stage I must be obtained. The following courses are required#:
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i. Biophysics 401 (3 hours, must be completed in the first year) ii.
Biophysics 595A (research seminar) and 595B (faculty seminar) (5 hours total,
must be completed in the first two years) iii. Biophysics 586 (2 tutorials,
1 hour each, must be completed before Preliminary Exam) iv. Biophysics 581-83
(3 lab rotations, 2 hours each, must be completed in the first semester) v.
MCB 580 - ethics course (1 hour, must be completed in the first year) vi.
Two 500-level courses from the pre-approved Biophysics course list* vii. Additional
400- and/or 500-level biophysics, science, or engineering courses to make up a
total of 32 hours in i. through vii. # Most of these requirements
should be completed during the first two years, and definitely should be complete
prior to the Preliminary Exam. *500-level courses in other departments
may be petitioned to count towards the Biophysics and Computational Biology course
requirement if they are not on the pre-approved list, if the main content is biophysical.
Center approval should be obtained by students before registering
for non-approved courses, if students wish to be given credit. The Biophysics
& Computational Biology Office has a pre-approved list of courses available
to students. I. Tutorials and Lab Rotations The basic requirement
is for 3 lab rotations (Biophysics 581-583, 5-weeks in length, 2 hours
each) and 2 tutorials (Biophysics 586, 7-weeks in length, 1 hour each).
Tutorials may not be taken on the same topic as a lab rotation, though you may
take a rotation and a tutorial under the same professor, however, you may not
complete a tutorial with your advisor. All required lab rotations
must be taken and completed by the end of the first semester. A short
written report of 6-10 pages is required for each rotation. On the basis of the
lab rotations, students must select a research advisor by the end of the first
semester. This includes ensuring acceptance by the advisor. {NOTE: If
necessary, students the Molecular Biophysics (MBTG) Training Grants, along with
University fellowships, will be allowed the first two semesters to choose a research
lab and may take additional rotations, if desired. However, an early decision
is strongly recommended.} Each tutorial constitutes of meeting
with a faculty member at least once a week for a 7-week period, and culminates
in a written paper of 6-10 pages. Students should expect to submit two or more
drafts, for advice on both scientific content and writing skills. It is possible
to complete two tutorials in a single semester, with the second beginning the
eighth week of classes.
Beginning Sp09, any student wishing to become
involved with the Biophysics K-12 Outreach Program may substitute one semester's
worth of outreach activities for one tutorial. Prior project approval from the
Biophysics Director is required. II. Seminars All first
year students must take Biophysics 595A (Seminar) and Biophysics 595B
(Faculty Research Topics Seminar) in their first semester. At least 80% of the
class meetings must be attended for a satisfactory grade. Biophysics 595B will
only be required in the first semester. Students are required to continue
to register for Biophysics 595A (research seminar) until the end of their second
year, for a total of four semesters. III. Ethics Requirement
Graduate students in the sciences at the University of Illinois are expected
to have training in professional ethics. For this purpose, graduate students in
the Center for Biophysics and Computational Biology are required to take the ethics
course offered by the School of Molecular and Cellular Biology, MCB 580.
For more information regarding the course, which is offered each spring semester,
visit www.life.illinois.edu/mcb/580.
Students must enroll in this course in their first year of study.
IV. Grades/Grade Point Average (GPA) The University of Illinois
grades on a 4.00 point plus & minus system (A=4.00; B=3.00; C=2.00; D=1.00;
F(fail)=0.00). In order for the University to calculate the overall Grade Point
Average (GPA), the number of hours for a course is multiplied by the numerical
equivalent of the letter grade received. This is done for all graded courses and
the sum of all graded courses is divided by the total number of graded hours.
This is the GPA. The Graduate College minimum GPA requirement for biophysics
is 3.00 in all coursework. If a student's overall GPA is below 3.00 for
a semester, a warning letter will be sent from the Graduate College. If, after
the completion of additional graded hours, the GPA has not been raised, the student
will be placed on limited status. If the student is still on limited status
the following semester, they will not be allowed to register for subsequent semesters.
