Iowa State University

The information in this document will provide general guidance about important issues related to the academic careers of students in this Graduate Program. Students should stay in close communication with their major professors regarding important curriculum and policy issues to stay up to date on these matters. Students should feel free to bring questions and comments to the Chair and members of the BCB Supervisory Committee at any time.

Administration and Contact Information

Bioinformatics and Computational Biology program activities are overseen by the Chair, Supervisory Committee, and Program Assistant. Please contact us if you have any questions about the program.

BCB Chair Volker Brendel 2112 MBB 294-9884 vbrendel@iastate.edu
BCB Program Assistant Trish Stauble 2014 Molecular Biology Building 294-5122 bcb@iastate.edu
BCB Program Office 2014 Molecular Biology Building 294-5122 bcb@iastate.edu www.bcb.iastate.edu Toll-free: 1-888-569-8509 Fax: 515-294-6790	BCB Supervisory Committee Volker Brendel (chair) Julie Dickerson (associate chair) Vasant Honavar Xiaoqiu Huang Jim Reecy Chris Tuggle (former chair) Drena Dobbs, (IGERT PI) Robert Jernigan (ex officio)

I. INTRODUCTION

Bioinformatics and Computational Biology

Interdepartmental Graduate Program

The Bioinformatics and Computational Biology (BCB) Program at Iowa State University is an interdepartmental graduate major offering outstanding opportunities for graduate study. The BCB program involves more than 60 nationally and internationally known faculty – biologists, computer scientists, engineers, mathematicians, physicists and statisticians – who participate in a wide range of collaborative projects.

Nearly 60 graduate students in the BCB Program have the opportunity to conduct research in all major research areas of computational molecular biology, including genomics, structural genomics, functional genomics, and computational systems biology, with access to some of the most modern experimental platforms.

BCB students are trained to develop an independent and creative approach to science through a highly interdisciplinary curriculum and thesis research projects that include both biological and computational/mathematical components. First-year students are appointed as research assistants and have the opportunity to do research exploration rotations in various laboratories to gain experience in both "wet" and "dry" lab environments before selecting the laboratory in which to do their graduate research. In the second year, students initiate a thesis research project under the guidance of two faculty mentors, one from the biological sciences and one from the quantitative/computational sciences. BCB students are encouraged to participate in internships with academic or industrial partners during their degree program. The M.S. and Ph.D. degrees are usually completed in two and five years, respectively.

General information about the BCB program is available throughout our website including information on our BCB faculty and their research interests as well as links to homepages for individual faculty and research groups. (back to top)

II. UPON ARRIVAL AT IOWA STATE

To help in the orientation process, new students should:

 

• Read this on-line handbook. It is especially important to read the section on Administrative Matters during your first few days. Email is the BCB program's most important means of communication, so students should register for email as soon as possible, and then check it daily.

• Refer to the publications and forms section regularly and examine these resources carefully. They contain information about University services as well as regulations and requirements for graduation. Links to important Graduate College resources are also listed including an orientation website which provides a comprehensive overview of student services.

 

III. GETTING STARTED –

THE FIRST YEAR

Graduate Student Orientation

For new graduate students, the academic year begins with a Graduate Student Orientation Week designed to ease the transition to graduate study at Iowa State. This is a time to become acquainted with the Bioinformatics and Computational Biology (BCB) program and its members and to prepare for registration and the start of classes. In addition to participating in the BCB orientation events, students also will take part in orientation activities offered by the Graduate College and International Student and Scholars Office. Students should refer to all schedules for information about Orientation activities.

New BCB students are admitted to the program in one of two categories:

• First year students admitted to BCB for research exploration rotations
New students admitted into BCB are supported during the first year on a BCB research assistantship or an NSF fellowship. They spend the first year taking classes, doing research exploration rotations, and choosing a major and co-major professor. A temporary advisor helps new students arrange rotations and choose courses to fulfill the BCB program requirements. New students do not have a "home department" until after they complete their rotations and choose a major professor, usually before the end of their second semester on campus. The student's home department is the same as that of his/her major professor.

• Current ISU students admitted to BCB as "transfers," "co-majors" or "concurrent degree candidates"
Students admitted to BCB as transfers from other ISU departments or programs, or as co-majors or concurrent degree candidates, are usually supported by their major professor and/or home department. They spend their first year as BCB majors initiating an interdisciplinary research project, taking classes, and choosing a co-major professor. The major professor helps the student choose courses to fulfill the BCB program requirements. The student's home department is the same as that of his/her major professor. In most cases, the sections of the BCB Graduate Handbook dealing with temporary advisors, research exploration rotations and choosing a major professor do not apply to these students. (back to top)

 

Assignment of a Temporary Advisor

Each new BCB student is assigned a temporary advisor who is usually a member of the BCB Supervisory Committee. Temporary advisors guide students in selecting courses during the first year, discuss research opportunities in Bioinformatics and Computational Biology, and suggest research groups/laboratories for research exploration rotations.

When a student is admitted to BCB as a transfer, co-major, or concurrent degree candidate, the major professor serves as advisor.

Registration for Classes

During Graduate Student Orientation week, students meet with their temporary advisors for counseling and preparation of class schedules for the upcoming semester. After consulting with advisors, students can register for classes through their AccessPlus accounts. If changes in course registration are necessary, course adds and drops, section changes and credit changes can be made on AccessPlus until the end of the first week of classes.

After the first week of classes, changes in class schedules must be submitted on a Request for Schedule Change or Restriction Waiver form (better known as an Add/Drop Slip), which is available from the BCB program office or from advisors. Once signed, this form needs to be taken to Room 10 Enrollment Services Center to formalize the change(s).

Students can register for future semesters through AccessPlus after meeting with their advisor to plan their schedules. Register for classes before the beginning of the semester to avoid late registration charges. There are also charges for schedule changes after the first week of classes. (back to top)

Research Exploration Rotations

An important aspect of the BCB training program is participation in Research Exploration Rotations. The rotations serve several purposes. They are designed to help students choose their future major professors and to help professors choose graduate students. In addition, exploration rotations provide students an opportunity to actively participate in research projects of BCB faculty laboratories and promote interaction and exchange of information among BCB research groups. Because rotations are necessarily brief, students are not usually able to "complete" a project, in either a biological or computational research group. Instead, during the research exploration rotation period, students should:

• get to know the professor and the students and postdocs working in the research group;
• learn as much as possible about the professor's research projects;
• obtain "hands on" experience in one of the group's research projects;
• attend research group meetings and journal club meetings; and
• read reprints, reviews, and grant proposals related to the group's research.

It is appropriate for a rotating student to ask the rotation advisor whether the advisor would consider accepting him/her as a graduate student, but the final decision should not be made until all rotations have been completed.

Participation in research exploration rotations is required for all first year BCB students: three rotations for Ph.D. students and two rotations for M.S students. 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.

Beginning in Orientation Week, students should take advantage of and make opportunities to meet individual faculty members and discuss their research. Students should arrange appointments with the professors whose work interests them most.

Students should make use of the following resources in selecting research groups and professors with whom to rotate:

• the list of BCB faculty who have expressed an interest in serving as mentors for research exploration rotation students, available on the rotations page of the BCB website and from the BCB program office;
• homepages of individual BCB faculty;
• discussions with individual faculty members. (This is very important.) Faculty can provide curriculum vitae, recent publications and grant proposals;
• research talks given by faculty in the BCB Faculty Orientation and Poster Session and in the various departmental seminars on campus;
• discussions with current BCB graduate students.

Students should compile a list of several BCB faculty with whom they would like to rotate; this can be done in consultation with the temporary advisor. Students should personally contact the faculty members to determine whether they are accepting rotation students and to schedule a rotation.

To assist both faculty and students in planning, students should attempt to schedule exploration rotations and submit a completed BCB Research Exploration Rotation Planning Form to the BCB office as early as possible.

