revised bioinformatics bs program - implementation request 2-26-2013

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NEW ACADEMIC PROGRAM – IMPLEMENTATION REQUEST

I. PROGRAM NAME, DESCRIPTION AND CIP CODE

A. PROPOSED PROGRAM NAME AND DEGREE(S) TO BE OFFERED Bachelor of Science in Bioinformatics

B. CIP CODE: 26.1103: Bioinformatics C. DEPARTMENT/UNIT AND COLLEGE – Indicate the managing dept/unit and college

for multi- interdisciplinary programs with multiple participating units/colleges.

Department: Computer Science College: Science

II. PURPOSE AND NATURE OF PROGRAM

The Departments of Computer Science (CSC), Ecology and Evolutionary Biology (EEB), and Molecular and Cellular Biology (MCB) propose to jointly offer a Bachelor of Science degree in Bioinformatics. Bioinformatics is an emerging area of interdisciplinary study that lies at the intersection of computer science and biology that aims to apply computational techniques to manage, analyze, and understand biological information. Technological advances in recent years have led to an explosion in the amount of biological data being created. The large variety of data sources, and the vast scale of the data, makes traditional approaches to data manipulation impractical. What is required, instead, is a combination of highly sophisticated computational algorithms and tools, together with the deep biological knowledge necessary to apply those tools effectively. The purpose of the proposed degree program is to provide students with the breadth of knowledge and expertise, spanning both computational and biological domains, that they need to function effectively in this rapidly-growing area. The organization of this degree program is motivated by the anticipated needs of the biological sciences in the 21st century.1 It contains four emphasis areas: in Computer Science, Ecology and Evolutionary Biology, Molecular and Cellular Biology, and Systems Biology. The first three areas emphasize material from the corresponding department. All

1 National Research Council, A New Biology for the 21st Century, National Academy of Sciences, 2009: “The New Biologist is not a scientist who knows a little bit about all disciplines, but a scientist with deep knowledge in one discipline and a `working fluency’ in several.”

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emphasis areas are supported by a core set of courses focusing on material that every bioinformaticist should know.

III. PROGRAM REQUIREMENTS – List the program requirements, including minimum number

of credit hours, required courses, and any special requirements, including subspecializations, subplans, theses, internships, etc.

The BS in Bioinformatics degree has a core curriculum in biology and computer science, and four possible areas of emphasis: an emphasis in (i) Molecular and Cellular Biology, (ii) Ecology and Evolutionary Biology, (iii) Computer Science, or (iv) Systems Biology. All four emphasis areas share the same core curriculum in the first two years, and then begin specializing in the third and fourth years. The Computer Science and Systems Biology emphasis areas also take a more advanced mathematics and statistics sequence in their second year. The degree proceeds by first covering the essential core curriculum of Molecular and Cellular Biology, Ecology and Evolutionary Biology, and Computer Science, and then moves on to upper-division courses specific to the field of bioinformatics. Students who are majors in the program take a 1-unit seminar course in their freshman and sophomore years that gives an overview of the field of bioinformatics, and provides majors an opportunity to get to know one another. We describe the BS in Bioinformatics curriculum by presenting four-year plans for each of the four emphasis areas. All specific courses listed in the plans are required for that emphasis area; where electives are available, they are noted, and are to be selected from a list of approved electives (provided later in Section III.A). All plans meet the University and College of Science degree requirements with respect to general education, mathematics, foreign language, and upper division requirements, and have a total of 120 units for the degree. The description of the four-year plans for the emphasis areas begins on the next page.

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BS in Bioinformatics: Molecular and Cellular Biology Emphasis

Year 1, Fall Year 1, Spring

CHEM 151 (General Chemistry I), 4** CHEM 152 (General Chemistry II), 4**

MATH 122A (Calculus I), 1 MATH 129 (Calculus II), 3

MATH 122B (Calculus I), 4 CSC 127B (Introduction to Computer Science II), 4

CSC 127A (Introduction to Computer Science I), 4 CSC 190 (Seminar in Bioinformatics), 1

ENGL 101 (First-Year Composition), 3** ENGL 102 (First-Year Composition), 3

Total 16 units Total 15 units


CHEM 241A (Organic Chemistry), 3** CHEM 241B (Organic Chemistry), 3**

CHEM 243A (Organic Chemistry), 1 CHEM 243B (Organic Chemistry), 1

MATH 263 (Introduction to Statistics and Biostatistics), 3

CSC 245 (Introduction to Discrete Structures), 4

CSC 250 (Essential Computing for the Sciences), 3 CSC 290 (Seminar in Bioinformatics), 1

