Bioinformatics Campus Certificate - University of Illinois

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1

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 posse
ss 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 Bioenginee
ring 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




2

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 concer
n 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, a
nd 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 backg
round 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 the
se 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 backgrou
nd, 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 suc
cessfully 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

3

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.





4




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 matr
iculated 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 approve
d 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, imp
lementation is set for Spring 2006.


RN:

Attachment


Cc:

R. Betts


C. Hulse

P. Banerjee


P. Uselengi


S. Laxpati


H. Lu


C. Williams


5

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 Certific
ate:



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. h
uilu@uic.edu









2.
uslenghi@uic.edu


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.
Loc
ation 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 cert
ificate 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 deman
d for the program;




1

Institutions may request approval to offer a program, simultaneously
, on
-

and off
-
campus, including
statewide. However, assessments of program objectives and outcomes should be developed that address all
of the locations and modes of delivery for which the institution is seeking approval. Note that “on
-
campus”
approval e
xtends to the entire region in which the main campus is located. New off
-
campus programs to be
offered outside the institution’s region require approval.


6



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 graduate
s 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, p
rovide 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 Engineerin
g. 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 emergi
ng 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
summati
on 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 eff
icient 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
s
tarted 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
av
ailable 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
certifica
te 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 a
n
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.


7

The regular bioinformatics certificate program does not have an
y 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 b
iotech 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 re
cently 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.

P
rovide 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 close
ly 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 fr
om 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 cons
ists 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)


8

*
Previously offered as
BIOE 494
.

^

Previously offered as
B
IO
E

594.



Course 1. Introduction to Bioinformatics (BIOE 480)


This is the general introductory course in bioinformatics. The main techniques cov
ered 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 bioi
nformatics. 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.

The algorithms and software involved include:



Sequence comparison algorithms and the software program FASTA as well as related
programs;



Sequence database searching with BLA
ST, PSI
-
BLAST, HMMER;



Functional database searches with GO and PFAM for gene identification and functional
assignment;



Biology database design using SQL/mySQL;



Programming to solve text processing another bioinformatics task with perl, and learning
how
to use the bioperl database to search for the available programs;



Phylogenetic analysis with program PHYLIP.

All these programs are widely used in industry and academia (in case a student might want to find
a job in a university), and learning how to appl
y them, as well as the theory of the algorithm
driving them; this will provide a

huge advantage over other workers in applying these tools
properly.


Course 2. Biostatistics (elective) (BIOE 439)


This course teaches the student biostatistics, which is a
popular branch in the

biotech and
pharmaceutics industry. The industry standard in statistics software, R and S++, will be taught to
the students. Also required is programming knowledge of Java (preferred) or Perl and C++. The
programming part won’t be h
ard for the IT professionals. Thus our goal in this course is to teach
them the application of basic algorithms and the theory behind the statistical analysis. We will
extensively use examples and small projects to teach them how to use R and Java to achi
eve their
bioinformatics tasks. Topics included here are: sample analysis; interval
-
censored survival data
analysis; longitudinal data analysis; multivariate analysis; theory of distributions in statistics;
experiment and design.


Course 3. Computational
Functional Genomics. (elective) (BIOE 582)

In this course we focus on the study and implementation of methods of data mining and machine
learning that are useful in the analysis of gene expression data from genome comparison,
microarray experiments and pro
tein function prediction. Students will gain practical skills
especially in the analysis of microarray data in addition to theoretical knowledge on the methods.
The topics covered in this course includes Microarray Technology, Microarray experiments,
Prepr
ocessing of Microarray data, statistical methods (hypothesis testing, resampling, bootstrap,
Multiple testing), distances and expression measures, feature selection, cluster and classification
analysis for microarray data, inferring genetic network. We wil
l use
R

and
Bioconductor

9

package

for the microarray data analysis and
Matlab
for other implementation tasks. All three
tools are widely used in industry for gene expression analysis.

Course 4. Molecular Modeling in Bioinformatics (elective) (BIOE 483)


Th
is course teaches the students how to elucidate the structure of a biopolymer using related
modeling tools and algorithms in bioinformatics. The targeted areas are in protein structure
modeling, structure based drug design, drug screening, cheminformatics
, and binding prediction.
Students will be able to learn the principle and applicability of each of the algorithms and
programs used in structure modeling.

