Degree Requirements for the PhD in BCB

Progressing through the BCB degree program

Information for students on how to progress through the main components of the BCB degree program are below.  The BCB Student Handbook also contains complete information on the degree requirements for students in the BCB Graduate Program. 

A summary of course requirements for the PhD and MS degrees, and for the minor and co-major degrees, as well as a timetable for completion of the course requirements, is also below.

The forms and publications page contains links to information and forms which are necessary to progress through your degree program.

Rotations

The Purpose of Rotations - An important aspect of the BCB training program is participation in Research Exploration Rotations. Participation in three research exploration rotations is required for all first year BCB students. The rotations serve several purposes:

  • They are designed to help students choose their future major professors and to help professors choose graduate students;
  • They provide students an opportunity to actively participate in research projects of BCB faculty laboratories; and
  • They promote interaction and exchange of information among BCB research groups.

Selecting a Lab for Rotation - The selection of labs for rotations should be guided by the following:

  • At least one rotation must be a "wet" laboratory experience (usually in a biological science laboratory using molecular biological, biophysical or biochemical techniques).
  • At least one rotation must involve a strong computational component (usually in a research group in computer science, mathematics, physics, statistics or engineering).
  • Students are strongly encouraged to participate in rotations in at least two different departments.
  • A discussion of available funding should take place before the rotation commences to make sure funding will not be an issue, if they join the lab.

Faculty interested in having students rotate through their labs this Fall and in Spring, 2016, are here. Faculty who had rotations in the past are also listed. Links to their home pages are provided so you can become familiar with their on-going research projects. Some also have brief descriptions of potential rotation projects you might be involved with if you rotate in their labs.

More information can be found on rotations here.  A helpful document can be viewed here: Rotation-How-Tos.pdf

Selecting a Major and Co-Major Professor

Much of the first year will be devoted to the important process of selecting a major professor. After completing research exploration rotations, students should contact their potential major professors to discuss the possibility of joining their laboratories. First-year BCB students must choose a major professor and notify the BCB program office of their choice by April 13 for the PhD.

The major professor will assist the student in choosing an appropriate co-major professor. BCB requires that the major and co-major professor (one from the biological sciences and one from the computational/quantitative sciences) actively serve as joint mentors for the student. The co-major professor must be chosen prior to filing the on-line Program of Study/Committee (POSC) form. The co-major professor should also be designated as a major professor on the POSC form.

The co-major professor plays an integral role in the mentoring of BCB students. Ideally, major and co-major professors have active research collaborations, and share the responsibility for funding the student (by arranging a research or teaching assistantship). BCB PhD projects typically emerge from research collaborations between the co-major professors and the student. If this is not the case, it is still expected that the co-major professor will meet regularly with the BCB student to help guide dissertation research. The selection of a co-major professor, therefore, is an important decision and should be given careful consideration.

More details are in the BCB Graduate Handbook and here is another page with more details on this topic.

Establishing a Home Department

For administrative purposes, the major professor's department becomes the student's Home Department. After choosing a major professor, students must initiate a Request to Establish a Home Department for Students Admitted to Interdepartmental Majors form (see the Forms section) and submit it to the BCB administrative office. All BCB students should have filed their Home Department forms by May 1.

On the Home Department form, in Section II, after "Comments," the major professor must note his or her agreement to accept the student and to provide or arrange funding. The major professor should then sign the "Major Professor" line.

Forming a Program of Study Committee (POSC)

After choosing the major and co-major professor, and establishing a home department, students should begin planning a suitable program for completion of the BCB graduate coursework. Before the end of the first year, students should determine the remainder of their Program of Study (POS) Committee members through discussions with their major and co-major professors. One form will be filed electronically with the Graduate College to form the POS Committee and to report the courses the student will take to complete their graduate coursework or POS.  More information on forming the Program of Study Committee (POSC) can be found here.

Initial and Annual POSC Meetings

Before submitting the POSC form, students must meet with their committee to discuss their research plan and the additional coursework they will take to support it. All BCB students must meet with their POS committees annually. More information on what takes place at the initial and annual POS meetings can be found here. A written synopsis of research progress should be provided to the committee in advance of the annual POS committee meeting.

For Ph.D. students, the first POS meeting must be scheduled before the end of the first semester of the second year. In each subsequent year, BCB recommends that Ph.D. students schedule their annual meeting during November. For annual meetings after the Ph.D. Preliminary Examination, only three committee members are required to be present. All committee members must be present for the Final Defense. Ph.D. students are expected to complete their degree work in approximately five years.

For M.S. students, the first POS meeting must be scheduled before the end of the first year (usually late Spring or early Summer semester.) M.S. degree students are expected to complete their degree work in approximately two years. If the M.S degree is not completed within two years, the POS committee should meet at the end of the second year to review student progress and set a target date for completion of the degree.