Students on limited status are also ineligible for degree conferral until the
limited status is lifted. In addition, the Center for Biophysics and
Computational Biology has a minimum GPA requirement of 3.00 for the courses in
i., iii.-vii above. If a student's GPA in these courses falls below 3.00
for a semester, a warning letter will be sent from the Biophysics Office. If,
after the completion of additional graded hours, the GPA has not been raised,
the student will be placed on probation, and can be asked to leave the Program.
Grades of S (satisfactory) and U (unsatisfactory) are given for seminar courses,
but not counted toward the GPA. Likewise, if a course is taken Credit/No Credit,
it is not counted toward the GPA. Hours for these courses will be counted toward
the total credit hours for the degree. 1. Deferred grades are
temporary grades given for work not completed for a lab rotation and for Thesis
Research (599). Thesis work will be graded DFR until the final examination is
passed, when an S or U grade will be granted. Incomplete work for a lab rotation
should be completed by the semester following the receipt of a DFR grade. The
professor must complete a Supplemental Grade Report form, assigning a letter grade,
before credit can be received for the course. 2. Excused grades
(I) are temporary grades given for courses where work is not completed before
the end of the semester. These must be cleared up before the reading day of the
following semester. "I"grades not cleared by the appropriate time will
become "FR" ("F by rule") and appear on the student's transcripts
as such. These are counted as F when computing GPA. Once the work is completed,
the professor must submit a grade change form to replace the FR with a letter
grade. V. Petitions For students who feel they have already
met a requirement through previous coursework; want to receive 500-level credit
for courses in other departments; want to be considered for an exception to a
requirement; or want to request an extension of time to complete a project or
degree; it may be possible to petition the Center for Biophysics and Computational
Biology and the Graduate College. Petitions must have the approval of the advisor,
the Center Director, and the Dean of the Graduate College. There are certain cases,
as with a departmental requirement (versus a university requirement), where only
the advisor and the Center Director need to approve the petition. An
official Student Petition Form must be completed by the student on the Graduate
College website (https://www.grad.illinois.edu/petitions/).
Once the student completes the form on-line, the document should be printed, and
the advisor's comments and approval obtained. The signed form must then be submitted
to the Biophysics and Computational Biology Office for the Director's signature.
The Biophysics and Computational Biology Office will submit the petition to the
Graduate College, if appropriate. The outcome of the petition will be forwarded
to the student (and the Biophysics and Computational Biology Office) electronically
by the Graduate College. B. TEACHING All Biophysics
and Computational Biology students are required to teach for a minimum
of one semester during their graduate career, though some students will be
asked to teach for additional semesters if their advisors do not have an alternative
means of support available. Students are strongly urged to complete this requirement
in their first few years in the program. There is a limited number of Teaching
Assistantships (TA) available through the Center for Biophysics and Computational
Biology itself. Most appointments are made through other departments, such as
Molecular and Cellular Biology and Physics. These TAships are highly competitive.
The Biophysics and Computational Biology Office will inform students
each fall and spring when the School of Molecular and Cellular Biology is accepting
applications. Students will be asked to complete an application on-line. Students
may also apply for TAships in other departments. Most applications are due the
semester prior to the proposed assignment (MCB TA applications for fall are due
in mid-April; those for spring are due in mid-November), so students should be
sure to submit applications to the appropriate departments well in advance for
full consideration. Sometimes TAships can be arranged through the advisor's lab.
This option should be discussed with the advisor directly. TA's are appointed
for 1 semester, though some departments offer an option to renew the next semester.
TAships are generally not offered over the summer, so other means of support must
be arranged. I. TA Orientation Before students are allowed
to act as TA's for a University course, they must pass the Graduate Academy
for College Teaching program. This program is usually held one week prior
to the beginning of classes in the fall and spring semesters. Students will attend
large and small group sessions; be videotaped teaching a short lesson; and have
the tape reviewed. (There are also follow-up sessions later in the semester that
offer further training opportunities. These are not required for Biophysics and
Computational Biology students, but may be attended if of interest to the students.)