The deadline for submitting the Rotation Planning form in Fall semester is September 14. Typically, the length of each rotation is approximately eight weeks for Ph.D. students, and about six weeks for M.S. students. Adherence to the following timetable is strongly recommended. It is critical that students choose a major professor and notify the BCB office of their choice on or before the deadlines indicated. (back to top)

Dates for Fall 2009/Spring 2010 Rotation Program

If a student realizes within the first two weeks of a rotation exploration that the rotation experience is not in an area of research he or she wishes to pursue, the student should consult with the temporary advisor. The temporary advisor will assist the student in scheduling another exploration rotation if assistance is needed.

Students obtain graduate credit for research exploration rotations by registering for BCB 697 - BCB Research Rotations for two semesters (Ph.D. students) or one semester (M.S. students). Rotation students usually register for two to five credits of BCB 697 per semester. The number of BCB 697 - Research Rotation credits is determined by the number of course credits for which the student is registered.

To satisfactorily complete BCB 697, students must submit a Rotation Evaluation form for each rotation which briefly describes their work in the rotation. The form requires faculty comment on each rotation experience, as well. The form is downloadable from the Administration webpage of the BCB website here.

All BCB graduate students should register for a total of 12 credit hours each Spring and Fall semester and a total of 5 credit hours each Summer semester. Although research will be conducted during the exploration rotations, completion of a project is not required. However, many faculty will use research productivity as one measure by which they determine whether to offer a student the opportunity to join their laboratory. It is therefore important to allow sufficient time in your schedule to actively engage in the intellectual activities of your host lab. (back to top)

Choosing a 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 May 7 for the PhD.

In Fall semester of 2008, the BCB faculty voted to institute a Core and Associate faculty membership for the BCB graduate program. This policy states that either the major or co-major professor must be a core BCB faculty member. Membership is listed on the faculty directory page and on the faculty research page.

NOTE:

• Students should not feel pressured to make a final decision about their future major professor until after all exploration rotations have been completed. BCB faculty are strongly encouraged to wait until new BCB students have had an opportunity to complete all scheduled rotations before making a commitment to any specific student. It is in the student's best interest to reserve a final decision until becoming fully informed about all available opportunities.

• It is important for students to discuss their future graduate assistantship support with potential major professors. During the exploration rotation period, BCB students are usually supported as Research Assistants (RAs) with funds provided by the BCB program or NSF fellowships. Typically, Ph.D. students receive 10.5 to 24 months and M.S. students receive up to 6 months of guaranteed assistantship support. After a student has chosen a major professor, responsibility for the student's assistantship funding lies with the major professor and home department. (For administrative purposes, the major professor's department becomes the student's home department.)

When a BCB faculty member agrees to serve as a student's major professor, the faculty member is expected to provide or arrange assistantship support for the remainder of the student's degree program, as long as the student remains in good standing and is making good progress toward the degree. Very few professors are able to "guarantee" a specific source of graduate assistantship support for several years. It is important, therefore, for each student to take an active role in discussing future assistantship funding with the major professor. Most students receive support as either a Research Assistant (RA) or a Teaching Assistant (TA), with funding supplied by the major professor and/or the home department. In some cases, students receive support from other sources, such as scholarships, training grants, or competitive research assistantships. (back to top)

 

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 7 (Ph.D.) or December 18 (M.S.).

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.

Choosing a Co-Major Professor

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 Committee Appointment 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. (back to top)

Appointing a Program of Study (POS) Committee

After choosing the major and co-major professors 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 appoint a graduate Program of Study (POS) Committee by filing a Recommendation for Committee Appointment form. The composition and responsibilities of the POS committee are in accordance with the Graduate College guidelines (see below).

The POS committee should include faculty whose knowledge and research interests can aid and complement the student's research interests, as well as faculty whose expertise will ensure a breadth of knowledge on the committee. For Ph.D. candidates, the POS committee must consist of at least five members of the Graduate College Faculty. The committee must have at least three faculty members – including the major professor and co-major professor – from within the Bioinformatics and Computational Biology major (i.e., who are members of the BCB faculty). The fourth member should be from outside the student's field of emphasis to provide relevant specialized knowledge or a different perspective helpful to the planning, execution, and reporting of research, or some aspect of intellectual diversity deemed important by the committee and/or major. The committee should indicate on the committee form who will serve as an outside member. The fifth member must be a member of the Graduate Faculty as must all other POS committee members.

For M.S candidates, the POS committee must consist of at least three members of the Graduate College Faculty. Both the major and co-major professors must be members of the BCB faculty. One member of the committee must be either outside the major (not a BCB faculty member) or outside the student's home department.

Concurrent degree candidates, both M.S. and Ph.D., must meet the standard committee requirements for their Ph.D. or M.S. degree, as stated above.

Special rules govern the composition of the POS committee for students seeking a co-major degree in BCB:

For students seeking a BCB Ph.D. co-major, both the major and co-major professors must be members of the BCB faculty, with one professor affiliated with the department of the student’s second major. The third member must be a BCB faculty member, and the fourth must be a faculty member of the student’s second major. The fifth member can be outside both majors or in one of the two major departments or programs.

For students seeking a BCB M.S. co-major, both the major and co-major professors must be members of the BCB faculty, with one professor affiliated with the department of the student’s second co-major. The third member can be outside both majors or in one of the two major department or program.  back to top

After the chosen members of the POS committee have agreed to serve, students should complete the Recommendation for Committee Appointment form, sign it, and obtain signatures of committee members. “Bioinformatics and Computational Biology” should be listed as “Major”; home department (major professor’s department) should be listed as “Department.” They should submit the form to the Bioinformatics and Computational Biology program office for approval. The BCB Program Assistant will obtain the signature of the BCB Chair, who is Director of Graduate Education (DOGE) for the BCB major, and will send the form to the Graduate College.

BCB Program Requirements Checklist

Students are required to use the BCB Program Requirements Checklist (see the Forms section) to track progress toward meeting BCB program requirements. An updated version of this checklist should be brought to each semester's schedule planning session with your advisor and to the BCB Annual Review interviews with the BCB program chair. Continued membership in the Bioinformatics and Computational Biology program and financial support is contingent upon satisfactory progress towards the degree. The BCB Program Requirements Checklist is one of the most important tools used by the program staff and BCB Chair to track student progress. (back to top)

IV. Academic Matters

Degrees Offered

The Bioinformatics and Computational Biology graduate program is designed to provide doctoral (Ph.D.) level training. In certain circumstances, students may be admitted as M.S. candidates. The M.S. degree is not a prerequisite for the Ph.D. program.

Students who are admitted to the Ph.D. program and who later wish to transfer to the M.S. program must make the transfer concomitant with selection of a major professor (before the start of the second year). Students will be financially responsible for their education after the transfer. Transfers after the first year require approval of the BCB Supervisory Committee.

Students who are admitted to the M.S. program and who wish to transfer to the Ph.D. degree program in BCB may request to do so. Applications for transfer are judged on the basis of the same criteria as new applications for direct admission to the Ph.D. program. Students who wish to enter the Ph.D. program in BCB after completion of the M.S. degree in BCB must reapply to the program. Such applications are judged on the basis of the same criteria as new applications to the BCB Ph.D. program. (back to top)

Academic Calendar

The BCB graduate program is a year-round program that includes Fall, Spring and Summer semesters. Students are expected to be registered and to participate in research and courses twelve months per year. A rotating student may take vacation with the approval of his or her temporary advisor and by notifying the Bioinformatics and Computational Biology program assistant. Each student must obtain the required approval and notify the BCB office prior to travel, in order to avoid potential interruption of graduate assistantship support and/or visa problems. See Leave in the Benefits section of this handbook for information regarding vacation.

Research Expectations

BCB students are trained to develop an independent and creative approach to science through an integrated curriculum and interdisciplinary research projects in the fields of bioinformatics, computational biology, and biological statistics.

Advanced degrees in BCB require that a student's research project be interdisciplinary, including both biological and quantitative/computational components. The POS committee is responsible for determining whether a student's research project meets this condition.