Preliminary Examination

The Graduate College requires that all Ph.D. students pass a Preliminary Examination before advancing to candidacy for the doctoral degree. To initiate this process, the student must file a Request for Preliminary Examination form with the Graduate College two weeks prior to the examination.  The form is not online yet and is  available from department and program administrative offices and the Graduate College. Both the major professor and BCB Chair need to sign off on this form.

BCB students should:

  • complete the Preliminary Examination before the end of the first semester of the third year,
  • complete at least two of the four BCB core courses before taking this examination, and
  • have an approved POSC in place the semester before the examination takes place.

All POS committee members must be present for the examination or an approved At-A-Distance form (see the Forms section) must be in place with the Graduate College prior to the exam for the member who is participating from a distance.

The examination must contain both a written and an oral component. The written component must include a "formal" Research Proposal in the format of an NSF, NIH or USDA research proposal. Master’s degree candidates are not required to take a Preliminary Examination. Research Proposals that serve as the written component of the Preliminary Examination should be submitted at least two weeks before the Preliminary Examination.

Preparing to Graduate - International Students

Are you thinking about graduation??  Optional Practical Training (OPT) is a visa requirement for those who want to continue working in the U.S. after graduation.  You must begin the application process for this at least four months in advance !!  Please register for the OPT workshop so you can become aware of all deadlines and requirements for this visa status.  A link to the workshop is on our forms and publications page.

Writing the Dissertation

BCB requires students’ research projects to be interdisciplinary, including both novel biological and quantitative/computational components. In addition, dissertations and theses written for Ph.D. and M.S. degrees in BCB must be in the “alternate format"; that is, they must include one or more papers designed for submission to a professional journal. As a guideline, the Ph.D. thesis is expected to include approximately three published or publishable original manuscripts.

A link to the alternate journal paper format is here. Writing in the alternate journal paper format provides important practice in writing publishable papers and shortens the time required for the final aspects of a student's thesis research to be published. If a student's POS committee feels that the alternate format is inappropriate for some reason, this requirement can be waived by petition from the POS committee to the BCB Chair.

The Graduate College has organized many resources to help you in all aspects of the preparation and writing of your manuscript. A link to this and many other Graduate College resources can be found on our forms and publications page.

Students should provide a pdf of the final thesis to the BCB program office.

Thesis Seminar

Students are strongly encouraged to present the final oral seminar during a regular BCB Seminar series or as part of a seminar series of their home department. At least two weeks prior to the seminar, students should provide the BCB office with the text of the formal seminar announcement.

Seminar posters will be distributed and an email message will be sent to BCB faculty and graduate students announcing the seminar.

Final Examination

The Final Examination for the Ph.D. or M.S. degrees is an oral defense of the Ph.D. dissertation or M.S. thesis.  Complete copies of the Ph.D. dissertation should be submitted to the POS committee at least two weeks before the Final Exam date. All committee members must be present for the Final Defense.

Students should file an electronic Request for Final Examination form after the dissertation or thesis work has been completed and all the other requirements have been met. To file this form:

  • Log into your Access Plus account. http://accessplus.iastate.edu/
  • Then select Graduation from the left side menu
  • Finally, select Application and fill out your Application for Graduation

To withdraw your application from the system:

  • Log into your Access Plus account: http://accessplus.iastate.edu/
  • Then select Graduation from the left side menu
  • Finally, select your Application and click on the Withdraw button

After receipt of this electronic form, the Graduate College will send a Report of Final Examination form directly to the program administrator who will send it to the major professor. The major professor is responsible for bringing this form to the final oral examination.

Following the public seminar (usually, but not always immediately afterwards), the final oral examination (closed to the public) will be given by the POS committee. All members of the POS committee must be present at this meeting. If a member of the POS committee cannot be on site for the exam, be sure to have a Graduate College At-A-Distance form (see the Forms section) filed and approved prior to the exam. This examination will review the dissertation or thesis and the candidate’s knowledge of relevant subjects.

Annual Review of BCB Student Progress

Continued participation in the Bioinformatics and Computational Biology program and financial support are contingent upon satisfactory progress towards the degree. The progress of all students in the BCB program is evaluated each year by the BCB Chair or members of the BCB Supervisory Committee. In the past, students were required to use the BCB Program Requirements Checklist (see the Forms section) to track progress toward meeting BCB program requirements. Directions will be given to students as to what document(s) they should provide to the program for their BCB Annual Student Reviews. The Annual Review also offers an opportunity for BCB students to provide feedback on the program.

Progress will be evaluated on the basis of the following criteria:
• Timely completion of BCB training requirements
• Satisfactory performance in laboratory exploration rotations or satisfactory progress in thesis research
• Satisfactory performance in required/recommended courses

BCB Program Grade Requirement

A minimum grade requirement for the BCB core courses was instituted for students entering in Fall 2009 and beyond. Students must obtain an average GPA of 3.0 in the core courses which includes BCB 567, 568, 570 and the advanced Biology Core Requirement. The minimum grade which is acceptable in these courses is a B-.

