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New Undergraduate Option
Genomics/Bioinformatics

Status: Approved and Processed

Proposal

Proposal ID: 2266
Type: New Option/Minor
Submission Date: January 3, 2006 4:19pm
Approval Date: September 20, 2006 11:06am
Effective Term: Spring 2006
Justification:
Justification:
The purpose of the proposed BRR G/B Option is to provide a research-based undergraduate major in Genomics/Bioinformatics.

The field of Genomics/Bioinformatics represents a research breakthrough basic enough to cause a paradigm change, with the potential to transform almost every area of research in natural resources and agriculture. As a result, this growing interdisciplinary field forms a central focus of OSU’s mission, and also plays a role in the College of Agriculture’s Strategic Plan. Many faculty members at OSU are currently performing cutting-edge Genomics/Bioinformatics research in fields as varied as environmental microbiology, forestry, crop genetics, and the study of plant, animal and human pathogens. The University-wide Computational and Genome Biology Initiative recognizes the growing importance of this field in Oregon, and is currently hiring more faculty in Genomics/Bioinformatics. The proposed undergraduate G/B Option will complement OSU’s research initiative and graduate programs, and will create organized undergraduate access to broad-based faculty research excellence in Genomics/Bioinformatics.

As far as we know, there is no other G/B undergraduate program in Oregon; there are only a small number of G/B undergraduate programs nationwide. There is a demand for an undergraduate program in this area at OSU. One BRR student has already completed a genomics/bioinformatics research project (in the Botany and Plant Pathology department). This student was awarded a Howard Hughes Fellowship and is currently a beginning graduate student in Microbiology. The new G/B Option will be a broadly interdisciplinary degree program at the undergraduate level, in which students do a thesis and are grounded in all the basic sciences in the context of a liberal education. The G/B Option will give undergraduates research experience in Genomics/Bioinformatics, preparing them for graduate school at OSU or elsewhere, or for entry into careers in such areas as the pharmaceutical, natural products, food products, crop genetics and biotechnology industries. Because Genomics/Bioinformatics is a relatively new field, graduates with bachelor’s degrees that have training in this area are extremely rare. OSU students with both training and research experience should be in a strong competitive position.

As well as completing BRR required coursework in biological and physical sciences, mathematics, and statistics, students in the G/B Option will be required to take option courses in four areas: Biochemistry/Molecular Biology, Genetics/Organismal Biology, Computer Science, and Statistics/Modeling. G/B students will also be required to do an internship in Biocomputing (BRR410). We chose these areas in consultation with genomics researchers, and we also examined G/B undergraduate and graduate curricula at other universities. Courses in Biochemistry/Molecular Biology will teach the students the chemical, biochemical and biological nature of genomics data and how they are generated. Courses in Genetics/Organismal Biology will give students the biological background to understand the interesting research questions in his or her area. Computer Science courses will provide the tools used for genomics analyses, and Statistics/Modeling courses will provide an understanding of the methods of analysis. Background courses in these four areas, therefore, will provide breadth of knowledge. For depth of understanding in the option, students will develop an area of emphasis by choosing one of the four areas and taking an additional 6 to 8 credits of upper-division courses in that area. Because of the broadly interdisciplinary nature of the field, we have provided a choice of courses within these four areas; this will allow students and their faculty mentors to tailor their programs to their specific research projects. The courses in each of the four areas were selected with advice from OSU faculty to cover important areas in the field. Several people we consulted had specific suggestions as to how to improve our original proposal, which we incorporated into the final proposal. Students also have unspecified electives in the option, allowing them to acquire the specific coursework they need for their research projects or for graduate school in their chosen fields.

The centerpiece of the BRR interdisciplinary major is a comprehensive undergraduate research experience. This differentiates BRR from several related undergraduate programs in science and natural resource areas. BRR students choosing the G/B Option will learn genomics/bioinformatics from their research projects. They will apply the knowledge they gained in course work to real problems; they will learn experimental design, the scientific method, analytical tools and computer skills by doing research. BRR students also participate in the lab or group meetings of their faculty mentor and learn from other students and more senior personnel.