The Ph.D. dissertation must: "demonstrate conclusively the ability of the author to conceive, design, conduct, and interpret independent, original, and creative research. It must attempt to describe significant original contributions to the advancement of knowledge and must demonstrate the ability to organize, analyze, and interpret data. Dissertation research should be worthy of publication and should appear in appropriate professional journals or in book form. Since satisfactory completion of the thesis or dissertation can constitute one of the most gratifying experiences in graduate study, the document should reflect the highest standards of scholarship, serving as a measure of quality for the student, major professor, and the program." (from the ISU Graduate College Handbook)

In BCB, the Ph.D. thesis is generally expected to include approximately three published or publishable original manuscripts. For additional details, see Writing the Thesis in the Progressing Through the Degree Program section of this Handbook.

The Ph.D. and M.S. degrees are usually completed in five and two years, respectively. (back to top)

Background Coursework

The foundation disciplines for BCB are genetics, molecular biology, mathematics, computer science, statistics and physics. Students entering the BCB program are expected to have a strong undergraduate background in at least one of these disciplines and additional coursework in another.

The following tables summarize the three areas in which BCB majors must demonstrate basic competence. A flow chart diagram of the prerequisite, background and core courses is also provided.

Students are strongly encouraged to take courses equivalent to the ISU courses listed under Course Prerequisites for Admission to BCB prior to enrollment in the BCB program, but will have the opportunity to make up deficiencies during the first year of BCB graduate training. Courses listed under BCB Background Coursework Requirements are prerequisites for BCB core courses. These background courses should be completed either prior to admission or during the first year of BCB graduate training. The temporary advisor or major professor helps each student determine whether additional courses are needed. The student's POS committee will evaluate competence in the three background areas during the student's second Annual POS Committee meeting.

Required Core Courses

All BCB majors must take at least one core course in molecular genetics and four core courses in computational biology.

Core courses in molecular genetics :

GDCB 511. Molecular Genetics. (Cross-listed with MCDB). (3-0) Cr. 3. S.Prereq: Biol 313 and BBMB 405. The principles of molecular genetics: gene structure and function at the molecular level, including regulation of gene expression, genetic rearrangement, and the organization of genetic information in prokaryotes and eukaryotes. (An equivalent or more advanced course may be substituted with approval of student's POS Committee.)

Core courses in computational biology :

BCB 567. Bioinformatics I (Fundamentals of Genome Informatics). (Cross-listed with Com S, Cpr E). (3-0) Cr. 3. F. Prereq: Com S 208; Com S 330; Stat 341; credit or enrollment in Biol 315, Stat 430. Biology as an information science. Review of algorithms and information processing. Generative models for sequences. String algorithms. Pairwise sequence alignment. Multiple sequence alignment. Searching sequence databases. Genome sequence assembly.

BCB 568. Bioinformatics II (Advanced Genome Informatics). (Cross-listed with GDCB, Stat, Com S). Cr. 3. S. Prereq: BCB 567, BBMB 301, Biol 315, Stat 430, credit or enrollment in Gen 411. Advanced sequence models. Basic methods in molecular phylogeny. Hidden Markov models. Genome annotation. DNA and protein motifs. Introduction to gene expression analysis.

BCB 569. Bioinformatics III (Structural Genome Informatics). (Cross-listed with BBMB, Com S, Math, Cpr E). Cr. 3. F. Prereq: BCB 567, Gen 411, Stat 430. Algorithmic and statistical approaches in structural genomics including protein, DNA and RNA structure. Structure determination, refinement, representation, comparison, visualization, and modeling. Analysis and prediction of protein secondary and tertiary structure, disorder, protein cores and surfaces, protein-protein and protein-nucleic acid interactions, protein localization and function.

BCB 570. Bioinformatics IV (Computational Functional Genomics and Systems Biology). (Cross-listed with Com S, GDCB, Stat, Cpr E). Cr. 3. S. Prereq: BCB 567, Biol 315, Com S 311 and either 208 or 228, Gen 411, Stat 430. Algorithmic and statistical approaches in computational functional genomics and systems biology. Analysis of high throughput gene expression, proteomics, and other datasets obtained using system-wide measurements. Topological analysis, module discovery, and comparative analysis of gene and protein networks. Modeling, analysis, simulation and inference of transcriptional regulatory modules and networks, protein-protein interaction networks, metabolic networks, cells and systems: Dynamic systems, Boolean, and probabilistic models. Ontology-driven, network based, and probabilistic approaches to information integration.

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Recommended (not required) Courses

It is recommended that all BCB graduate students who have not had laboratory experience in biological sciences take at least two 1-credit modules of BCB 542 (Introduction to Molecular Biology Techniques). Similarly, BCB graduate students who come in with a biology undergraduate degree take at least two modules of Bioinformatics Techniques, BCBio 442X, which has four techniques modules on sequence databases, protein structure; phylogenetic analysis and microarray analysis techniques.

Advanced Group Requirements

In addition to the five core courses, students must complete at least six credits of advanced coursework. Courses should include three credits from Category I (Molecular Biology) and three credits from either Category II (Computer Science) or Category III (Mathematics/Statistics). The table below provides a list of some of the courses that can be used to fulfill this depth requirement. Not all the listed courses are suited to all programs of study. Students should consult with their POS committees to determine which courses from this list, or not from the list, are most appropriate. Check the table below for new course offerings and updated course lists.

Required Seminars and Activities

Workshops and Symposia

• BCB 593 - Workshop in Bioinformatics and Computational Biology. (1 cr. each time taken) (Fall, Spring, Summer) Current topics in bioinformatics and computational biology research. Lectures by off-campus experts. Students read background literature, attend preparatory seminars, attend all lectures and meet with lecturers.

Seminars

• BCB 690 - Student Seminar. (1 cr.) (Spring) Students present an account of their annual research progress to peers and to two faculty mentors who promote group discussions of experimental procedures and analysis.
• BCB 691 - Faculty Research Seminar. (1 cr.) (Fall) BCB faculty members present summaries of current research in their groups.

In addition, BCB students are expected to participate in a seminar series in their home department and to make an oral presentation (either in a research seminar or journal club) at least once each year.

Student-Sponsored Seminars

BCB students are encouraged to recommend invited speakers for Bioinformatics, Computational Biology and Biological Statistics seminars on campus. Funding is available for at least one student-sponsored seminar by a top-caliber visiting scientist each year (i.e., students invite and make arrangements for hosting the speaker).

Scientific Ethics and Good Science and Bioethics Training
All BCB majors are required to attend the Scientific Ethics Workshop, which is part of new student orientation each Fall semester. In this workshop, students are introduced to the concepts of ethical behavior and good practice in science. Discussion includes proper research methods, ways to avoid self-deception in the practice of science, and scientific misconduct.

In addition to attending the Scientific Ethics Workshop, BCB students are required to take BCB-approved bioethics courses or course modules. Students seeking M.S. degrees are required to take at least one BCB-approved bioethics course/module (0.5 credit minimum). Ph.D. students are required to take at least two bioethics modules or another BCB-approved bioethics course (1 credit minimum). The required sessions in general scientific ethics offered during Fall orientation (above) do not count toward this bioethics course requirement. Students supported by special training grants may have additional bioethics training requirements.   (back to top)

BCB-approved bioethics courses include:

Agron/Gen/Pl P/VMPM 565 - Professional Practice in the Life Sciences (usually offered Spring)
1. Professional Practices in Research
2. Intellectual Property and Industrial Interactions
3. Life Science Ethics

Please see BCB Courses in the BCB website for additional information.

Language Requirements
Language requirements are determined by the student's Program of Study Committee.

Graduate English Requirements
Graduate students whose native language is not English must take the English Placement Test at the beginning of their first semester of enrollment. This test is administered by the Department of English. It must be taken in addition to TOEFL (Test of English as a Foreign Language), which is required as part of the admissions process.

A student who does not pass this examination is assigned to one or more courses in the English 99 or 101 series. This coursework must be completed during the first year of study.

