January 6, 2006
TO: Robert Mrtek, Chair
Senate Committee on Educational Policy
FROM: Roger Nelson
Assistant Vice Chancellor for Academic Affairs
RE: Bioinformatics Certificate
As you know, the UIC Faculty/Student Senate voted at its December 2, 2005, meeting to table the proposal for the Bioinformatics Certificate and to remand it to the Senate Committee on Educational Policy. The Senate requested the proposers of the certificate program to address a basic concern that applicants, who will possess a bachelor’s degree in engineering or in a closely related science discipline, may not have adequate preparation in the fundamentals, particularly in biology, of the courses required for the certificate.
Professor Hui Lu of the Department of Bioengineering and one of the authors of the proposal submitted his response, which is attached here. In addition to his response, I am also attaching a copy of the proposal for the Bioinformatics Certificate.
RN:
Attachments
Cc: C. Hulse
R. Betts
P. Banerjee
P. L. E. Uslenghi
H. Lu
UNIVERSITY OF ILLINOIS AT CHICAGO
Response to Questions Raised at the UIC Faculty/Student Senate
Meeting of December 2, 2005, Concerning the Proposed
Certificate in Bioinformatics, College of Engineering
The essential concern expressed by one of the senators at the December 2, 2005, UIC Faculty/Student Senate meeting about the proposal for the Bioinformatics Certificate is that the certificate program does not require any prior knowledge of the fundamentals to the required or elective courses proposed for the certificate program.
Response
As an interdisciplinary field, bioinformatics covers a variety of subjects including math, physics, chemistry, biology, computer science, etc. In most cases, incoming students are from one of these fields, and gain knowledge of other disciplines in our graduate courses. For example, in 2005, the background of our PhD students was distributed as follows: 31% from engineering, 16% from biology, 15% from computer science, 8% from math/stats, and 8% from chemistry; only 10% had both biology and computer science backgrounds. These students are publishing in top journals, getting various awards and fellowships, and have good jobs when they finish. We have shown that students who lack certain background training can learn the necessary information through our courses, which are the same as those in the certificate courses.
Some specific points:
1. Do the students admitted to the Bioinformatics Certificate program need to have background in all of these fields: biology, genetic, math, CS, etc?
Students need to have background education in one of the following: engineering, math, physics, chemistry, or biology. What is essential for admission is that they performed well in an engineering or science major and have computer programming experience.
2. Can students, without prior knowledge of biology, successfully complete the courses for the Bioinformatics Certificate program?
Yes. Our regular graduate students, who come from a pure engineering background, are able to acquire the necessary biology knowledge in our courses. Of course, they will not have the same biology knowledge as graduate students in the biology department, but the amount of knowledge we teach in these courses is enough for them to successfully complete the program, find jobs and do research.
3. Pre-requisite knowledge for BioE 483, Molecular Modeling in Bioinformatics.
Answer: The biology knowledge needed for BioE 483 is taught in the required BioE 480 (Introduction to Bioinformatics). The students will have adequate preparation for BioE 483 and will deepen their knowledge of biology through this course.
4. Unique design of our courses.
The concerns raised at the Senate meeting actually reflect the strength of our curriculum. To train the students in the new discipline of bioinformatics, we have to work with the fact that most incoming graduate students don’t have all of the background needed or desired. This includes both the certificate students and the PhD/MS students. As a result, these courses have been designed to draw upon each student’s strengths and add knowledge that was not part of their baccalaureate training.
5. Goal of the Bioinformatics Certificate program
Our intention is to give the students enough training in three (3) courses for them to find entry-level bioinformatics-related jobs. The contract training program will be assessed on the number of jobs and promotions we provide for the trainee. Thus we are very careful in setting the standard of admission.
6. Relationship of BioE 439, Biostatistics, in the Department of Bioengineering to BSTT 400, Biostatistics I, in the School of Public Health.
The BioE 439, Biostatistics, course has been offered in College of Engineering, Department of Bioengineering, for many years. It is a required course for the BIOE undergraduate curriculum and it is an elective course for the graduate curriculum. The Bioinformatics Certificate program uses exactly the same course materials.