MCB 181R (Introductory Biology I), 3 ECOL 182R (Introductory Biology II), 3

MCB 181L (Introductory Biology I), 1** ECOL 182L (Introductory Biology II), 1

Gen Ed, 3***



BIOC 385 (Metabolic Biochemistry), 3 PHYS 103 (Introductory Physics II), 3

PHYS 102 (Introductory Physics I), 3 PHYS 182 (Introductory Laboratory II), 1

PHYS 181 (Introductory Laboratory I), 1 MCB 304 (Molecular Genetics), 5

CSC 345 (Analysis of Discrete Structures), 4 ECOL 346 (Bioinformatics), 4

Gen Ed, 3*** Gen Ed, 3***


Year 4, Fall and Spring

MCB 305 (Cellular and Developmental Biology), 4

MCB 315 (Key Concepts in Quantitative Biology), 4

Gen Ed, 12***

Foreign Language, 6****

Electives (at least 1 upper-division MCB elective), 3*

Total 29 units (for 2 semesters)

Notes * To complete a second major in Molecular and Cellular Biology, students would need to ensure the elective courses meet the MCB Lab, Writing-Emphasis, and Core Elective requirements. ** Honors options for these courses include ENGL 109H, MCB 181M, CHEM 105A, CHEM 105B, CHEM 106A, CHEM 106B, CHEM 242A, and CHEM 242B. *** Students should select upper-division Tier-Two General Education courses to meet the 42 overall upper-division units requirement. **** Students who satisfy the second-semester foreign language proficiency requirement out of high school will replace these foreign language units with approved upper-division electives in the program.

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BS in Bioinformatics: Ecology and Evolutionary Biology Emphasis











MATH 263 (Introduction to Statistics and Biostatistics), 3

CSC 245 (Introduction to Discrete Structures), 4

CSC 250 (Essential Computing for the Sciences), 3 CSC 290 (Seminar in Bioinformatics), 1

MCB 181R (Introductory Biology I), 3 ECOL 182R (Introductory Biology II), 3

MCB 181L (Introductory Biology I), 1** ECOL 182L (Introductory Biology II), 1

Gen Ed, 3***



PHYS 102 (Introductory Physics I), 3 PHYS 103 (Introductory Physics II), 3

PHYS 181 (Introductory Laboratory I), 1 PHYS 182 (Introductory Laboratory II), 1

CSC 345 (Analysis of Discrete Structures), 4 ECOL 335 (Evolutionary Biology), 4

ECOL 320 (Genetics), 4 ECOL 346 (Bioinformatics), 4

Gen Ed, 3*** Gen Ed, 3***



ECOL 302 (Ecology), 4

ECOL 465 (Phylogenetic Biology), 3

Gen Ed, 12***


Electives (at least 1 upper-division EEB elective), 4*


Notes

* To complete a second major in Ecology and Evolutionary Biology, students would need to ensure the elective courses meet EEB requirements. ** Honors options for these courses include ENGL 109H, MCB 181M, CHEM 105A, CHEM 105B, CHEM 106A, CHEM 106B, CHEM 242A, and CHEM 242B. *** Students should select upper-division Tier-Two General Education courses to meet the 42 overall upper-division units requirement. **** Students who have already satisfied the second-semester foreign language proficiency requirement out of high school will replace these foreign language units with approved upper-division electives in the program.

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BS in Bioinformatics: Computer Science Emphasis











MATH 254 (Introduction to Ordinary Differential Equations), 3

MATH 363 (Introduction to Statistical Methods), 3

CSC 250 (Essential Computing for the Sciences), 3 CSC 245 (Introduction to Discrete Structures), 4

MCB 181R (Introductory Biology I), 3 CSC 290 (Seminar in Bioinformatics), 1

MCB 181L (Introductory Biology I), 1** ECOL 182R (Introductory Biology II), 3

ECOL 182L (Introductory Biology II), 1



CSC 345 (Analysis of Discrete Structures), 4 CSC 445 (Introduction to Algorithms), 3

MCB 304 (Molecular Genetics), 5; or ECOL 320 (Genetics), 4

MCB 305 (Cellular and Developmental Biology), 4; or ECOL 335 (Evolutionary Biology), 4

Gen Ed, 6*** ECOL 346 (Bioinformatics), 4

Gen Ed, 6***

Total 14-15 units Total 17 units


CSC 450 (Algorithms in Bioinformatics), 3

Gen Ed, 9***


Electives (including at least 2 upper-division Computer Science electives), 9-10

Total 27-28 units (for 2 semesters)

Notes

** Honors options for these courses include ENGL 109H, MCB 181M, CHEM 105A, CHEM 105B, CHEM 106A, CHEM 106B, CHEM 242A, and CHEM 242B. *** Students should select upper-division Tier-Two General Education courses to meet the 42 overall upper-division units requirement. **** Students who have already satisfied the second-semester foreign language proficiency requirement out of high school will replace these foreign language units with approved upper-division electives in the program.