Two waivers allow some non-native English speakers to be exempt from this test:

1) Students who already have a B.A., M.A., or Ph.D. degree from an accredited four-year college or university within the U.S. are not required to take the English Placement Test; and

2) Non-native English speaking ISU students who meet or exceed any of the following test scores: Paper-based TOEFL (PBT) 640 (and above); Computer-based TOEFL (CBT) 270 (and above); Internet-based TOEFL (iBT) 105 (and above). Contact the Graduate College Office, 1137 Pearson, in order to be certified.

Teaching Requirements
Teaching requirements are determined by the home department. All graduate students are encouraged to participate in teaching seminars and obtain teaching experience as part of their training.

Testing of Nonnative Speaking Students Who Teach
SPEAK/TEACH testing is required of graduate students who fit both of the following categories:

• those who are not native speakers of American English (i.e., learned another language first), and
• those who are to be appointed to or considered for teaching assistantships, or who will have some teaching responsibilities even if they are not teaching assistants (TAs).

The SPEAK/TEACH tests of oral proficiency are given before the beginning of Fall and Spring semesters. Department offices have a schedule of SPEAK/TEACH testing dates. Registration for the test is held the day before the test is administered. Complete information about the SPEAK/TEACH program can be found at http://www.grad-college.iastate.edu/speakteach/. Questions about SPEAK/TEACH testing should be directed to the SPEAK/TEACH office, 1116 Pearson , 515-294-1958, 515-294-7996 or itas@iastate.edu.

A prospective teaching assistant who does not pass these tests is required to successfully complete coursework and be retested. Sections of University Studies 180 are designed to help new teaching assistants. These courses focus on pronunciation, listening, question handling, teaching and lecturing skills, and an introduction to the culture of U.S. university life. Because enrollment in University Studies 180 is restricted, TAs cannot register for the courses through online registration. TAs must appear at the SPEAK/TEACH Office, 1116 Pearson on the first or second day of classes for Fall or Spring semester to obtain permission to enter the course by completing a course add slip. (back to top)

Additional Research Training Opportunities

Participation in International Scientific Conferences and Symposia
Attendance and presentation of research results at professional meetings are an essential part of the BCB graduate training program. Students should attend at least one national or international meeting during their degree program. All BCB students are eligible for financial assistance from the BCB program (as well as from other ISU sources) for conference-related expenses. For additional information, see Grants for Professional Travel in Section VII. Financial Matters.

Internships
BCB students are encouraged to participate in industrial internships as part of their training for careers in industry, government or the public sector. Recent internships for students have taken place with Merck, Syngenta and Novartis. In the past, Pioneer Hi-Bred International has offered Graduate Research Fellowships with an eight week internship during the summer of a student’s first year of study. Additional internships in subsequent years were arranged between the student and Pioneer. For additional information, please refer to the BCB Internship webpage.

International Experiences
BCB students also are encouraged to enrich their educational experience and establish international contacts by participating in international research experiences. The BCB program has had working relationships with four institutions (three in Europe and one in China) with which international training experiences were arranged in the past. Speak with your major professor about arranging these opportunities.   back to top

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 a GPA of 3.0 in the core courses which includes GDCB 511 and the minimum grade which is acceptable in these courses is a B-.

Graduate Minor

A graduate minor in BCB requires:

• completion of two core BCB courses, BCB 567, 568, 569 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 section) has much additional information.

Summary of First Year Course Requirements for BCB Majors

All first year Ph.D. and M.S. degree candidates must:

• take courses to complete BCB Background Coursework Requirements;
• take the required BCB core courses suggested by temporary adviser;
  • BCB 567 - Fundamentals of Genomic Informatics and
  • BCB 568 - Advanced Genomic Informatics and
  • GDCB 511 - Molecular Genetics (or equivalent)
• attend BCB 691 - BCB Faculty Research Seminar (Fall) if it does not conflict with Stat 430
• participate in BCB 690 - BCB Student Research Seminar (Spring); and
• participate in Fall Scientific Ethics Workshop and take courses to fulfill the BCB Bioethics training requirement.

After the First Year

• Students should register for BCB 699 - Research (rather than BCB 697 - Research Rotation) every semester. Number of credits for BCB 699 will vary depending on other courses taken; students should register for a total of 12 credits every Fall and Spring semester, and a total of 5 credits every Summer semester.
• Students should register for courses to complete Advanced Group Requirements, following the recommendations of their major and co-major professors and POS committee.
• Students should refer to the Summary of BCB Requirements (above) for specific credit hour requirements for seminars, workshops, etc.

Sample Curricula for First and Second-Year BCB Graduate Students

Three examples of first and second year programs for students with prior training in computer science and biological sciences .

V. PROGRESSING THROUGH THE

DEGREE PROGRAM

Forms listed in this section can be found in the Forms section of the Administrative webpage. The Graduate College also has many forms available on the web at http://www.grad-college.iastate.edu/forms/forms.html.

The BCB Program Requirement Checklist (see the Forms section) summarizes the coursework requirements of the BCB program and provides a timetable for completion of degree requirements. ISU Graduate College requirements for the Ph.D. and M.S. degrees are summarized in the ISU Graduate College Handbook.

First Year Activities

Activities completed during a student's first year in the BCB program are described in Section III. Getting Started – The First Year.

Approval of the Program of Study (POS)

After choosing major and co-major professors and establishing a POS committee, students must file a Program of Study form. The Graduate College Program of Study form serves as a contract between the student and the Graduate College, indicating the minimum coursework that must be completed for the Ph.D. or M.S. degree. Links to most BCB program forms as well as Graduate College forms can be found here.

Students should prepare a tentative Program of Study in consultation with their major professor and arrange a meeting of their POS committee to discuss the proposed Program of Study and research plans. All committee members must be present. The student's first Annual Progress Report is also reviewed at this meeting (see below).

In preparing the Program of Study, the student and major professor should refer to the BCB course requirements to ensure that the planned coursework: 1) meets all BCB requirements, 2) meets all Graduate College requirements, and 3) is appropriate, based on the student’s planned research project. The POS committee will approve the POS form if these conditions are met. If courses listed on the POS form do not meet all BCB course requirements, the POS form will NOT be approved by the BCB program chair (unless a memo of justification is provided by the POS committee).

Transferability of Credits from Other Institutions

The transferability of credits from other institutions is determined on a case-by-case basis by the student's POS committee and the BCB Chair. To waive a course requirement, the student must attach to the POS form a memo signed by his or her major professor (on behalf of the POS committee) and the instructor of the course the student wishes to waive. The memo must state that the student has already received satisfactory instruction in the subject matter covered by the required course. Credits for seminars, workshops and colloquia are not transferable. (back to top)

Tips for Scheduling POS Meetings

Scheduling POS committee meetings can be challenging, but there are ways to simplify the task. In consultation with the major professor, the student should select four or five potential meeting timeslots, and then email the other POS committee members asking which times they could be available to meet.

Following the advice of the major professor, the student should indicate the expected duration of the planned meeting (usually about one hour) in the email message to POS committee members. This email request should be sent several weeks prior to the proposed date of the first POS meeting. Arrangements for the Preliminary Exam and Final Defense (which require longer time slots) should be made at least one month in advance. After obtaining faculty responses, the student should select a time when everyone can meet, reserve a conference room, and notify the POS committee members of the date, time, and location of the meeting. The whole scheduling process should be completed within two to three days so that timeslots available during the initial inquiry remain available. Email is the most efficient means of scheduling these meetings.

It is important (and courteous) to send an email reminder of the meeting time and place to POS committee members two to three days prior to the scheduled meeting.

First POS Committee Meeting

In most cases, a student's POS form is approved during the first POS committee meeting. Approval of the POS must be obtained before the end of the first semester of the student’s second year (Ph.D.) or before the end of the first year (M.S.)