November 14, 2005
TO: Robert Mrtek, Chair
Senate Committee on Educational Policy
FROM: Roger Nelson
Assistant Vice Chancellor for Academic Affairs
I am submitting for review and action by the Senate Committee on Educational Policy the attached proposal for the Bioinformatics Campus Certificate.
This certificate was first offered in Fall 2005 as part of an agreement signed with Chicago Technology Park. The College of Engineering plans to offer the certificate to regular students who would pay the online hourly rate of $535/credit hour once matriculated into the program. This proposal is being sent to you for approval under the new guidelines for certificate programs. Requiring 12 hours, this post-baccalaureate certificate is classified as a campus certificate.
The certificate has been approved by the Graduate College. As a campus certificate, it does not require action by the Graduate College Executive Committee. The College of Engineering EPC approved the proposal on November 7. If approved by the Senate by the end of the Fall 2005 term, implementation is set for Spring 2006.
RN:
Attachment
Cc: R. Betts
C. Hulse
P. Banerjee
P. Uselengi
S. Laxpati
H. Lu
C. Williams
REQUEST FOR A NEW UNIT OF INSTRUCTION: Certificate
BACKGROUND
1. Name of Institution: University of Illinois at Chicago
Department and/or College Sponsor: Bioengineering/College of Engineering
List unit approvals with dates: Educational Policy Committee Approval, College of Engineering,
November 7, 2005
2. Title of Proposed Certificate: Bioinformatics Campus Certificate
3. Contact Persons: 1. Hui Lu, Assistant Professor, Department of Bioengineering
2. Piergiorgio L. E. Uslenghi, Associate Dean, COE
3.1. Telephone 1. 312-413-2021
2. 312-996-6059
3.2. E-mail 1. 2.
3.3. Fax 1. 312-413-2018 (HL) 2. 312-996-8664 (PU)
4. Level of Proposed Certificate
__ Undergraduate Certificate (1-2 years) X_Post-Baccalaureate Certificate
__ Undergraduate Certificate (2-4 years) __ Post-Master’s Certificate
__ First Professional Certificate
5. Requested CIP Code (6-digits) ______(to be supplied by the Office of Academic Programs)
6. Proposed Date for Implementation: Spring 2006
7. Location Offered[1]: On-Campus ___
Off-Campus ___: Region Number(s)______or Statewide___
Online _X_
8. MISSION, OBJECTIVES AND PRIORITIES
8.1 Describe specific objectives and measurable contributions the certificate will make to the university’s mission, paying particular attention to the program’s consistency with the university’s priorities. Such objectives and contributions may include:
· serving a distinct student population;
· occupational and student demand for the program;
· collaborating with and/or supporting other programs at the institution;
· meeting the needs of state agencies, industry, business, health care providers, other educational institutions, and/or society; and
· increasing the number of graduates in a high demand or emerging field of study.
8.2 Explain how the certificate will meet regional and state needs and priorities.
8.3 Discuss estimated future employment opportunities for completers of this certificate program. Where appropriate, provide documentation by citing data from such sources as employer surveys, current labor market analyses, and future workforce projections.
This certificate program is offered by the Department of Bioengineering and MEng program in College of Engineering. It consists of a cluster of four courses that are offered online to students in the Master of Engineering degree program, among which the students will take three to earn the certificate. The knowledge taught in the program relates to current and emerging topics in bioinformatics such as DNA sequencing, gene function annotation, drug design, gene expression analysis, and statistical analysis.
The Bioinformatics Campus Certificate program will provide us the chance to design courses and train Information Technology (IT) professionals for them to enjoy the new opportunities in biotechnology. Bioinformatics is an integration of mathematical, statistical and computer methods to analyze biological, biochemical, and biophysical data. It is not a simple summation of biology and programming. On one hand, industry badly needs well-trained bioinformatics workers; while on the other hand, we see certain so-called “bioinformatics” workers laid off from their jobs. The key goal in this certificate program is to teach and train the students in a proper way, the bioinformatics way.
The specific knowledge a student needs to master to have a successful job in industry is based upon the understanding and application of the core principles of bioinformatics. The specific knowledge a student must master in the proposed program is listed below in three groups: foundations, bioinformatics, and computational methods. All of this knowledge will be integrated by us in the four courses in bioinformatics. This will be the most efficient way of training IT professionals.