The popular software used in industry include:

Protein
-
ligand (drug) binding: DOCK, AUTODOCK,

Gen
eral packages aimed at structure modeling: SYBYL, QUANTA, INSIGHT II

Molecular dynamics Simulations: CHARMm, AMBER



Graduation requirements




Students must complete the required course (BIOE 480) and two out of three elective
courses within three semeste
rs (summers included) from admission into the program. A leave of
absence of up to one year may be granted once, upon petition and for a reason acceptable to the
Director of the Master of Engineering degree program and Academic director of Bioinformatics
c
ertificate. A grade
-
point
-
average of at least B is required for graduation. No credit is given for
courses in which a grade below C is received. If a grade lower than a C is earned, a course may
be repeated once, in which case only the higher of the two gr
ades is considered as meeting the
requirement.


9.2

Describe the strategies to be incorporated into the proposed certificate to promote
student learning.


Strategies


Besides the standard online audio teaching, there are five strategies we will implement t
o
promote student learning:

1. We are assigning homework and online quizzes that the students need to finish on a
weekly basis.

2. There will be monthly meetings with trainees in the form of either an industry seminar or
a review session about the course

content. For the students who cannot attend, the
recording of the meeting will be posted online in the blackboard.
We also plan to use a
synchronous conference component, such as Centra Symposium, to make this optional
meeting available to geographically
distant students.

3. Computers
, funded by Chicago Tech Park,

are provided for
bitmap contract training
students to remote login finishing the programming and software training.

4. TAs are available 20 hours a week to meet students, talk to them on the pho
ne, or answer
questions online

for bitmap trainees
.

The availability of
a
TA to regular certificate students
depends on the

number of
enrollment
s in

each course.


5. We are starting to provide a job list database for bioinformatics related openings. Our
trainees will have access to this database.

On the side, Chicago Technology Park will help trainees find internships after they finish
the course work. Although UIC is not responsible for this internship, this opportunity
motivates a lot of students to ap
ply and learn well.



10

9.3 Objectives: Explain what students are expected to know and/or be able to do upon
completion of the certificate program.


Learning objectives


Recipients of this certificate program will be technically up to date in the vast and
very rapidly
changing field of bioinformatics. They will be able to work with minimal or no additional
training in industries dedicated to analyzing biological data such as database search, genome
sequence, gene function, microarray gene expression, proteo
mics, interpreting experiment output
or processing health care related data such as patient’s response to drugs.




9.4 Assessment: Describe how the above objectives will be assessed, such as:



End
-

or near
-
end
-
of
-
program assessment of studen
t learning, in addition to
course
-
by
-
course assessment such as: (1) evaluation of capstone experiences
(projects, recitals, exhibits, portfolios, etc.); (2) pre
-

and post
-
testing (value
-
added
assessment);



Multiple performance measures, if necessary, that
reflect the uniqueness of the
certification program and discipline such as: (1) standardized or other
comprehensive examinations; (2) certification examinations.


Strategies and assessment




The value of the courses will be measured in three ways. First
, the course can be measured
by the sum of the difficulty of all its lessons. That is, by evaluating how well each student is
progressing, we can determine how to adjust the amount and type of material for the next round
of the course. For example, our c
lassroom courses have been created to suit a wide variety of
backgrounds; these courses will serve as the templates for our online courses with the bias
towards the IT background students. Now, if we observe that our average students from IT
professions b
reeze through some sections and plod through others, we will adjust the details of
the content accordingly. Students are monitored and evaluated in a manner consistent with all
graduate courses. They are assigned homework, class projects, midterm and final

examinations.
Reliable monitors are secured at all off
-
campus locations where examinations occur, in order to
verify student identity and preclude cheating. Feedback on the quality of the program is obtained
from student evaluations of course content and
instructor at the end of each term.

The second metric used to evaluate our courses is the student survey. Recognizing that
situations may arise that cannot be accounted by observing trends in grading, we will ask
the
students how they felt about certain
aspects of the course. This is a proven method to reveal
hidden obstacles or benefits unforeseen at the time the course was created. We are able to fine
tune the courses during the teaching if necessary.

The final metric will be industry. By sending ou
r prospective students into the field for an
internship or job, we hope to gain feedback from industry to illuminate the strengths and
weaknesses of our program. This is a very important indicator of the success of our program. By
tailoring our program t
o the industry standard, we hope to gain a large percentage of placement of
our students into new careers. This will also help us to determine how hard to push our students
and how selective we need to be in order to gain potential employer’s approval.