At least one week prior to the scheduled POS committee meeting, students should prepare the following documents:

• Proposed POS form
• Description of Proposed Research

The Description of Proposed Research should be concise (usually 2-3 pages) and summarize the major objectives of the research project and planned approaches to achieve these objectives. Because the POS must be approved soon after the student has chosen a major professor, the research description is expected to be preliminary; it is understood that the student's plans may change as the research progresses. The written proposal should be viewed as a tool to help the student plan the dissertation or thesis research and to aid the POS committee members in evaluating whether the proposed POS coursework is appropriate. The research project of BCB students must be interdisciplinary, comprised of both biological and computational/mathematical components. The Description of Proposed Research should be emailed to the committee members one week prior to the first meeting.

Students should be prepared to make a brief oral presentation at the first POS committee meeting. Typically, the student describes his or her academic background (undergraduate institution, previous degrees, research experience, research interests, career goals) during the first few minutes of the meeting. The student then briefly summarizes the proposed research and solicits input from committee members. The POS committee is responsible for ensuring that the proposed research project is interdisciplinary, including both biological and computational/mathematical components. In addition, the POS committee is responsible for ensuring that the POS coursework: 1) meets all BCB requirements, 2) meets all Graduate College requirements, and 3) is appropriate, based on the student’s planned research project. If no changes in the proposed POS are required, the meeting concludes with members of the committee signing the POS form. If changes to the proposed POS are required, the student must modify the form and obtain signatures of POS committee members as soon as possible after the meeting. Immediately after the POS is signed by committee members, the student must submit the completed and signed POS form to the BCB office for approval by the BCB Program Chair and the Graduate College.

After the Program of Study has been approved by the Graduate College, changes to the POS may be made only with the approval of the POS committee and the Graduate College.

Annual POS Committee Meetings

All BCB students must meet with their POS committees annually. 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 October. 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. All committee members must be present for the Final Defense.

Complete copies of Ph.D. dissertation should be submitted to the POS committee at least two weeks before the Final Exam date.

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. This evaluation is based primarily on information within the BCB Program Requirements Checklist. 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 (see BCB Program Requirements Checklist in Forms section)
• Satisfactory performance in laboratory exploration rotations or satisfactory progress in thesis research
• Satisfactory performance in required/recommended courses

Satisfactory Completion of BCB Courses

The POS committee is responsible for: 1) ensuring that a student's coursework fulfills the BCB requirements, and 2) determining whether required/recommended BCB courses have been satisfactorily completed. In addition, all BCB students must meet the Graduate College Grade Requirements, as described below.

Graduate College Grade Requirements

A cumulative GPA of at least 3.0 is required by the Graduate College for one-half tuition support by the Graduate College. The grading scale at ISU is as follows: A (4.0), A- (3.67), B+ (3.33), B (3.0), B- (2.67), C+ (2.33), C (2.0), C- (1.67), D+ (1.33), D (1), and F (0). Research grades (699, 697) do not count toward the GPA.

BCB Program grade requirements were instituted for Fall 2009 and beyond and are here.

Preliminary Examination (Ph.D. only)

The Graduate College requires that all Ph.D. students pass a Preliminary Examination before advancing to candidacy for the doctoral degree. Before a BCB student can take the Preliminary Examination, they must have completed at least two of the four BCB core courses. The Preliminary Examination meeting should be completed before the end of the first semester of the third year. All POS committee members must be present.

To initiate this process, the student must file a Request for Preliminary Examination form (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.

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.

Writing the Dissertation or Thesis

BCB requires students’ research projects to be interdisciplinary, including both 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.

Writing in alternate 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.

If research data from other students or researchers is included in the thesis (e.g., the student is one of several co-authors on a manuscript included in the thesis), instructions on how to clearly indicate co-authors’ roles in the research and/or preparation of the manuscript is available from the Graduate College. Their webpage on electronic theses/dissertation submission includes links to critical formatting information.

Students must provide a hardbound copy of the final thesis to the BCB program office. The BCB copy does not require special paper, and can be printed on either one or both sides of the page. Thesis binding services are provided for a nominal charge by Printing and Publications or by the Memorial Union Copy Center.

Application for Graduation

Students must submit an Application for Graduation form to the Graduate College indicating the expected semester of graduation. This form must be completed by midterm of the semester preceding the graduation semester. If a student does not graduate at the expected time, a new application must be submitted for a subsequent semester. The Graduate application form is available at http://www.grad-college.iastate.edu/forms/forms.html.

Thesis Seminar and 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. This includes a required formal seminar presentation of thesis research to the Bioinformatics and Computational Biology faculty, students, and other members of the Iowa State academic community.

Students should submit a Request for Final Examination form after the dissertation or thesis work has been completed and all the other requirements have been met. After receipt of this form, the Graduate College will send a Report of Final Examination form directly to the major professor. The major professor is responsible for bringing this form to the final oral examination.

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. Following the public seminar (usually, but not always immediately afterwards), an 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. This examination will review the dissertation or thesis and the candidate’s knowledge of relevant subjects.

BCB Exit Interview

After receiving the Graduate Student Approval Slip for Graduation from the Graduate College, students should schedule a 30-minute exit interview with the BCB Chair. The Chair’s signature (as Director of Graduate Education [DOGE] for BCB) is required on the Approval Slip. If a bound copy of the thesis has not already been provided to the BCB office, it should be given to the BCB Chair at the exit interview.

After Graduation

Letters of Recommendation
When letters of recommendation are needed for future employment or grant proposals, students should directly contact faculty to ask whether they are willing to serve as referees. If so, students should provide the following:
• adequate advance notice (at least three to four weeks);
• a copy of the job posting or job description;
• a current Curriculum Vitae; and
• an email reminder one week before the recommendation deadline.
It is courteous (and wise) to send referees a complete numbered list of the letters needed, with deadlines clearly indicated AND pre-addressed labels. An electronic copy of this address list is usually appreciated.

Dismissal

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.

Dismissal Criteria
A student may be dismissed, that is, removed from the degree program and not permitted to register as a BCB student, for the following reasons:

• Failure to progress satisfactorily in his/her degree program

This may be evidenced by a lack of research progress, a lack of aptitude or a failure to maintain satisfactory academic standing, as defined by the Iowa State University Graduate College Handbook.

• Lack of a major professor

Because graduate degrees in Bioinformatics and Computational Biology at ISU are centered about a mentored research project, it is impossible to complete a degree without a research mentor (major professor). To maintain good standing and earn a degree in BCB, a student must have a BCB faculty member serving as major professor.

A student admitted to BCB on rotation has up to 12 months (Ph.D.) or 6 months (M.S.) from the date of entry into the program to find a faculty member willing to serve as his or her major professor (unless otherwise designated at the time of admission). If the student desires assistance, the BCB Chair will help the student search for a major professor; however, final responsibility for finding a major professor rests with the student.

Occasionally, a faculty member who has agreed to serve as a major professor becomes unable or unwilling to serve. A faculty member who wishes to terminate service as major professor for a BCB student may do so by notifying the student and the BCB Chair in writing. A student who has lost his or her major professor has up to three months (after the date the BCB Chair was notified) to identify another BCB faculty member willing to serve. (In BCB, the co-major professor usually would be the logical choice to replace the major professor; if he or she agrees, a new co-major professor should be appointed.) The BCB Chair will help the student search for a new major professor, if the student desires.

• Academic dishonesty

The proper conduct of science requires the highest standards of personal integrity. Because of this, the University and BCB consider dishonesty in the classroom or in the conduct of research to be a serious offense. Students accused of academic dishonesty will be dealt with according to the procedures outlined in the University Catalog and the Faculty Handbook. Possible punishments can include dismissal from the program and expulsion from the University, depending on the severity of the offense.

Dismissal Procedures
A student’s POS committee – or, if the student has no POS committee, the student’s major professor, temporary advisor, or a member of the BCB Supervisory Committee – can recommend dismissal of a student for any of the reasons listed above. Recommendations for dismissal are made to the BCB Chair and are acted on by the BCB Supervisory Committee.