II. English Proficiency Requirements 1. All non-native English
speaking international students must pass the Speaking Proficiency English
Assessment Kit (SPEAK) test before they can be enrolled in an orientation
session or be appointed as a Teaching Assistant. It is also a graduation requirement
of the University and of the Center for Biophysics and Computational Biology.
Even U.S. citizens or permanent resident aliens must sit for the exam if English
is not their native language. An exemption from the exam can be granted only if
a student attended both high school and college in English speaking institutions.
If any of the following have been passed prior to enrollment at UIUC,
the scores will be accepted in lieu of the SPEAK test:
TSE passed
with a score of 50 iBT* speaking sub-section passed with a score of 24
IELTS* speaking sub-section passed with a score of 8 *scores must be
less than 2 years old on the 1st day of class the semester the student enters
the U of I The SPEAK test is offered in March, July, and October only. Information
will be disseminated from the Biophysics and Computational Biology Office regarding
test dates and times. The exam is held at the Foreign Language Building and the
exams start promptly at the time indicated. Students taking the exam need to bring
a picture ID card and will need to arrive at least 15 minutes early to check in.
Results of the exam are sent to the Biophysics and Computational Biology
Office approximately two weeks after the test date. A score of 50 or higher is
passing. If a passing grade is not earned, the exam must be taken again the following
semester, but only after participation in language improvement activities have
occurred. These improvement activities include: taking an English as a Second
Language course (ESL 504 or 506 may be repeated); taking the Language Improvement
Workshop; or hiring a private, OIR-approved tutor for a minimum of 10 hours to
help improve English abilities. An appeal may be undertaken after receiving a
failing grade. Please see the Biophysics and Computational Biology Administrative
Coordinator for more information about the appeal procedures. Students are
required to take the SPEAK test each semester until they pass it, and it is a
requirement for successful passage of the BQE. As of 2002, the University
of Illinois only allows a student to take the SPEAK test three times. If the student
fails the exam the third time, they will be required to take one of the alternate
exams at their own expense until a passing score is achieved. 2. If
a student receives a score of 610 or less on the TOEFL test (253 on the computer
based test; 102 on iBT), they will also be required to take the ESL Placement
Test (EPT) when they arrive on campus. The score received on the EPT determines
the need for any ESL courses at the University of Illinois. These courses must
be completed before the student will be allowed to TA or graduate.
C. EXAMINATIONS There are three exams to be passed during the
program leading to a Ph.D. degree in Biophysics and Computational Biology.
I. Biophysics Qualifying Examination The first of these is
the Biophysics Qualifying Exam (BQE), which must be passed before the end
of the fourth semester of residence in the program. Students are expected to take
the exam in their first year. The exam is administered every spring semester and
may be taken twice, if necessary. The BQE has both written and oral
parts. The written BQE tests the student's general knowledge of Biophysics and
Computational Biology. It contains three sections (Experimental; Computational;
Fundamentals of Biophysics). Six questions (out of 12 available) must be attempted,
with at least one in each section. The oral BQE reviews biophysics knowledge further,
especially in areas not mastered on the written exam, and determines the student's
progress in course work, research, and other programmatic matters. The BQE committee
recommends to the faculty whether or not a student should pass and thus be admitted
to Ph.D. candidacy. Passage of Biophysics 401 (or equivalent) as well as biochemistry
and physical chemistry (or equivalent) are strongly suggested before attempting
to take the BQE. Regular attendance at seminars; study of past exams; and a good
knowledge of the Biophysics and Computational Biology faculty's research have
also proven to be helpful. Final decisions on admission of a student
to Ph.D. candidacy are made by the Biophysics and Computational Biology faculty,
and are based not only on the recommendation of the BQE committee, but also on
the total academic record, the student's research potential, and the nature of
the student's objectives and motivation. Formal admission to the Ph.D. candidacy
also requires that the student be accepted into the research group of a Biophysics
and Computational Biology faculty member who then serves as the student's official
advisor. As noted earlier, non-native English speaking international
students must pass the SPEAK test in order to satisfy the requirements of the
Qualifying Examination.