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BS in Bioinformatics: Systems Biology Emphasis











MATH 254 (Introduction to Ordinary Differential Equations), 3

MATH 363 (Introduction to Statistical Methods), 3

CSC 250 (Essential Computing for the Sciences), 3 CSC 245 (Introduction to Discrete Structures), 4

MCB 181R (Introductory Biology I), 3 CSC 290 (Seminar in Bioinformatics), 1

MCB 181L (Introductory Biology I), 1** ECOL 182R (Introductory Biology II), 3

ECOL 182L (Introductory Biology II), 1



BIOC 385 (Metabolic Biochemistry), 3 MCB 304 (Molecular Genetics), 5

CSC 345 (Analysis of Discrete Structures), 4 ECOL 346 (Bioinformatics), 4

ECOL 302 (Ecology), 4 Gen Ed, 6***

Gen Ed, 3***



ECOL 335 (Evolutionary Biology), 4

MCB 305 (Cellular and Developmental Biology), 4

MCB 480 (Introduction to Systems Biology), 3

Gen Ed, 12***

Electives (including at least 1 upper-division MCB or EEB elective), 7*


Notes

* To complete a second major in Molecular and Cellular Biology, or Ecology and Evolutionary Biology, students would need to add 2 semesters of physics (PHYS 102, 181, 103, and 182), and additional MCB or EEB electives to meet the respective MCB or EEB requirements. Students who have not already satisfied the second-semester foreign language proficiency requirement out of high school will replace some of these elective units with foreign language units. ** Honors options for these courses include ENGL 109H, MCB 181M, CHEM 105A, CHEM 105B, CHEM 106A, CHEM 106B, CHEM 242A, and CHEM 242B. *** Students should select upper-division Tier-Two General Education courses to meet the 42 overall upper-division units requirement.

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A. CURRENT COURSES AND EXISTING PROGRAMS -- List current courses and existing university programs which will give strengths to the proposed program.

The degree curriculum builds upon existing strengths in the Molecular and Cellular Biology, Ecology and Evolutionary Biology, and Computer Science programs. Courses currently taught by these programs that are in the core curriculum of the Bioinformatics BS include the following:

CSC 127A (Introduction to Computer Science I), 4 CSC 127B (Introduction to Computer Science II), 4 CSC 245 (Introduction to Discrete Structures), 4 CSC 345 (Analysis of Discrete Structures), 4 CSC 445 (Introduction to Algorithms), 3 CSC 450 (Algorithms in Bioinformatics), 3 ECOL 182R and 182L (Introductory Biology II), 4 ECOL 302 (Ecology), 4 ECOL 320 (Genetics), 4 ECOL 326 (Genomics), 3 ECOL 335 (Evolutionary Biology), 4 ECOL 346 (Bioinformatics), 4 ECOL 465 (Phylogenetic Biology), 3 MCB 181R and 181L (Introductory Biology I), 4 MCB 304 (Molecular Genetics), 5 MCB 305 (Cellular and Developmental Biology), 4 MCB 315 (Key Concepts in Quantitative Biology), 4 MCB 480 (Introduction to Systems Biology), 3

(Note: ECOL 346, Bioinformatics, will become a 4-unit course beginning Spring 2014.) Other existing courses that provide electives for the degree include the following:

ABE 416 Statistical Bioinformatics and Genomic Analysis BIOC 385 Metabolic Biochemistry CSC 337 Web Programming CSC 352 Systems Programming and Unix CSC 372 Comparative Programming Languages CSC 422 Introduction to Parallel and Distributed Programming CSC 436 Software Engineering CSC 460 Database Systems ECOL 345 Biodiversity and the Tree of Life ECOL 409 Evolution of Infectious Diseases ECOL 426 Population Genetics ISTA 420 Applied Cyberinfrastructure Concepts to Enable Extreme Science ISTA 421 Introduction to Machine Learning ISTA 454 Informatics in Biology PHIL 321 Medical Ethics

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B. NEW COURSES NEEDED -- List any new courses which must be added to initiate the program; include a course prefix, number, title, catalog description and number of units for each of these courses.