Procedures for dismissal are as described in the ISU Graduate College Handbook. Before a dismissal is decided, the BCB Chair must give the student a written notice explaining why dismissal is being considered. The BCB Chair must also discuss the situation with the student – as well as with the POS committee, major professor, temporary advisor, and/or Supervisory Committee – in an attempt to find a satisfactory resolution. This discussion constitutes the “informal conference” as described in the Graduate College Handbook. If a satisfactory resolution cannot be reached and the Supervisory Committee votes to dismiss the student, either party may bring the issue to the attention of the Associate Dean of the Graduate College for a decision. The student may appeal the decision of the Associate Dean, as described in the Graduate College Handbook.

Responsibilities of BCB and the Major Professor
It is the responsibility of BCB to counsel students who are having academic difficulties, to help students search for an acceptable major professor or, if students are unable to overcome these difficulties, to help the students identify and apply to other appropriate degree programs. It is the responsibility of the major professor and his/her department to seek funds for a student’s assistantship and for the conduct of research.

Relationship between Status in BCB and Termination of Financial Support
Although students in BCB are normally supported on graduate assistantships, this is not a requirement for continued participation in BCB. Students not on assistantship will continue to have regular status in the major so long as they remain in good standing and are registered.

Because assistantship support at Iowa State requires that a student be a member of a graduate program, dismissal from BCB requires that assistantship support be terminated unless the student is able to transfer to another graduate program at ISU.

Students with any doubt about their assistantship status should discuss their situation with their major professor, the department or program providing their assistantship support and/or the BCB Chair. For further information on termination of assistantship appointments, see the Graduate College Handbook.

Appeal Process
The University has established appeal processes for student grievances. These vary depending on the nature of the grievance, and are described in the Graduate College Handbook. Generally, these procedures begin with the program chair or the appropriate Department Executive Officer. It is usually best for all parties if a satisfactory resolution can be reached without initiating a formal appeal process. The Associate Dean of the Graduate College is available to consult informally with students and faculty.

VI. CAMPUS RESOURCES

ISU/BCB Computer Services/Resources

Iowa State University has outstanding computational and biological research facilities that support collaborative research groups in the life sciences, bioinformatics and computational biology, computer and information sciences, engineering, and complex adaptive systems.

Links to a number of campus resources for bioinformatics, computational biology and biological statistics are available on the BCB website under Resources. For a compilation of some of these resources, visit: http://www.bcb.iastate.edu/Resources.html . Some of these resources include:

• Information Technology (IT) at Iowa State Univeristy -- manages a campus-wide network, which augments the various departmental computing facilities. Major computational research facilities include the Center for Bioinformatics and Biological Statistics, the Virtual Reality Applications Center, the Scaleable Computing Laboratory, and the Artificial Intelligence, Database, and Distributed Computing Research Laboratories in the Department of Computer Science.

General information about the computing facilities at Iowa State University can be found at http://it.iastate.edu/ or call the Solution Center located in 195 Durham, at 294-4000.

Laptop checkout is available from the Solution Center at 195 Durham Hall. Checkout is free for three days and is done on a first-come, first-serve basis. Find more information here: http://www.it.iastate.edu/checkout/.

• ISU Library - Andrea Dinkelman, Asst. Professor and Science and Technology Librarian, has a page devoted to bioinformatics resources. Find that at: http://instr.iastate.libguides.com/bcb.

• The BCB Lab - a student-led initiative in the BCB Program which provides a forum for the exchange of experience, knowledge, and resources to enhance research activities. Visit their website.

• The BCB Library - BCB has purchased a number of books and started a modest library operation to benefit BCB students. The library is currently housed in 2014 Molecular Biology Building. A link to the BCB Library’s list of the books is here: http://www.bcb.iastate.edu/documents/BCB-Booklist-June09.pdf

In addition, Current Protocols in Bioinformatics is available in the BCB Library which is a 2,000 page resource by Wiley that is updated with new material every three months.

Laurence H. Baker Center for Bioinformatics and Biological Statistics

The mission of the Laurence H. Baker Center is to facilitate the bioinformatics work of students and faculty by providing computer support, fostering communications among the students and faculty at ISU and with external laboratories and granting agencies, and providing leadership in bioinformatics activities. Faculty in the Center are engaged in research that either: 1) produces large amounts of biological data or 2) develops computational, graphical, or algorithmic methods to interpret and glean information from large biological data sets. Such data sets stem from molecular, cellular, anatomical, physiological, population, and ecological studies. Additional information is available at: http://www.bioinformatics.iastate.edu

Graduate and Professional Student Senate (GPSS)

The Graduate and Professional Student Senate (GPSS) represents the graduate and professional students' perspective on campus issues and serves as a liaison between graduate/professional students and the university administration. Each department/program is permitted to elect or choose 1 Senator for every 50 students in the department up to 5 Senators. Typically, senators are elected by the department's students or are selected by the Graduate Student Organization, if one exists.

For Fall 2009, Sasha Kemmet, CIO, for the organization, called for programs to fill their Senate seats. BCB does not have representation at this time. All senators need to be selected and forms must be submitted by September 11 to serve in the 2009-2010 Senate. Since GPSS also holds an August meeting, it is beneficial if Senators can be elected by August 21. If you are interested in serving, contact the BCB program assistant.

For more information, visit: http://www.grad-college.iastate.edu/gpss/index.html. The GPSS office is located in the West Student Office Space J, Memorial Union, email: gpsscio@iastate.edu

Student-Sponsored Seminars

BCB students are encouraged to recommend invited speakers for Bioinformatics, Computational Biology and Biological Statistics seminars on campus. Funding is available for at least one student-sponsored seminar by a top-caliber visiting scientist each year (i.e., students invite and make arrangements for hosting the speaker). The 1414 Molecular Biology Building Classroom which has a capacity of 199 is available to BCB for Seminars on Wednesdays at 4:10.

VII. FINANCIAL MATTERS

Graduate Appointments and Assistantships

Most students in Bioinformatics and Computational Biology receive some form of financial support. However, both the source of the support and the responsibilities associated with it vary from situation to situation. New BCB students are admitted to the program in one of two categories discussed in Section III. Students entering Bioinformatics and Computational Biology for exploration rotations usually receive a Research Assistantship (RA) funded by Bioinformatics and Computational Biology during the first year or by an NSF two-year fellowship. Typically, Ph.D. students receive 10-24 months of guaranteed assistantship support, and M.S. students receive up to 6 months. Stipends for students admitted as transfers, co-majors, or concurrent degree candidates are provided by major professors or home departments and are governed by departmental policies. The responsibilities associated with a stipend depend on the type of assistantship (Research Assistantship or Teaching Assistantship). Information about these forms of support is available in the Graduate College Handbook.

It is important for students to discuss their future graduate assistantship support with potential major professors. After a major professor has been chosen, the primary responsibility for a student's assistantship funding lies with the major professor and home department. (For administrative purposes, the major professor's department becomes the student's home department.)

All graduate students on assistantships sign a Graduate Assistantship Letter of Intent that lists the terms and conditions of their appointment. Generally, graduate assistantship appointments are on a "one-half time" basis. "Half-time" is the maximum time appointment for graduate students; the remaining "half-time" is spent as a student in graduate studies and research. Appointments can be terminated by mutual consent or for reasons as described in the Graduate College Handbook. Any questions regarding graduate appointments should be directed to the BCB office (2014 Molecular Biology Building).

• Financial constraints and program changes may result in adjustment in specific responsibilities and/or sources of funds during the period of appointment.
• The Graduate Assistantship Letter of Intent is based on the University fiscal year and does not imply that support will terminate on the end date noted in the Letter of Intent.
• BCB students will receive continued Graduate Assistantship support (either as a Research Assistant or Teaching Assistant) for the duration of Ph.D. degree work, as long as students remain in good standing. The specific source(s) of funding may vary depending on resources available to the major professor.
• If a student transfers from the BCB Ph.D. program to the BCB M.S. program, the student will be financially responsible for his/her education after the transfer.