Rules for BQE Grading In order
to avoid confusion with complicated schemes of combinations of scores, here are
the simple BQE Guidelines:
A. 4 or more passes (out of 6 written questions
attempted): Students who receive 4 or more passes on the written BQE will
not be required to retake the written BQE. However, students may be asked
to retake the oral exam, depending upon their performance during the oral exam
on any of the questions they did not pass, and/or any unanswered questions about
their proposed research, progress with other program requirements, and related
matters. B. 3 or more fails (out of 6 written questions): Students who
receive 3 or more fails on the written BQE unconditionally must retake both the
written and oral portions of the BQE. C. All other scores Students
receiving scores not falling into either category A. or B. above should be prepared
for a thorough oral examination on the BQE questions. The BQE Committee will decide
the final outcome of the exam based on the performance at the oral: retaking the
oral, or retaking both the written and oral parts of the BQE. II.
Preliminary Exam The second exam, the Preliminary Exam,
examines the student's thesis proposal and his or her knowledge and ability to
pursue in-depth research in their chosen area. The primary purpose of the Preliminary
Exam is to examine the validity of the thesis proposal and to test the student's
fitness to carry out independent research. Students are expected to take the Preliminary
Exam before the end of their third year in the Program. Students are also expected
to have completed all coursework and tutorials prior to their prelim.
The exam is oral and is administered by an ad hoc committee recommended by the
student's advisor, who serves as the chair of the committee. The committee is
appointed by the Graduate College with the recommendation and consultation of
the Director of the Center for Biophysics and Computational Biology. A majority
of the four or more members of this committee must be members of the Graduate
College. A majority must also be members of the Biophysics and Computational Biology
faculty. It is the student's responsibility to ensure that the committee is appointed
at the appropriate time, at least three weeks prior to the proposed exam date.
The student requests that his/her advisor initiate the appointment of the committee
through the Center for Biophysics and Computational Biology Office. Additionally,
the Biophysics Office will need a copy of a Project Summary Report from the student
for their file. This is a one page, double-spaced summary, which can be used to
introduce research to the committee on prelim day! The Preliminary Exam
is based on a 20-30 page (double-spaced) thesis proposal presented to the committee.
The proposal should include an Introduction, Methods and Materials, Preliminary
Results, Proposed Work, and References. Figures and captions should be incorporated
into the text. It is the student's responsibility to see that the thesis proposal
is in the hands of the committee at least two weeks before the committee meets.
At the start of the oral exam, the student presents a 20- to 30-minute outline
of the proposed work. The committee then examines the student regarding facets
of the proposal that need clarification, and makes suggestions which may facilitate
the approach to the problem. Finally, the committee may raise questions of a more
general nature, to test the adequacy of preparation for the proposed work, and
general knowledge of Biophysics and Computational Biology. At the conclusion
of the oral examination, the chairperson of the committee will announce one of
four possible decisions: a. Passed b. The examination is adjourned
and will be reconvened at a later date. c. Failed, but the committee believes
that further preparation may enable the student to pass. At least one semester
of additional work must be allowed for such preparation. d. Failed and the
student will not be admitted to another examination. III. Final Exam
The third exam is the Final Exam, which is a presentation
and defense of the student's thesis work. The Final Exam committee is appointed
by the Graduate College upon the recommendation of the Director of the Biophysics
and Computational Biology and the student's thesis advisor. The student requests
his or her advisor to initiate the appointment of this committee through the Biophysics
and Computational Biology Office. The composition of the committee for the Final
Exam has the same requirements as for the Preliminary Exam and is usually the
same as that for the Preliminary Exam; however, a change in the direction of the
thesis may require changes in the committee. The Final Exam may not be taken sooner
than 6 months after the Preliminary Exam. Doctoral candidates must complete all
requirements for the degree so as not to exceed five years after their first registration
in the Graduate College. (See Petition section for exception to this rule.)