Success of the program requires knowledge of what the industry needs, not just now but also in the near future. As a fast developing field, the industry requirements change quickly, and we need to prepare students for the current needs as well as near future changes. We are training them to learn the spirit and way of thinking about bioinformatics through the combination of theory and application. The application provides them with immediate knowledge getting them started in their jobs, and the theoretical foundation they learn will help them gauge opportunities or keep their current jobs when the interests shift in the industry.
Although the design of the courses have been offered online and therefore have been available to students worldwide, we are focusing on Chicago area trainees who will benefit from our person-to-person help from teaching assistants (TAs), industry seminars, and services to provide local internship opportunities.
This certificate program has two components: the first is the contracted training with funding from Department of Labor through Chicago Technology Park (bitmap program); the second is a regular online training certificate similar to the current three other post-baccalaureate certificate programs offered by the MEng program in the College of Engineering.
The bitmap program offered us funding to develop the courses and provide TA help. We are contracted to train at least 128 students in the next 2 and half years. The trainee has to be an American citizen or permanent resident, with an IT background. The tuition for the bitmap trainees is paid by Chicago Tech Park and the COE, thus the trainees will be offered free training.
The regular bioinformatics certificate program does not have any restrictions. The COE has full control on the admission, and the trainees will pay the regular UIC online tuition rate.
There is a growing need for well-trained bioinformatics workers in the Chicago area, and the Midwest in general. We have contacted biotech and pharmaceutical companies in Chicago and nearby areas and got very positive responses. There are already several companies committed to take our trainees for a one-semester internship after they finish the courses. Master’s degree students who recently graduated from our bioinformatics program all found jobs in this field easily. One of our trainees in the program already got a job offer in Milwaukee after enrolling in our courses for 2 months. He will finish the certificate while working in that new position.
9. PROGRAM DESCRIPTION
9.1 Provide a brief narrative description of the certificate program, including a list of its central academic objectives. Explain how the curriculum is structured to meet the certificate’s stated objectives. Provide a complete catalog description for the proposed certificate, including:
· program admission and academic policies
· policy on the acceptance of transfer credit to apply to the certificate program
· complete listing of course and other requirements; note that new courses should be
listed as such and forwarded concurrently through the Course Request System (CRS)
· course descriptions from the UIC web catalog
Admission requirements
Applicants must have a bachelor’s degree in engineering or in a closely related discipline, such as chemistry, mathematics, physics or biology from an accredited institution of higher education, and a solid undergraduate background in programming. A minimum grade point average of 3.0 is required for admission. Applicants from non-English-speaking countries must have a minimum TOEFL score of 550 (paper-based) or 213 (computer-based). The online course will be in the format of html with audio insertions. The students are required to have access to a computer with a sound card and an internet connection. Software requirements are a web browser (Internet Explorer or Netscape) and basic editing software.
Transfer of credits
No transfer of credits is allowed into the Certificate Program.
Course Requirements Description
The campus certificate in Bioinformatics provides training in bioinformatics theory and applications, such as DNA sequencing, gene function annotation, drug design, gene expression analysis, proteomics data analysis, biostatistics.
The certificate program consists of the following three courses for a total of twelve semester credit hours:
--- BIOE 480 – Introduction to Bioinformatics (4 hrs.)
--- Two out of three:
BIOE 439 – Biostatistics (4 hrs.),
BIOE 483*– Molecular Modeling in Bioinformatics (4 hrs)
BIOE 582^ –Computational Functional Genomics (4 hrs)
* Previously offered as BIOE 494.
^ Previously offered as BIOE 594.
Course 1. Introduction to Bioinformatics (BIOE 480)
This is the general introductory course in bioinformatics. The main techniques covered here are related to sequence analysis, which is still a routine job in industry: gene identification, genome sequencing, sequence comparison, database searching, and phylogenetic tree analysis. However, the course achieves more than just teaching bioinformatics. It also serves as the course in which we introduce relevant molecular biology knowledge. We are going to discuss the central dogma of molecular biology, DNA sequences, and protein sequences. The students will learn enough biology to understand the applications of bioinformatics algorithms and software taught in this course.