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Program in Biophysics Graduate Student Handbook

Doctoral Degree Requirements

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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#:

  • 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.