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BENG 3000

Bioinstrumentation
Spring, 2016

Class time/room

Tuesday 3:00 pm to 3:50pm; Thursday: 3:00-5:50pm @ ENGR 205


Lab session#1: Tuesday 4:00 pm 5:50 pm;
Lab session#2: Thursday 4:00 pm 5:50 pm;

Instructor:

Prof. Anhong Zhou,


Email: Anhong.Zhou@usu.edu (preferred)
Tel: 797-2863;
office: ENGR 402N
TAs: Carson Sparks
carson.sparks@aggiemail.usu.edu
Stephanie Lawanto
stephanie.lawanto@gmail.com
Han Zhang
han.zhang1985@aggiemail.usu.edu
Wei Zhang
wei.zhang@aggiemail.usu.edu

Office hours
Textbook:
Grading:

By appointment
J.G. Webster Bioinstrumentation text & lab experiments.
No exams. Final grade will be counted by three major components:
Class attendance (10%)
Quiz (20%)
Assignments and Lab reports (30%)
Final Research/Design project (40%)

Prerequisites:

ECE 2200 or TEE 2300 (pending approval) or instructor consent

Bioinstrumentation is traditionally defined as a field that applies the fundamentals of


measurement science to biomedical instrumentationemphasizing common principles
and unique problems associated with making measurements in living systems. [J.G.
Webster]. Bioinstrumentation (BENG 3000) is a laboratory based course that introduces
students to methods of obtaining and processing information relating to biological
systems. A series of virtual and lab experiments are to be conducted in this course.
Bioinstrumentation (BENG 3000) will thus focus on instrumentation applicable to
biomedical, bioenvironmental, and bioprocess areas accordingly. The guest lectures will
be presented. Also keep in mind there is often overlap and a technique presented in a
biomedical context likely has applications in other Biological Engineering subdisciplines. The design project will allow students to focus on an area related to their
interests. The goal of this course is to provide students with hands-on experience using
state of the art instrumentation. Good laboratory practice, experimental design and
technical writing are also integral parts of this course.
Textbook:
1. John G. Webster, Bioinstrumentation, John Wiley & Sons, Inc. 2004.

(W)
1

Readings materials:
2. J.B. Olansen, E. Rosow, Virtual Bio-instrumentation: Biomedical, Clinical, and
Healthcare Applications in LabView, Prentice-Hall, Inc. 2002. (VLV)
3. LabVIEW 6i, Student Edition, Prentice-Hall, Inc. 2001 (including software). (LV)
4. Handouts containing contents in these readings materials will be distributed before
class
Tentative schedule for BENG 3000 (subject to changecheck Box postings!)
Week
No.
(date)
1

Lectures/class discussions
(Tuesday)

Lab experiments
(Thursday)

Syllabus & course overview

Lab Orientation & Safety

(Jan 12)

(Jan 14)

3-3:50 pm Meas. Systems;


4- 5 pm Basics of electronics

(Jan 19)

3-3:50 pm Cellometer Demo


Dr. Kelsey McCulley from Nexcelom
Bioscience, Inc.
4- 5 pm Basics of electronics

Text
Chpt. and
reading*

Comments

W-ch1,
W-ch2

(Jan 21)
3

3-3:50 pm Basics of electronics


4- 5 pm LabVIEW Overview

3-3:50 pm Pressure measurement


4- 5:50 pm Lab 1: Spectrophotometry
(Co/Cr mixture)

(Jan 26)

(Feb 02)
3-3:50 pm Quiz-1 (wk1-wk4)

4- 5:50 pm Lab 2: LabVIEW

(Feb 09)
6

Make up Mondays class


No class

(Feb 16)
3-3:50 pm Pulse oximetry &

Electromyography (EMG)
4- 5:50 pm Lab 3: DAQ hardware &
software

(Jan 28)
4- 5:50 pm Lab 1: Spectrophotometry
(Co/Cr mixture)

PPT slides
Lab notes

(Feb 04)
3-3:50 pm Electroencephalography
(EEG)
4- 5:50 pm Lab 2: LabVIEW

(Feb 11)

EEG-W-ch7.1
& 7.2; ECG-,
W-ch8.2, VLV
ch 3, p75-85

3-3:50 pm Electrocardiography
(ECG)

Lab 1 report
due Feb 18

(Feb 18)
3-3:50 pm HPLC/MS (or field
tour local hospital?)
4- 5:50 pm Lab 3: DAQ hardware &
software

(Feb 25)
3-3:50 pm Guest lecture/tour: NMR

4- 5:50 pm Lab 4: EEG/ECG

PPT slides,
W-ch3.1,

3-3:50 pm Temperature meas.