The degree program has two new required courses that are not currently offered at the University: CSC 250 (Essential Computing for the Sciences), and CSC 190/290 (Seminar in Bioinformatics), both of which are described below. The course CSC 250 would become a prerequisite for the core bioinformatics course in the degree that is currently taught at the University: ECOL 346 (Bioinformatics). CSC 250 has no prerequisites, but its content does require some academic maturity, and hence it is numbered at the 200-level. The course CSC 190/290 is a freshman and sophomore seminar-style course that introduces students who are majors in the program to the field of bioinformatics.

CSC 190/290, Seminar in Bioinformatics (1 unit). Prerequisites and corequisites: none. This seminar-style course provides an overview of and introduction to the field of bioinformatics. Talks by faculty who do research in bioinformatics and computational biology, as well as by scientists from the biotechnology industry, give a sense of the current directions in the field.

CSC 250, Essential Computing for the Sciences (3 units). Prerequisites and corequisites: none. This course teaches essential computational skills for students in scientific disciplines, such as bioinformatics, biology, chemistry, and physics. The content focuses on three computational skills: (i) basic programming in a scripting language such as Python, and knowledge of supported data structures; (ii) facility with the UNIX operating system environment, including file structure, regular expressions, and job control; and (iii) essential database skills, including database accession and interfacing through the SQL query language.

C. REQUIREMENTS FOR ACCREDITATION -- Describe the requirements for accreditation if the program will seek to become accredited. Assess the eligibility of the proposed program for accreditation.

No program accreditation will be sought. D. DISTANCE LEARNING – Indicate whether this program will be offered via distance

learning and which courses are available via distance learning.

The program will not be offered via distance learning.

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IV. STUDENT LEARNING OUTCOMES AND ASSESSMENT A. STUDENT OUTCOMES -- Describe what students should know, understand,

and/or be able to do at the conclusion of this program of study.

Graduates of the BS in Bioinformatics program would: (i) have a breadth of competency in both Computer Science, and Molecular and Cellular Biology or Ecology and Evolutionary Biology, from having completed the basic core curriculum in both disciplines; (ii) have achieved depth in one of these disciplines through the coursework in their chosen emphasis area; and (iii) have completed advanced training in bioinformatics through specialized courses in the major such as ECOL 346 (Bioinformatics), CSC 450 (Algorithms in Bioinformatics), and MCB 408 (Introduction to Systems Biology). This is congruent with the view from the National Research Council report2 that states, “The New Biologist is not a scientist who knows a little about all disciplines, but a scientist with deep knowledge in one discipline and a `working fluency’ in several.” All graduates would be fluent in computer programming, and have a well-grounded knowledge of computer science up through data structures and fundamental algorithms; would have vital knowledge of biology from the molecular level, to the genomic level, up through the cellular level, and a sound understanding of evolution and genetics; and would have basic essential skills in chemistry, mathematics, and statistics. Depending on their emphasis area, students would have further knowledge in algorithm design, biochemistry, quantitative biology, and systems biology. Graduates with an emphasis in Molecular and Cellular Biology, or Ecology and Evolutionary Biology, would be informed users of bioinformatics software tools, be able to process and transform the output from analyses using such tools, and have the domain knowledge necessary to evaluate the biological validity of the results. Graduates with an emphasis in Computer Science would be able to develop new bioinformatics tools and analysis methods, and have the core biological knowledge to be effective in interactions with teams involving biologists and domain experts. Students with a BS in Bioinformatics, furthermore, will be well-prepared to go on for graduate study in bioinformatics with no deficiencies.

B. STUDENT ASSESSMENT -- Provide a plan for assessing intended student

outcomes while the students are in the program and after they have completed the degree.

The curriculum across all emphasis areas is common in the first year, while in the second year students with an emphasis in Computer Science or Systems Biology take a more

2 National Research Council, A New Biology for the 21st Century, National Academy of Sciences, 2009.

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advanced mathematics and statistics sequence. Students in the BS will be assessed and advised toward the end of their second semester on whether to continue with the MATH 254 (Ordinary Differential Equations) and MATH 363 (Statistical Methods) sequence, or conclude with MATH 129 (Calculus II) and take the less calculus-intensive statistics course MATH 263 (Introduction to Statistics and Biostatistics). Similarly students will be assessed and advised in their fourth semester on which emphasis area they will choose for their third and fourth years. Student outcomes will be assessed through a combination of reviewing student performance in courses, feedback provided by students, and career opportunities available to students (such as graduate school and job offers). We will consult with UA’s Office of Instruction and Assessment (OIA) for feedback on our assessment efforts.