The final form of the thesis, at the time of deposit after a successful defense,
must conform to the rules specified by the Graduate College. At the time of the
defense, the thesis must be in essentially final form, except for binding, which
may be of any convenient type. The Final Exam is a public exam,
and the recommended format is a 50-minute formal presentation as a public seminar,
with a short question period from the audience. The examination committee will
then question the candidate in detail in a private meeting. At the conclusion
of the oral examination, the chairperson of the committee will announce one of
four possible decisions: a. Passed, and the committee will sign the Certificate
of Committee Approval forms. b. Passed, but with revisions and the committee
will sign the approval forms at a later date. c. Failed, but the committee
believes that further preparation may enable the student to pass. At least one
semester of additional work must be allowed for such preparation. d. Failed
and the student will not be admitted to another examination. The Graduate
College provides a handbook for thesis preparation and submission, which can be
picked up in Coble Hall, or accessed via the web at: www.grad.illinois.edu/thesis/thesishandbook/index.asp.
D. REQUIREMENTS FOR THE MASTER OF SCIENCE DEGREE Students
are not admitted into a program leading to a Master's degree. The Master's degree
is not normally awarded to students continuing toward the doctoral degree in the
program, or to students who are transferring to another PhD program on campus.
However, under certain circumstances, a student may be awarded a Master of Science
degree. The requirements for this are as follows: -
a total
of 32 hours of credit in biophysics courses and related subjects. -
10 hours of 500-level biophysics courses with a minimum GPA of 3.25. This 10
hours does not include seminar courses (Biophysics 595A/B) and/or research units
(Biophysics 590/599) and can include no more than 2 hours of tutorials (Biophysics
586). 500-level courses in other departments count towards this 500-level formal
course requirement if they are on the approved Biophysics course list. -
At least 4 hours of research (Biophysics 590 or 599) is required, with the
work presented as a thesis (which is submitted to the Graduate College after the
advisor's approval) or research paper (which is submitted only to the advisor
and/or Center Director). The paper should be a concise account of the student's
research, in the style and format of an appropriate scientific journal, except
that it should include a more detailed introduction to the area of investigation,
and it may include a greater degree of speculation in the discussion. Bibliographic
references should include complete titles. The paper should be between 10-50 typed,
double-spaced pages, excluding figures and numbered references, which should be
attached to the paper. The evaluation of the paper will be made by the
student's Biophysics 590/599 advisor. The advisor has the option of calling for
an oral examination based on the research paper/thesis. Additionally, the Center
Director will review the paper. After the evaluation of the paper, one of three
possible decisions will be made by the Center Director: a. The paper
is approved, and the student passed the examination. b. The paper should be
revised and resubmitted within one month. c. The student failed the examination.
E. SATISFACTORY ACADEMIC PROGRESS Unless there are
very unusual circumstances, the following conditions must be met in order for
a graduate student to be considered as making satisfactory academic progress,
and to be eligible for reappointment as an assistant or trainee: o A student
should give evidence of continuous effort and progress. Beginning with the end
of the first academic year, and thereafter, the student should give evidence of
continuous effort and progress in research. -
A student should
complete 32 hours of courses by the end of three semesters, following the outlines
of the program requirements (above). If this condition is not fulfilled, he/she
will not be appointed as a graduate assistant/trainee after that time without
special permission from the Center for Biophysics and Computational Biology Director.
This rule does not apply to special status students. -
Students
should enroll for the maximum amount of course credit (including 590 and 599)
for which they are eligible, usually 12-16 hours per semester (8 hours in the
summer). A minimum of 8 hours of course work is required at all times, except
with permission from the Center Director. International students must maintain
an enrollment of 12 hours for the fall and spring terms to maintain their visa
status. -
A doctoral student should complete all requirements
for the degree not later than five years after entering graduate school with the
B.S. degree. Continuation beyond this time requires special permission from the
Center for Biophysics and Computational Biology Director and the Graduate College,
in response to a petition from the student's research advisor. -
A student who has a GPA below 3.0 after two semesters will be considered as
making unsatisfactory academic progress. -
A graduate assistant
who performs inadequately, or irresponsibly, in a teaching or research position
may be removed from the position with no commitment of alternative support.
Annual Review
The Center for Biophysics and Computational Biology
holds annual reviews for all students. This process helps keep students on track
toward the timely completion of their degree. The initial stage of review consists
of a written Progress Report from the Biophysics & Computational Biology Office
each year, which lists all requirements met and those still outstanding.