BRR students take required foundation courses in the biological and physical sciences. In addition, they perform 2 full years of research (a minimum of 14 credits) in the laboratory or program of a faculty mentor, culminating in a senior thesis and seminar. Students and their faculty mentors develop a list of relevant advanced courses tailored to their chosen options and research. The BRR program is one of the top research-based undergraduate programs in the nation. 60% of BRR graduates go on to graduate school; others have used their training to gain employment in research, environmental consulting and engineering, and governmental positions. 100% of BRR graduates are employed or in graduate school.

BRR students can select research mentors from among participating faculty mentors in a broad variety of departments and colleges such as Biochemistry, Biology, Bioengineering, Botany and Plant Pathology, Chemistry, Crop and Soil Sciences, Environmental and Molecular Toxicology, Environmental Science, Fisheries and Wildlife, Forest Sciences, Forest Resources, Microbiology, Natural Resources, Oceanography, Public Health, and Zoology.

The proposed G/B curriculum substitutes MTH 231 and 232 for MTH 251 and MTH 252 (the latter two courses are on the regular BRR curriculum). This is because MTH 231 and 232 are prerequisites for computer science courses. It also substitutes BB 490 and BB 491 for BB 450 and BB 451 (the latter two courses are on the regular BRR curriculum). BB 490 and BB 491 are prerequisites for BB 492. The BB 490-492 sequence provides students with a rigorous training in biochemistry, molecular biology and protein structure. This substitution was suggested by members of the Biochemistry Department at the curriculum planning meeting.

It seems likely and desirable that courses and programs in Genomics/Bioinformatics will be developed in departments such as Biochemistry, Microbiology, and Computer Science. For example, Dr. Dan Rockey offered an experimental undergraduate course in genomics during summer term 2005 (as BB/MB 405). Although Dr. Rockey will be unable to continue this course, it is likely to be picked up and developed by others. Another need is a course in Biocomputing; concepts needed for modern biocomputing are currently not presented in an organized fashion, but instead scattered through a large number of computer science courses or not taught at OSU. New undergraduate courses will strengthen the proposed BRR G/B option and can be added to the BRR G/B curriculum when appropriate. However, even if another department starts a Genomics option or major, BRR is unique in offering a substantive research experience. A BRR student could double-major or minor in a new Genomics track or major to obtain the academic background of the new program, while completing the BRR major in order to gain the research experience.

There are currently several graduate courses in topics related to genomics/bioinformatics (for example, MB 668, Genomics and Cellular Evolution). While undergraduate enrollment in these courses is at the discretion of the instructor, we will encourage BRR G/B students to participate if they can obtain permission.
Comments:
There is no syllabus because this proposal is for an option, not a course.

The following four files are atttached:
1. A list of option courses for the proposed BRR Genomics/Bioinformatics option: G/B Option Courses.doc
2. The BRR curriculum: BRR Curriculum.doc
3. The memo that was sent out for formal liaison: Liaison Memo genomics.doc
4. The responses received to the liaison memo: Responses to Liaison GB.doc

Originators

Name Title Department/School
Katharine Field Professor Microbiology (Science)
CN\tuckeral

Contacts

No contacts

Liaisons

No Liaisons

Program Information

Program Title: Genomics/Bioinformatics 
College/Department or College/School: College of Agricultural Sciences 