Dismissal Information

Continuing registration as a graduate student at Iowa State University is contingent upon maintaining good standing in a graduate major. The Bioinformatics and Computational Biology program expects BCB students to complete their degrees in a satisfactory and timely manner. However, there are certain situations that may require severing the relationship between a student and the BCB program. More information on resignation and dismissal policies can be found here.

Summary of BCB Course Requirements for PhD - Fall 2017

Most students do not have preparation in all courses required to establish optimal foundational information for the BCB curriculum.  Students may be required to take background coursework.  See more information about these courses here.

Requirement

Course Number
(Semester Offered)

Course Name

Ph.D.

Variable
Background coursework

Variable
Stat 430 (F)

Variable
Empirical Methods for Computer Science

~15 cr
3 cr

BCB core courses

BCB 567 (F)
BCB 568
BCB 570 (S)

Fundamentals of Genomic Informatics
Advanced Genomic Informatics
Systems Biology

3 cr
3 cr
3 cr

Advanced Biology Core
Requirement

Variable

Examples:

GDCB 511, Molecular Genetics
AnSci 556, Current Topics in Genome Analysis
EEOB 561, Evolutionary and Ecological Genomics
EEOB 563, Molecular Phylogenetics

3 cr.

Advanced group requirements

Variable

Variable

6 cr.

Workshops and symposia

BCB 593a

BCB Workshop

1 time

Student research seminar

BCB 690 (S)

BCB Student Research Seminar

2 timesb

Faculty seminar

BCB 691 (F)

BCB Faculty Research Seminar

1 timed

Research rotation
(first year only)

BCB 697 (F S)

BCB Research Rotations

3 labs

Research

BCB 699 (F S SS)

Research

Variable cr.

Bioethics training

GR ST 565 (F)

BCB-approved bioethics course/modules

1 cr.

Graduate English

Variable

(for non-native English speakers only) Determined by placement exam

Total Credit Hours

 

 

72

 

  a BCB 593 Workshop is offered various semesters (F S SS), but at least once each year.
  b Student must make at least two oral presentations.
  d As of Fall 2017, students will be required to take it once.

 

Summary of Degree Requirements for the BCB Minor

A graduate minor in BCB requires:

  • completion of two core BCB courses, BCB 567, 568 or 570 (6 credits);
  • Statistics 430 (3 credits);
  • 1 credit each in BCB Workshop, Faculty Seminar and Student Seminar; and
  • completion of 3 credits in courses listed under BCB Advanced Group Requirements. The Program of Study Committee must approve the selected courses.

In addition:

  • the planned POS must be reviewed by the BCB Chair prior to POS committee approval;
  • at least one member of the POS committee must be a BCB faculty member; and
  • application for minor must be made prior to PhD preliminary examination.

Co-major or Concurrent Degree Requirements

Students who are admitted to the BCB program as co-major or concurrent degree candidates must fulfill the requirements of the BCB program in addition to those of the co- or concurrent degree program.

Seminar requirements for co-majors may be modified as follows if the POS committee and BCB chair agree:

Co-majors may take just one BCB faculty research seminar (BCB 691) if the other major requires at least one faculty research seminar in the other discipline and they may take one BCB student seminar (BCB 690) if the other major requires at least one student seminar in the other discipline.

The Graduate College Handbook (see the forms and publications page) has much additional information.

Timetable for Completion of BCB Degree Requirements

 

PhD

MS

Attend Lab Safety Orientation Orientation week Orientation week
Take Graduate English Examination (for nonnative speakers only) Orientation week Orientation week
Start rotation 1 September 11 September 11
Start rotation 2 October 30 October 30
start rotation 3 January 8 Not applicable
Make major professor decision April 13 December 1
File Home Department form April 27 December 15
Select Program of Study Committee members Before end of  1st year Before end of  1st year
Hold first POS Committee meeting and file POSC form By 1st semester of 2nd year Before end of 1st year
Hold annual POS meeting By November By November
Take Oral English Certification Test (was Speak/Teach) Int’l: At least 1 semester prior to expected TA Int’l: At least 1 semester prior to expected TA
Take preliminary examination By 1st semester of 3rd year Not applicable
Submit thesis to POS committee 2 weeks prior to defense 2 weeks prior to defense
Provide research seminar information, title and abstract to BCB office 2 weeks prior to seminar 2 weeks prior to defense

General degree requirements overseen by the Graduate College for the Ph.D. and M.S. degrees are summarized in their handbook, a link to which can be found here.

Links to some important sites on the Graduate College website can be found here dealing with thesis requirements and graduation forms and deadlines.

 

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