Student performance We will monitor student performance, e.g., in the form of drop rates for individual courses, student GPAs, and retention rates for the program as a whole, to assess the content, structure, and difficulty level of individual courses as well as their relationship to each other. Student feedback We will solicit feedback from students regarding both the courses and the program as a whole. We will conduct exit interviews with graduating students to obtain a retrospective assessment of their coursework as well as the BS program overall. Career opportunities We will use UA Career Services survey data to track, to the extent possible, the fraction of our students who go on to pursue graduate degrees in this or related disciplines as well as the fraction of students getting job offers on graduation.

V. STATE'S NEED FOR THE PROGRAM

A. HOW DOES THIS PROGRAM FULFILL THE NEEDS OF THE STATE OF ARIZONA AND THE REGION? -- Explain.

In the ten years since the Arizona Bioscience Roadmap of 2002,3 Arizona has invested a great deal in the biosciences and has become a national leader in this area.4 It is natural and timely to ask what needs to be done to continue and reinforce this leadership into the coming decades. A study by the National Research Council states that a strong

3 Battelle Memorial Institute. Platform for Progress: Arizona's Bioscience Roadmap. (Prepared for the

Flinn Foundation.) December 2002. www.flinnscholars.org/file/arizona_biosci_roadmap_revised_540.pdf.

4 The Flinn Foundation. Distance Traveled: The Bioscience Roadmap Turns 10. 2011 Progress on Arizona's Bioscience Roadmap. http://www.flinn.org/file/2011_progress_brochure.pdf.

http://www.flinnscholars.org/file/arizona_biosci_roadmap_revised_540.pdf.

http://www.flinn.org/file/2011_progress_brochure.pdf

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integration of the biosciences and the information sciences is crucial for this.5 The proposed Bioinformatics degree program aims to provide this integration and prepare students with the training and skills to be productive in the biosciences workplace of the 21st century.

This degree will prepare students for graduate studies in either a bioinformatics-related field or in a traditional discipline, as well as for immediate entry into the job market. Some career opportunities in related fields are:

Life sciences: scientific curator, gene analyst, protein analyst, phylogeneticist, computational biologist, research scientist/associate.

Computer science and engineering: database programmer, bioinformatics software developer, network administrator/analyst.

Applied science: molecular modeler or structure or biomechanics analyst, biostatistician.

Pharmaceutical science: cheminformatician, pharmacogeneticist, research scientist/associate.

B. IS THERE SUFFICIENT STUDENT DEMAND FOR THE PROGRAM? -- Explain and

please answer the following questions. 1. What is the anticipated student enrollment for this program? (Please

utilize the following tabular format).

5-YEAR PROJECTED ANNUAL ENROLLMENT

1st Year 2nd Year 3rd Year 4th Year 5th Year

Number of Majors 10 25 40 60 100

2. What is the local, regional and national need for this program? Provide

market analysis data or similar evidence of the need for this program. Include an assessment of the employment opportunities for graduates of the program during the next three years.

While employment in this sector, like most other sectors, has been hit by the recession and the slow economic recovery, there are indications that job growth in this area is picking up. An industry study of the bioinformatics market outlook to 2015 states:

“During the past decade, the bioinformatics market has significantly evolved across the globe on the back of the rising genomics industry. The increasing application of genomics in biotech and pharmaceutical research and

5 National Research Council, A New Biology for the 21st Century, National Academy of Sciences, 2009.

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development has created a huge commercial market for bioinformatics worldwide. As per our latest research report’s estimation, the global bioinformatics market, which reached the mark of around US $3 Billion in 2010, will expand at a CAGR of around 25% during 2012-2015 as the declining cost of human genome sequencing and increasing public and private sector investment will give a significant boost to the industry.”6

We expect that the growth in markets will be accompanied by a corresponding growth in jobs. Initial signs suggest that this is happening, e.g., a search of job trends at www.simplyhired.com, a job postings website, indicates a 224% increase in Bioinformatics jobs from December 2010 to May 2012.7 A Battelle study of demand for bioscience workers in Arizona8 indicates that 71% of the jobs in health/bio-informatics will require at least a BS degree, and 19% requiring a more advanced degree, indicating employer demand for students with this degree.

3. Beginning with the first year in which degrees will be awarded, what is

the anticipated number of degrees that will be awarded each year for the first five years? (Please utilize the following tabular format).