Students who at the end of the certificate program wish to continue their studies toward the
Master of Engineering degree or Bioinformatics graduate degree (MS or PhD) are allowed to
transfer to that degree those certificate courses in which they received
a grade of at least B.


10.

RESOURCES



11


10.1 Complete Table II. Indicate on the appropriate lines in the table all sources of funds,


both state and non
-
state, and reallocations that will support the certificate program.


10.3

Provide a narrative budget statement that explains the source(s) of funds and how the




funds are to be used to support the certificate program (e.g., additional faculty and



staff, equipment, space, library resources).




10.4 What tuiti
on rate will be charged for this program (range tuition or online hourly)?



10.5 Is this a contract program? If so, please identify the contracting agency or
organization.


This certificate program has two funding mechanisms. The first mechanism: the
bitmap program,
which is a type of contract program. This component is supported by external funding through a
bitmap contract signed by Chicago Technology Park and the Board of Trustees. The second
mechanism: the regular bioinformatics certificate is embe
dded into the Master of Engineering
degree program, and as such does not require any additional resources, with the exception of the
minor cost of printing the certificate awards
.

Specifically, no additional faculty, staff, equipment,
space, or library res
ources are needed

besides those supported by the contract program

and those
that
already exist in MEng program
.
In the second mechanism, students will pay the online hourly
$535/credit hour tuition rate.
In both mechanisms, the online lectures are delivere
d using the UIC
Blackboard system.


11.
AFFECT ON UIC UNITS



11.1 Explain the involvement of other units at UIC in the certificate program. Have these




units approved of their participation? Provide evidence of support.



11.2 Explain the effec
t of the program on other UIC units’ programs. Have these units been


notified of this effect? (Provide evidence of this notification.)


This certificate program’s participants are from Department of Bioengineering and MEng
program in Colle
ge of Engineering.

This certificate program has no effect on other UIC units, except for the Master of Engineering
degree program in which it is embedded and Bioinformatics program in Department of
Bioengineering.


12.
OFF
-
CAMPUS/ONLINE CERTIFICATE PROG
RAMS ONLY


In addition to responding to the above questions, if all or part of the proposed certificate is to be

delivered off
-
campus and/or via the Internet, provide the following:



12.1 Describe the certificate’s mode(s) of delivery. If some courses w
ill be delivered online


(fully online or hybrid) list those courses.



12.2 Describe the process for assuring the quality of the off
-
campus/online program in the



following areas: (a) faculty qualifications and evaluation; (b) s
tudent access to




necessary library resources; (c) where appropriate, student and faculty access to




technical support, including computing.



12


12.3 For programs requesting off
-
campus approval only: has this certificate been approved




fo
r on
-
campus delivery?


All courses in this certificate program are delivered online. At some future time, it is possible that
some sections of these courses will be delivered live, as part of an evening/weekend on
-
campus
program.


The instructors in the ce
rtificate program are faculty in Department of Bioengineering in
the College of Engineering. Periodic evaluations of the instructors are conducted via the
questionnaires that the students in the program are required to complete anonymously at the end
of ea
ch course. Each faculty member has been teaching the corresponding regular courses before
they started to develop the online version of the same course.


The course material is contained in textbooks that all students in the course must acquire.
If additi
onal instructional material is needed, it is posted on the web by the course instructor. All
students must have access to a personal computer with certain minimal hardware and software
requirements, as specified on the web for all students in the Master of

Engineering program.


This certificate program has not been formally approved for either on
-
campus or off
-
campus delivery.



13


TABLE II



TOTAL RESOURCE REQUIREMENTS FOR THE NEW UNIT

Bioinformatics Campus Certificate (bitmap contract)

All dollar a
mounts expressed in thousands




Current

Budget

2
nd

3
rd

4th

Year

Year

Year

Year

Year

1

Total Resource Requirements


619.6

619.6

464.5

304.4

Contract
ends

2

Resources Available from
Federal Sources
1







3

Resources Available from Other
Non
-
Sta
te Sources
1


619.6

619.6

464.5

304.4


4

Existing State Resources
2







5

Resources Available through
Internal Reallocation
3







6

New State Resources Required
4


0

0

0

0



Breakdown: New State
Resources Required






7

FTE Staff
5







8

Personal
Services







9

Equipment and Instructional
Needs







10

Library







11

Other Support Services
6








1
These lines reflect funds available (not incremental funds) from non
-
state sources in any given year

2
Existing state resources in each successi
ve year are equal to the sum of the previous year’s existing state
resources (line 4); plus resources made available through internal reallocation (line 5); plus new state
resources (line 6). If state resources allocated to a program in any given year (li
ne 4) exceed state resource
requirements needed to support the program in the following year, state resource requirements should be
reduced with a negative dollar adjustment on line 5. The sum of lines 2 through 6 will always equal line 1.