If deemed necessary, the director or advisor can call for a more thorough review
by a small faculty committee, consisting of two to four members. This committee
can be a potential Prelim and/or Final Exam committee. These reviews will help
facilitate working relationships between faculty and students, and provide the
student with more contacts who may be aware of new or alternative methods or studies,
something a single advisor may be unaware of. The reviews by progress
report and/or committee are mandatory for all students. If requested, students
are to provide their committee with a two-page synopsis of the work that has been
completed, and the progress they have made each year. This synopsis will be reviewed
by the committee and discussed with the student at a brief meeting, to be arranged
by the student. The Biophysics and Computational Biology Office will
monitor the review process. The Office will remind the appropriate students to
make preparations for these annual meetings, and keep records of the recommendations
of their committees. F. DEGREE CONFERRALS When it is
time to set up the final defense, students should first arrange a meeting with
the Center Administrative Coordinator, as early as possible to verify that all
the Center requirements necessary to graduate have been fulfilled.
Please be sure to verify all deadline dates with the Center Administrative
Coordinator or Graduate College early in the semester prior to the
planned graduation, to ensure the timely deposit of the appropriate forms and
paperwork. Ph.D. degrees are conferred three times a year: May, October and
December. (Ph.D.'s, unlike Master's degrees, are not conferred in August.)
As mentioned before, copies of the Handbook for Graduate Students
Preparing to Deposit booklet are available from the Graduate College, which
is located on the 2nd floor of Coble. It is also located on the web at www.grad.illinois.edu/thesis/thesishandbook/index.asp.
The Handbook gives complete instructions on the official University policies,
procedures and preparation of the thesis. - Students should indicate,
while registering via UI Integrate/Enterprise that they plan to graduate
in the appropriate semester, or alternatively, an Application for Degree
(pink) form can be completed and submitted to the Graduate College by the designated
due date. This should be done early in the semester the student plans to
graduate. If a student fails to meet the requirements for a certain degree conferral
date, a new form must be completed again the following semester to add the name
to the degree list - it will not automatically roll over to the following degree
list.
- Students, working with their research advisor, must select
the final committee and inform the Biophysics and Computational Biology Office,
at least three weeks before the exam. Arrangements for the defense date,
time, and location of exam must also be made by the student. The Biophysics
and Computational Biology Office will complete the required paperwork and submit
to the Graduate College. Please leave plenty of time to meet the Graduate College
final examination date. The Graduate College approves of the committee members
and sends the Result of Examination form to the Biophysics and Computational
Biology Office. Arrangements must be made to pick up this form from the office
on the date of the exam.
- A copy of the thesis must be
submitted to the Center Office for the department format check, after the final
defense. At that time, the department format check form for thesis submittal
to the Graduate College will be completed.
- The Final Exam
must be passed at least one and one-half months before the graduation date.
Students must be registered during the semester that the final defense is taken.
[NOTE: If a student is registered for the summer and defends prior to the final
degree examination date for the fall semester, the student does not need to register
for the fall. However, if the thesis is not deposited until the appropriate deadline
(generally in early October or December - depending on what graduation date is
anticipated) the decision not to register will affect student insurance and any
RA appointments held, both of which require the student to be registered.] Please
see the section on Exams for specific information on the Final Exam process.
- The thesis committee will need to sign the Certificate of Committee
Approval forms, as well as the result of examination form, at the time of
the final exam. Certificate of Committee Approval forms can be found on the web
at www.grad.illinois.edu/forms/certificate/index.htm.
It is the student's responsibility to prepare at least 2 of these forms for
their committee's signature. The result of examination form must be returned
to the Center office immediately after completion of the oral exam, for submission
to the Graduate College.
- The final thesis, signed Certificate
of Committee Approval forms, and department format check must be deposited,
by the student, to the Graduate College at least two and one-half weeks
before the graduation date. Please be sure to make arrangements for the Center
Director to sign the Certificate of Committee Approval forms, as they are invalid
without the department head's signature.
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