PROJECTED DEGREES AWARDED ANNUALLY

1st Year 2nd Year 3rd Year 4th Year 5th Year

Number of Degrees 7 15 25 35 50

IV. APPROPRIATENESS FOR THE UNIVERSITY -- Explain how the proposed program is consistent with the University mission and strategic direction statements of the university and why the university is the most appropriate location within the Arizona University System for the program. The new BS in Bioinformatics degree is directly aligned with the strategic plan and mission of the University. As the most recent strategic plan9 for the University states in its Executive Summary, two of the ten emphasis areas listed under strategic directions are (i) biosciences and biotechnology, and (ii) biomedical and behavioral health. The discipline of bioinformatics directly impacts both of these two areas, as bioinformatics faculty perform research in the biosciences and biotechnology, often with biomedical applications, and graduates will go on in their employment to work in the biosciences and biomedicine, and develop new biotechnology.

6 ReportLinker.com. Bioinformatics Market Outlook to 2015.

http://www.reportlinker.com/p0795432-summary/Bioinformatics-Market-Outlook-to.html. 7 Simplyhired.com. Bioinformatics job trends. http://www.simplyhired.com/a/jobtrends/trend/q-

bioinformatics. 8 Battelle Foundation. Arizona Bioscience Workforce Strategy: Preparing for the Future. Oct. 2003. 9 University of Arizona, “Five-Year Strategic Plan: Expanding our Vision, Deepening our Roots, 2012-

2016.”

http://www.simplyhired.com/

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The University of Arizona is a Research I institution well known for its emphasis on interdisciplinary programs, with a premier record of research excellence such as the iPlant Collaborative, a five-year, $50 million National Science Foundation-funded center for cyberinfrastructure in the plant sciences. Health sciences at the University of Arizona, furthermore, has underway a new initiative in big data and biomedical informatics, which can greatly leverage faculty and students in bioinformatics. V. EXISTING PROGRAMS WITHIN THE ARIZONA UNIVERSITY SYSTEM

A. Arizona University System -- List all programs with the same CIP code definition

at the same academic level (Bachelor's, Master's, Doctoral) currently offered in the Arizona University System. (Please utilize the following tabular format).

CIP CODE1

PROGRAM

LOCATION

University & Site

PROGRAM ACCREDITATION?

YES/NO

1

2

1 Contact Patti King ([email protected] or 621-4107) for CIP Code information. [Patti King will fill this out when the application is received]

VI. EXPECTED FACULTY AND RESOURCE REQUIREMENTS

A. FACULTY

1. Current Faculty -- List the name, rank, highest degree, primary department and estimate of the level of involvement of all current faculty members who will participate in the program. If proposed program is at the graduate level, also list the number of master's theses and doctoral dissertations each of these faculty members have directed to completion. Attach a brief vita for each faculty member listed.

Below is a listing of faculty from the departments of Computer Science, Molecular and Cellular Biology, and Ecology and Evolutionary Biology, who will participate in the new degree program. For each faculty member, the listing gives their: (a) rank; (b) primary department; (c) highest degree; as a brief vita, (d) the institution and year they received their PhD for tenure-track faculty; and for their level of involvement, (e) an estimate of the percentage of their faculty FTE that they will devote to the

mailto:[email protected]

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new degree program. The FTE percentage of involvement for a faculty member was estimated from the amount of their total teaching FTE (which is generally 40% for tenure-track faculty and 80% for lecturers) that will be devoted to teaching a course that is a required or elective course in the BS in Bioinformatics curriculum, plus any amount of their total service FTE (generally 20% for most faculty) that will be spent helping to administer the degree program. While all faculty listed below have some level of involvement in the program, we have highlighted those faculty that are expected to have a high level of involvement (for example, through teaching a required course in the curriculum) by following their name with an asterisk. Those faculty with the highest level of involvement (for example, faculty who will oversee the program, and are involved in the design and improvement of the program) are highlighted with a double-asterisk.