3
Numbers can be

either positive (allocated to the program) or negative (allocated away from the program).

4
Reflects the level of state funding requested in the referenced year. Dollars reported are incremental.

5
Reflects the number of FTE staff to be supported with requ
ested funds. Not a dollar entry.

6
Other dollars directly assigned to the program. Do not include allocated support services.


14

TABLE II



TOTAL RESOURCE REQUIREMENTS FOR THE NEW UNIT

Bioinformatics Campus Certificate (regular)

All dollar amounts
expressed in thousands




Current

Budget

2
nd

3
rd

4th

Year

Year

Year

Year

Year

1

Total Resource Requirements


15.0

15.0

15.0

15.0

15.0

2

Resources Available from Federal
Sources
1







3

Resources Available from Other
Non
-
State Sources
1







4

Existing State Resources
2




15.0

15.0

15.0

5

Resources Available through
Internal Reallocation
3


15.0

15.0




6

New State Resources Required
4


0

0

0

0

0


Breakdown: New State
Resources Required






7

FTE Staff
5







8

Personal Services







9

E
quipment and Instructional Needs







10

Library







11

Other Support Services
6








1
These lines reflect funds available (not incremental funds) from non
-
state sources in any given year

2
Existing state resources in each successive year are equal t
o the sum of the previous year’s existing state
resources (line 4); plus resources made available through internal reallocation (line 5); plus new state
resources (line 6). If state resources allocated to a program in any given year (line 4) exceed state
resource
requirements needed to support the program in the following year, state resource requirements should be
reduced with a negative dollar adjustment on line 5. The sum of lines 2 through 6 will always equal line 1.

3
Numbers can be either positive (a
llocated to the program) or negative (allocated away from the program).

4
Reflects the level of state funding requested in the referenced year. Dollars reported are incremental.

5
Reflects the number of FTE staff to be supported with requested funds. Not a

dollar entry.

6
Other dollars directly assigned to the program. Do not include allocated support services.


15

Catalog Descriptions for existing courses:

BIOE
480

Introduction to Bioinformatics

3 OR 4 hours.

Computational analysis of genomic sequences and ot
her high throughput data.
Sequence alignment, dynamic programming, database search, protein motifs, cDNA expression
array, and structural bioinformatics. 3 undergraduate hours. 4 graduate hours.
Prerequisite(s)
:
BIOS 100 and CS 201; or consent of the instr
uctor.

BIOE 439

Biostatistics

3 OR 4 hours.

Statistical treatment of data, model estimation, and inference are treated in a
framework of biological experiments and attributes of data generated from such experiments. 3
undergraduate hours. 4 graduate hours
. Credit is not given for BIOE 439 if the student has credit
for BSTT 400. Extensive computer use required.
Prerequisite(s)
: MATH 210 and CS 108 and
consent of the instructor. Recommended background: Knowledge of MATLab.


The following two courses are pen
ding department and/or college approval. Until such approval
is received, students register for BIOE 494 (for BIOE 483) and BIOE 594 (for BIOE 582), which
are approved topics courses offered by the Department of Bioengineering.


BIOE 483 Molecular Modeling

in Bioinformatics


3 OR 4 hours.

Basic structural and dynamics tools in protein structure prediction, structure
comparison, function prediction, Monte Carlo and molecular dynamics simulations.
3
undergraduate hours. 4 graduate hours.
Prerequisite(s)
:
Grade

of B or better in BIOE 480.


BIOE 582 Computational Functional Genomics


4 hours.

Modern statistical and computational methods relevant to functional genomics.


Cell
function, gene regulation and protein expression.


Microarray technology and use; cluster

analysis; prediction of protein function.
Prerequisite(s)
:
BIOE 480.
Recommended Background:

Basic knowledge of probability, statistics, vector algebra, calculus and cell biology.