The University payday is the last workday of each month, with pay deposited directly into students’ bank accounts. Direct deposit and any bank account changes can be done on a student’s AccessPlus account. Deductions are made for Federal and State income taxes and Social Security, if applicable.

Competitive Fellowships for Enrolled Students

In addition to the fellowships available for new students entering the BCB program, fellowship opportunities also exist for currently enrolled BCB students. See www.bcb.iastate.edu/students/fellowships.html for additional information on fellowships for both new and enrolled students. Below is information on two awards for currently enrolled students.

Pioneer Hi-Bred International/Baker Center Graduate Research Fellowships
The Pioneer Fellowships provide a stipend of $20,000 per year for two years, plus tuition, benefits and fees. Pioneer Fellows work as interns at Pioneer Hi-Bred for eight weeks during the summer of their first year of support. Subsequent internships can be arranged by agreement of both parties.

Ph.D. students who have completed at least their first year of graduate training are eligible to apply. Eligibility is not limited to students in the Bioinformatics and Computational Biology graduate program, those receiving IGERT or MGET support, or those with major professors affiliated with the Baker Center. Students in any program or department with a research interest in computational molecular biology and bioinformatics are eligible.

The Pioneer Fellowships are awarded to deserving students with strong records of research accomplishment or evidence of great potential.

James Cornette Research Fellowships in Bioinformatics and Computational Biology
The Cornette Fellowships provide $10,000 six-month research assistantships plus tuition, benefits, and fees.

Ph.D. students majoring in Bioinformatics and Computational Biology who have completed at least their first year of graduate training are eligible to apply. Each student is eligible for a maximum of two Cornette Research Fellowships during his or her graduate program. Students must have met their program timeline requirements for academic, course, and training requirements and other required activities. (These requirements will vary for students depending on their program and their year of graduate study.)

The Cornette Fellowships are awarded to deserving students with strong records of research accomplishment or evidence of great potential. The awards are made in the Fall and begin on January 1.

Grants for Professional Travel

Attendance and presentation of research results at professional meetings are an essential part of the BCB graduate training program. Students should attend at least one national or international meeting during their degree program.

Financial assistance is available through Professional Advancement Grants from the Graduate College and the Graduate and Professional Student Senate, from major professors and home departments, and from the BCB program. Students interested in attending a conference should:

• discuss conference opportunities with their major professor and ask about the availability of funding provided through the major professor and the home department;
• plan conference attendance well in advance to ensure the best pricing for registration and airfares, and to secure funding;
• complete the Professional Advancement Grant (PAG) application for funding from the Graduate College and the Graduate and Professional Student Senate. The form and instructions are on the GPSS site: http://www.grad-college.iastate.edu/gpss/PAG/index.html
• submit the original of the PAG form to the Home department administrative office; and a copy of the PAG form to the BCB office, 2014 MBB. The home department typically will submit the form to the Graduate College for you.

The copy of the PAG form will serve as the application for BCB conference funding. Funding is available from the BCB program according to the following schedule, up to a maximum of $1,000 over a five-year period for a Ph.D. student or $400 over a two-year period for an M.S. student:

• $200 per year, when presenting research
• $100 per year, when not presenting research

Professional Advancement Grants

The Graduate and Professional Student Senate provides funds not only to support attendance at professional meetings, but also to support graduate student research and childcare. Information and forms are available on the GPSS website at http://www.grad-college.iastate.edu/gpss/, under Professional Advancement Grants.

Benefits

Student Health Insurance
Single student coverage under the Iowa State University Student Health Insurance Plan is provided free of charge to all graduate assistants at ISU. Insurance sign-up for new students takes place during Orientation. New students should not discontinue any other insurance before ISU coverage begins. Students also can arrange for insurance coverage for their family; this option is available only through payroll deduction.

AETNA Health Insurance will provide the 2009-2010 ISU Students and Scholars Health Insurance Program. For information, contact the ISU Student & Scholar Health Insurance Program (SSHIP) office at 0570 Beardshear Hall; phone: (515) 294-2394 or email: isusship@iastate.edu. Their website is at: http://www.hrs.iastate.edu/sship/.

All international students, whether on assistantship or not, are required to carry the ISU Student Health Insurance or to be covered by another health insurance policy. For more information, contact the International Student and Scholars office in Suite 250/252 Memorial Union (294-1120).

Prescription Drug Benefit Program
Graduate students receive single coverage free of charge in a prescription drug benefit program that reduces the cost of generic and prescription drugs available at the Student Health Center. For information, contact the Student Health Center Pharmacy (294-7983).

Health Service
All students have access to services provided by the ISU Student Health Service. A mandatory health fee of $85 per semester ($42.50 for summer session) and a health facility fee of $8 per semester ($4 for summer) are assessed to all students registered for five or more credits. This health fee pays for some services offered at the Student Health Center. The health facility fee applies to the cost of the new Student Health Center. The health center fee is optional for students enrolled for fewer than five credits. The health fee can be increased without notice.

Additional information about the student group plan medical insurance and the benefits of the mandatory health fee can be obtained from the Thielen Student Health Center (294-5801). Information about the Student Health Service also is available in the ISU General Catalog and on the web at www.public.iastate.edu/~health/homepage.html.

Leave
During the exploration rotation period, BCB research assistants with half-time appointments earn vacation at a rate of eight hours per month (equivalent to two calendar days per month). A student may take vacation with the approval of the temporary advisor and by notifying the BCB office.

After students’ Home Department forms are approved, leaves (including maternity/paternity) are handled by the major professors and home departments, which develop and implement their own policies. Vacation time accumulated prior to joining home departments is not carried forward.

The Graduate College Handbook states only:

Arrangements for a leave of absence are made between the graduate assistant and that assistant’s supervisor. When a graduate student employee needs to be absent either for personal reasons or illness, the supervisor should be understanding and accommodating to that need. At the same time, the graduate assistant should attempt to plan personal leave so that it does not interfere with or cause neglect of the duties associated with his or her appointment. Supervisors of graduate assistants are responsible for ensuring that their assistants do not exceed reasonable limits for leave.

All ISU students with assistantship appointments are employees of ISU and, as such, are allowed the regular university holidays (New Year's Day, Martin Luther King Day, Memorial Day, Independence Day, Labor Day, Thanksgiving Day, the Friday after Thanksgiving Day, and Christmas Day, plus one additional day each year determined by the university administration). Absences for other time off must be arranged with the temporary or major professor as outlined above.

Injuries and Injury Reports
If a student is injured while performing duties as a Graduate Assistant, he or she must submit a First Report of Injury as soon as possible. This form is available from ISU’s Environmental Health and Safety department or from ISU’s Forms page located at http://www.adp.iastate.edu/forms/other.html. Usually the University's Worker's Compensation insurance carrier will pay for medical care. (back to top)

VIII. ADMINISTRATIVE MATTERS

Administrative Assistance

The main administrative office for Bioinformatics and Computational Biology graduate students is the BCB program office in 2014 MBB. Office hours are 10 a.m. to 5 p.m. Monday through Friday. The BCB Program Assistant can be contacted at 294-5122 or bcb@iastate.edu.

Communications

It is vital that students maintain good contact with Bioinformatics and Computational Biology personnel throughout their graduate program. There are a number of ways to do this:

Student Contact Information
The BCB program maintains a record of each student's current email address, local home address and telephone number, as well as campus address and telephone number. It is important that students advise the BCB program office of any address changes.

Email
Students should check email at least daily, as this is the primary means of keeping students informed about BCB program activities.

Internet
The Bioinformatics and Computational Biology website contains most of the information pertaining to ongoing program events, and is updated regularly. Students should visit the website regularly at www.bcb.iastate.edu.

Campus Mail Service
All first-year Bioinformatics and Computational Biology graduate students can use the program office, 2014 Molecular Biology Building, as their temporary mailbox in the Molecular Biology Building during the exploration rotation period. After the student chooses a major professor, the student’s home department will arrange a permanent campus address and mailbox.

Telephone
Local calls can be made on most campus phones. Long distance calls can be made on University phones only with the prior approval of the person to whom the phone is assigned.