Program Type: Undergraduate Option 
Description:  
There are currently 10 options in the Bioresource Research interdisciplinary sciences major (BRR); this proposal would create an option in Genomics/Bioinformatics (G/B). Computational advances and the development of high throughput sequencing methods have led to a virtual explosion of genomic and proteomic data. These data provide the material needed to ask questions and undertake experiments in biosciences that have never before been possible. The computer-aided analysis of these data with new tools from information science comprises the field of Genomics/Bioinformatics. The purpose of the proposed BRR G/B Option is to provide a research-based undergraduate major in this field. Students are required to take one or two course in each of four areas: Biochemistry/Molecular Biology, Genetics/Organismal Biology, Computer Science, and Statistics/Modeling. In addition, students will obtain depth by choosing one of these four areas as their area of emphasis and taking an additional 6 to 8 credits of upper-division courses in that area, plus additional upper-division electives. Finally, students are required to do an internship in Biocomputing, as a prerequisite to, or concurrent with starting, their research projects.
Requirements:  
Proposed curriculum:\n\n Genomics/Bioinformatics Option (29 credits): Students are required to take one or two course in each of four areas: Biochemistry/Molecular Biology, Genetics/Organismal Biology, Computer Science, and Statistics/Modeling. In addition, students will obtain depth by choosing one of these four areas as their area of emphasis and taking an additional 6 to 8 credits of upper-division courses in that area, plus additional upper-division electives. Finally, students are required to do an internship in Biocomputing, as a prerequisite to, or concurrent with starting, their research projects. Courses are listed below, followed by the credit hours (in parentheses):\n\n (A) Mathematics: Substitute MTH 231 Elements of Discrete Mathematics (4) and MTH 232 Elements of Discrete Mathematics II (4) for MTH 251 and MTH 252.\n (B) Biochemistry/Molecular Biology: Choose one course: BI 314 Cell and Molecular Biology (4) or BB 331 Introduction to Molecular Biology (3). Students choosing the Biochemistry/Molecular Biology emphasis will choose 6 to 8 additional credits: BI 315 Cell and Molecular Biology Lab (4) or MB 310 Bacterial Molecular Genetics (3) or MB 311 Molecular Microbiology Laboratory (3) or BB 494 Biochemistry Laboratory (3) or BB 481 Biophysics (3) or equivalent upper-division courses approved by research mentor.\n (C) Genetics/Organismal Biology: Choose one course: CSS 430 Plant Genetics (3) or BOT 321 Introduction to Plant Systematics (4) or ANS 378 Animal Genetics (4) or FS 444 Forest Genetics or MB 302 General Microbiology (3). Students choosing the Genetics/Organismal Biology emphasis will choose 6 to 8 additional credits: MB 310 Bacterial Molecular Genetics (3) or MB 454 Genome Organization, Structure and Maintenance or MB 668 Genomics and Cellular Evolution or equivalent upper-division courses approved by research mentor.\n (D) Computer Science: CS 161 Introduction to Computer Science (4) and CS 162 Introduction to Computer Science II (4). Students choosing the Computer Science emphasis will choose 6 to 8 additional credits: CS 261 Data Structures (4) or CS 325 Analysis of Algorithms (4) or CS 420 Graph Theory (3) or equivalent upper-division courses approved by research mentor to fulfill the Computer Science emphasis.\n (E) Statistics/Modeling: Choose one course: BRE 471 Biosystems Modeling Techniques (3) or CSS 490 Field-Plot Techniques (4) or ST 352 Introduction to Statistical Methods (4). Students choosing the Statistics/Modeling emphasis will choose 6 to 8 additional credits: ST 411 Methods of Data Analysis (4) and ST 412 Methods of Data Analysis (4) or ST 421 Introduction to Mathematical Statistics (4) and ST 422 Introduction to Mathematical Statistics (4) or ST 441 Probability, Computing, and Simulation in Statistics (4) or equivalent upper-division courses approved by research mentor.\n (F) Electives: 3-6 additional credits of upper division courses approved by Research Mentor, for a total of 29 credits.\n (G) BRR 410 Biocomputing Internship (3)\n

Documents

File Name File Size Comment Date Added
G:B Option Courses.doc 28.00 Kb Dec 31, 1969 4:00 pm
Liaison Memo Genomics.doc 113.50 Kb Dec 31, 1969 4:00 pm
Responses to liaison GB.doc 41.00 Kb Dec 31, 1969 4:00 pm
BRR curriculum.doc 20.50 Kb Dec 31, 1969 4:00 pm
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