Computer Science Faculty

Christian Collberg, Associate Professor, CS, PhD (U. Lund, 1992), 20% Saumya Debray,** Professor and Head, CS, PhD (SUNY Stony Brook, 1986), 25% Alon Efrat,* Associate Professor, CS, PhD (Tel Aviv, 1998), 20% John Hartman, Associate Professor, CS, PhD (UC Berkeley, 1994), 20% Patrick Homer,* Senior Lecturer, CS, PhD, 40% John Kececioglu,** Associate Professor, CS, PhD (U. Arizona, 1991), 30% Stephen Kobourov,* Associate Professor, CS, PhD (Johns Hopkins, 2000), 20% David Lowenthal, Professor, CS, PhD (U. Arizona, 1996), 20% Lester McCann,* Senior Lecturer, CS, PhD, 40% Rick Mercer,* Senior Lecturer, CS, MS, 40% Bongki Moon,* Professor, CS, PhD (U. Maryland, 1996), 20% Todd Proebsting, Professor, CS, PhD (U. Wisconsin, 1992), 20% Richard Snodgrass, Professor, CS, PhD (Carnegie Mellon, 1982), 20%

Molecular and Cellular Biology Faculty

Carol Bender, Director UBRP and BRAVO, MCB, MS (Boston U., 1973), 15% Molly Bolger, Assistant Professor, MCB, PhD (Duke U., 2006), 23% Andrew Capaldi,* Assistant Professor, MCB, PhD (U. Leeds, 2001), 25% Lisa Elfring, Associate Professor, MCB, PhD (UC Santa Cruz, 1994), 25% Johnny Fares, Associate Professor, MCB, PhD (UNC, 1995), 18% Ryan Gutenkunst,* Assistant Professor, MCB, PhD (Cornell, 2008), 40% Jeffrey Laney, Associate Professor, MCB, PhD (Yale, 1995), 20% Lisa Nagy,** Associate Head and Professor, MCB, PhD (U. Washington, 1991), 30% Joyce Schroeder, Associate Professor, MCB, PhD (UNC Chapel Hill, 1998), 40% Tricia Serio,** Head and Professor, MCB, PhD (Yale, 1997), 5% Frans Tax, Associate Professor, MCB, PhD (U. Washington, 1994), 41% Ted Weinert,* Professor, MCB, PhD (Yale, 1984), 45% Guang Yao,* Assistant Professor, MCB, PhD (U. Wisconsin-Madison, 2002), 8% Daniela Zarnescu, Associate Professor, MCB, PhD (Penn State, 2000), 40%

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Ecology and Evolutionary Biology Faculty Alexander Badyaev, Professor, EEB, PhD (U. Montana, 1999), 10% Michael Barker,** Assistant Professor, EEB, PhD (Indiana U., 2009), 20% Kevin Bonine,* Adjunct Assistant Professor, EEB, PhD (U. Wisconsin, 2001), 15% Judith Bronstein,* Univ Distinguished Professor, EEB, PhD (U. Michigan, 1986), 15% Peter Chesson,* Professor, EEB, PhD (U. Adelaide, 1978), 15% Katrina Dlugosch,* Assistant Professor, EEB, PhD (UC Santa Cruz, 2006), 15% Anna Dornhaus, Associate Professor, EEB, PhD (U. Wurzburg, 2002), 10% Renee Duckworth, Assistant Professor, EEB, PhD (Duke U., 2006), 10% Brian Enquist, Professor, EEB, PhD (U. New Mexico, 1998), 10% Regis Ferriere,* Associate Professor, EEB, PhD (U. Paris, 1995), 15% Jeremiah Hackett,* Assistant Professor, EEB, PhD (U. Iowa, 2005), 15% Katrina Mangin, Director, Science Education Outreach, EEB, PhD (U. Arizona, 1991), 10% Joanna Masel, Associate Professor, EEB, PhD (U. Oxford, 2001), 10% Richard Michod, Professor and Head, EEB, PhD (U. Georgia, 1978), 10% Michael Nachman, Professor, EEB, PhD (U. Michigan, 1990), 10% Daniel Papaj, Professor, EEB, PhD (Duke U., 1984), 10% Peter Reinthal,* Adjunct Associate Professor, EEB, (Duke U., 1987), 15% Robert Robichaux,** Distinguished Professor, EEB, PhD (UC Davis, 1980), 20% Michael Rosenzweig, Professor, EEB, PhD (U. Pennsylvania, 1966), 10% Scott Saleska, Associate Professor, EEB, PhD (UC Berkeley, 1998), 10% Michael Sanderson,* Professor, EEB, PhD (U. Arizona, 1989), 15% William Schaffer,* Professor, EEB, PhD (Princeton, 1972), 15% Matthew Sullivan,* Assistant Professor, EEB, PhD (MIT, 2004), 15% Lawrence Venable, Professor, EEB, PhD (U. Texas, 1979), 10% Bruce Walsh,* Professor, EEB, PhD (U. Washington, 1983), 15% Noah Whiteman,* Assistant Professor, EEB, PhD (U. Missouri, St. Louis, 2006), 15% Michael Worobey, Professor, EEB, PhD (U. Oxford, 2001), 10%

2. Additional Faculty -- Describe the additional faculty needed during the next three years for the initiation of the program and list the anticipated schedule for addition of these faculty members.