Transportation

Bicycles
Bicycle racks are located throughout campus. Except for walks labeled as bike paths, bicycle riders are prohibited from using campus sidewalks. Lock your bike to a bike rack. Do not park your bike at medical ramps, trees, fences, or poles…any bike not locked to a bike rack is subject to impounding. Impounded bikes can be released from room 27 Armory for a $5 fee.

To assist in recovering lost or stolen bicycles, students should register bicycles at Ames City Hall ( 515 Clark Avenue) and through an on-line form available at the ISU Department of Public Safety (Armory) here: http://www.dps.iastate.edu/wordpress/?page_id=88

Buses
CyRide is the Ames bus system. Students can ride all CyRide routes free of charge upon presentation of a current ISU card. During the school year the buses leave from most locations every 20 minutes. Schedules are widely available throughout campus. Further CyRide information can be found at http://www.cyride.com/.

Cars and Parking
The Department of Public Safety (http://www.dps.iastate.edu/ ) has a Parking Division located in 27 Armory. Parking is scarce on campus and students can consult with them about these options:

1. Commuters can register their cars and apply for a permit for one of the two commuter lots on campus. One lot, 29, is located north of Molecular Biology and lot 29B is across Stange from Frederiksen Court.
2. Commuter Lot at Iowa State CenterCommuters can park at the parking lots at the Iowa State Center for free and take Cy-Ride’s Orange Route into campus. Cars cannot remain in the Iowa State Center lots past 10:00 p.m.
3. Paying on Campus Commuters have the option of paying to park each time they come to campus. Pay-by-the-hour machines are available in lot 100 on the east side of campus and lot 21 on the west end. There are also meters in some of the lots, but carefully read the signs and meters as some have time limits that do not accommodate classes.

Technological Resources for the Iowa State community

Information Technology, http://www.it.iastate.edu/ provides numerous services and resources to the ISU community. Contact the Solution Center, 195 Durham Center at 294-4000 for additional information or visit their website to learn where computer labs are on campus, what short courses are available, and much, much more.

Computer Checkout
Information Technology offers laptop checkout for temporary use. For more details, check their webpage here: http://www.it.iastate.edu/checkout/ .

Professional Ethics

During Orientation activities, students are required to attend an introduction to the concepts of ethical behavior and good practice in science. Included is discussion of proper research methods, ways to avoid self-deception in the practice of science, and scientific misconduct.

Bioethics training is a critical component of the BCB graduate program requirements. Every BCB student receives copies of Honor in Science and The Responsible Researcher: Paths and Pitfalls, which should be read carefully.

It is imperative that every student understand the ethical standards of science and conduct his or her scholarly activities accordingly. Scientists who commit unethical acts, whether from carelessness, ignorance, or malice, quickly lose the respect of the scientific community and may be prevented from receiving funding support. Scientific misconduct includes such activities as:

• falsification of data, ranging from fabrication to deceptively selective reporting, including the purposeful omission of conflicting data with the intent to falsify results
• plagiarism…representation of another’s work as one’s own
• misappropriation of the ideas of others…unauthorized use of privileged information
• misappropriation of funds or resources for personal gain
• falsification of one’s credentials

At ISU, these acts are taken very seriously and constitute “academic misconduct” (ISU Faculty Handbook, Fall 1999). Individuals found guilty of academic misconduct may suffer a variety of penalties, up to and including expulsion from the university.

If a student is aware of a potentially unethical situation, he or she should seek the advice of a trusted professor. Students may also contact the BCB Chair or a member of the BCB Supervisory Committee. All discussions with the Chair and the Supervisory Committee members will be confidential. Alternatively, students may go directly to Associate Vice Provost for Research, who is responsible for investigating charges of academic misconduct on campus. It is very important to protect the rights of the individual whose actions are questioned. Frivolous accusations of misconduct and vicious spreading of rumors are just as unethical as fabrication of data or plagiarism.   back to top

NON-DISCRIMINATION AND AFFIRMATIVE

ACTION STATEMENT

IOWA STATE UNIVERSITY

(July 28, 2008 Reaffirmation)

Iowa State University is committed to developing and implementing a program of nondiscrimination and affirmative action, a responsibility the university accepts willingly because it is the right and just thing to do. Because an educational institution exposes the youth of Iowa and of the nation to a multitude of ideas that strongly influence their future development, it is an area of our society where removing barriers is critical. We insist on promoting the concept of inclusion and participation.

This commitment is part of a larger commitment to developing a safe and supportive climate for all members of the ISU community in classrooms and laboratories, in offices, in the residence hall system, and throughout the campus. Iowa State University recognizes that a non-discriminatory environment complements a commitment to academic inquiry and intellectual and personal growth.

The goal is to provide a non-discriminatory work environment, a non-discriminatory living and learning environment and a non-discriminatory environment for visitors to the campus. Iowa State University herein recommits itself to comply with all federal and state laws, regulations, and orders, including the policies of the Iowa Board of Regents, which pertain to nondiscrimination and affirmative action.

All administrators and personnel providing input into administrative decisions are directed to ensure that all decisions relative to employment, conditions of employment and access to programs and services will be made without regard to race, color, age, religion, national origin, sexual orientation, gender identity, sex, marital status, disability, or status as a U.S. veteran. Exceptions to this directive may be made in matters involving bona fide occupational qualifications, business necessity, actions designed to eliminate workforce underutilization, and/or where this policy conflicts with federal and state laws, rules, regulations, or orders.

Iowa State does not discriminate on the basis of race, color, age, ethnicity, religion, national origin, pregnancy, sexual orientation, gender identity, sex, marital status, disability, or status as a U.S. veteran. Inquiries can be directed to the Director of Equal Opportunity and Diversity, 32100 Beardshear Hall, (515) 294-7612. Iowa State University will base employment decisions so as to further the principle of equal employment opportunity and diversity.

No otherwise qualified person will be denied access to, or participation in, any program, activity, service, or the use of facilities on the basis of factors previously enumerated. Reasonable accommodation will be made to facilitate the participation of persons with disabilities in all such activities consistent with applicable federal and state laws, orders and policies.

Further, all supervisory personnel will be responsible for maintaining an environment that is free of discrimination and harassment. Acts by anyone that adversely affect another person's employment, conditions of employment, academic standing, receipt of services, and/or participation in, or enjoyment of, any other activity, will be regarded as a violation of university policy and thereby subject to appropriate disciplinary action. Retaliation against persons filing complaints, for bringing the violation of this policy forward for review, or for assisting in a review, pursuant to a filed complaint or grievance, is prohibited.

Iowa State University 's commitment to nondiscrimination and affirmative action is of the highest priority and is to be adhered to as such. It applies to all university-sponsored programs and activities as well as those that are conducted in cooperation with the university.

Iowa State University has designated Carla R. Espinoza as the affirmative action officer and assigns overall program responsibility to her as the Director of Equal Opportunity and Diversity. Questions regarding complaints and/or compliance with affirmative action or equal opportunity should be directed to her at 3210 Beardshear Hall, Iowa State University, Ames, IA 50011-2024, (515) 294-7612.

IX. ISU Basics

AccessPlus

Iowa State University's AccessPlus is a personalized secure university information resource that provides on-demand accessibility to your confidential information. Much university business for students can be handled through their AccessPlus accounts. The menu options for students include:

Account/U-Bill
Address Change
Admissions
Campus Housing
Campus Org Events
Class Registration
Class Schedule
Current Student Information
CyCash
Dining Services
Direct Deposit
Enrollment Cert
Financial Aid
Grad Student Status
Grades & Transcripts
Health Insurance
Student Job Board
Tax Info (1098)
Telephone Services
Third Party Access
Votes and Surveys
Web Based Training

 

The University phone directory is updated each Fall; copies can be purchased at the University Bookstore, Memorial Union. The directory includes a two-year calendar of academic dates and deadlines. The online directory is updated regularly throughout the year.

The Iowa State University homepage is at http://www.iastate.edu/.            back to top