The present faculty listed above are sufficient to initiate the BS program, and no additional faculty are required for the program. It is anticipated, however, that within the next three years, the University will very likely hire new faculty within the area of bioinformatics, in order to further strengthen research programs on campus, and such new hires in bioinformatics will be incorporated into the BS program.

3. Current Student and Faculty FTEs -- Give the present numbers of Student

FTE (identify number by graduate and undergraduate students) and Faculty FTE in the department or unit in which the program will be offered.

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The home department for the BS in Bioinformatics program will be Computer Science, as listed earlier. As of Fall 2012, the total number of undergraduate student FTEs in Computer Science (counting both majors and pre-majors) is 655. The total number of faculty FTEs in Computer Science is 15.

4. Projected Student and Faculty FTEs -- Give the proposed numbers of

Student FTE and Faculty FTE for the next three years in the department or unit in which the program will be offered.

We project the following estimates of faculty FTEs in the Department of Computer Science (the home department for the program), starting from the current academic year 2012-13 and continuing with the next three academic years through the 2015-16 academic year: 15, 16, 17, 17. We project the following student FTEs in the Computer Science Department, from the current 2012-13 year through the 2015-16 year: 655, 688, 722, 758. (This projection is based on a very conservative 5% annual rate of growth.)

B. LIBRARY

1. Acquisitions Needed -- Describe additional library acquisitions needed during the next three years for the successful initiation of the program.

No new library acquisitions will be needed for the degree program. (Current journal subscriptions are sufficient.)

C. PHYSICAL FACILITIES AND EQUIPMENT

1. Existing Physical Facilities -- Assess the adequacy of the existing physical

facilities and equipment available to the proposed program. Include special classrooms, laboratories, physical equipment, computer facilities, etc.

The current physical facilities and equipment are adequate for the instructional needs of the degree program. No new classrooms, laboratories, physical equipment, or computer facilities are needed.

2. Additional Facilities Required or Anticipated -- Describe physical facilities

and equipment that will be required or are anticipated during the next three years for the proposed program.

No new physical facilities or equipment are required for the proposed degree program.

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D. OTHER SUPPORT

1. Other Support Currently Available -- Include support staff, university and non-university assistance.

Current support staff from the Department of Computer Science include our advising staff of Holly Brown, and Christina Dentel; and our laboratory staff of Phil Kaslo, Eneida Lima, and Tom Lowry. Support staff from the Department of Molecular and Cellular Biology will be Jennifer Cubeta. Support staff from the Department of Ecology and Evolutionary Biology will be Elizabeth Oxford.

2. Other Support Needed, Next Three Years -- List additional staff needed

and other assistance needed for the next three years.

Over the first three years of the program, as the number of majors in the BS in Bioinformatics degree ramps up, we anticipate a need for hiring one additional advising staff person in the second year of the degree program.

VII. FINANCING

A. SUPPORTING FUNDS FROM OUTSIDE SOURCES -- List.

No supporting funds from outside sources are identified.

B. BUDGET PROJECTIONS FORM -- Complete the budget projections form describing the current departmental budget and estimating additional costs for the first three years of operation for the proposed program. Please note that these costs for each year are incremental costs, not cumulative costs.

Please see the attached budget projection form.

VIII. OTHER RELEVANT INFORMATION In other information relevant to the degree proposal, we note that the proposed curriculum for the BS in Bioinformatics degree was developed through joint discussions among three departments: the Department of Computer Science, the Department of Ecology and Evolutionary Biology, and the Department of Molecular and Cellular Biology. We anticipate that RCM from the new degree program will be distributed among these three departments as follows:

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Credit for SCH will be assigned according to the home department in which each course in the degree is taught.

Credit for graduates and majors in the new degree program will be assigned to these three departments according to the emphasis area chosen by each graduate, except credit for graduates in the emphasis area of Systems Biology will be split equally between the Molecular and Cellular Biology Department and the Ecology and Evolutionary Biology Department.

During the first three years of the new program, we plan to have these three departments fully assess the program together. In particular, in the second and third years of the program, we will consider adding new advanced courses that have been created on campus that are relevant to bioinformatics, to meet the evolving educational needs of the majors in the program.

revised bioinformatics bs program - implementation request 2-26-2013

Documents

new biology

computer science college

systems biology emphasis

evolutionary biology

cellular biology mcb

bachelor of science

program requirements

proposed program