3-3:50 pm Lectures - PCR & Gel


electrophoresis (Dr. Miller)

Dr. Simon Sham (Chem Dept)


4- 5:50 pm Lab 4: EEG/ECG

EMG-VLV ch
3, p58-75; Wch7.12

PPT slides,
Lab note

Lab 1 report
due Feb 23 or
Feb 25

PPT slides,
Lab note

(March 03)
Spring Break! (03/07-11)

3-3:50 pm Surface Analysis -1


SEM/TEM & AFM

3-3:50 pm 3-3:50 pm Quiz-2


(wk5-wk7)

4- 5:50 pm Lab 5A: PCR;


Lab 5B: Gel electrophoresis

4- 5:50 pm Lab 5A: PCR;


Lab 5B: Gel electrophoresis

(March 15)
11

4- 5 pm LabVIEW Overview

(Feb 23)

(March 01)

10

3-3:50 pm UV-vis spectrophotometry

3-3:50 pm Guest lecture cell


physiology measurement (Prof.

(March 17)
3-3:50 pm MATLAB -1
4- 5:50 pm SEM lab tour (SER-006)

Lab note

Lab 3 due
March 15 or
March 17

W-ch4.3.14.3.2

Lab 4 due
March 22 or

Tim Gilbertson)

March 24

(March 24)

4- 5:50 pm SEM lab tour (SER-006)

(March 22)
12

MATLAB-2
(March 29)

Biomedical Imaging I (X-ray,


CT)
(March 31)
3-3:50 pm Quiz-3 (wk8-wk13)

Lab 5 due
March 29 or
March 31

Biomedical Imaging II MRI


Or guest lecture from U of U?

IBE Conference travel (April 7 -9)

(April 05)
Project design/lab
(April 12)

(April 07)
Project design/lab
(April 14)

15

Project design/lab
(April 19)

Project design/lab
(April 21)

16

Project design/lab
(April 26)

Project final
presentation/submission
(April 28)

13
14

17

May 02 May 06

W-ch7.3(Xray), 7.4(CT),
7.5(MRI)

April 21st,
mid-term prog.
mtg

* The order of lectures/labs is subject to change depending individual guest presenters


schedule
Assignments:
Students will work on (1) several class assignments to read the text and references
and solve problems; (2) formal laboratory reports; and (3) a report of design
project.
Evaluation Methods:
All assignments, projects and exams will be expected to be professional quality.
Quizzes will be held in No late work will be accepted without prior approval from
the instructor. Assignments and lab reports will be turned in (to instructor or
teaching assistant) at the time of next lecture class. Any late work without
approval from instructor will result in losing 5 points in your final grade. Three
or four students will form a group to complete your project designs. Grades will
be determined as the spreading percent mentioned in the first of this syllabus.
Announcements:
E-mail will be used to post important announcements. Please be sure to let the
instructor know your frequently used email address, preferably using
aggiemail.usu.edu. Its your responsibility to check e-mails regularly.
Since USU IT Helpdesk is updating our university email system, you should
contact IT Service people to make sure your email address that you are going to
use in this class will be active.
In order to avoid the compatibility problem between Office 2007 and Office 2003,
Please download a compatibility package for Office 2003 if you are using this old
version of software in your computer.
3

Students with disability:


If you need an accommodation due to a disability, please make arrangements to
discuss this with the instructor during first two weeks of the semester.

Format of Lab Report


All labs will be written up on 8-1/2 x 11 paper and should be submitted in hard copy with
the following sections included:
a. Title page (10 points):
Class Code and name (2 points)
Name (2 points)
Date (2 points)
Lab title (2 points)
Group member (smaller font size) (2 points)
b. Introduction (15 points):
literature review or background of this lab
Theory (if applies)
Scheme/illustrations (if applies)
Equation (if applies), using Word Equation Editor or the software to type the
equation, and give an equation number after the equation. You have to explain
or give the definition (units) of each parameter involved in the equation.
c. Experimental (20 points):
list of equipment (including its model number)
list of (bio)chemicals used and their concentrations
ensure the abbreviations of each (bio)chemicals are given full chemical name, not
just use the abbreviation like TNT.
Experiment procedures (step by step) could be adapted (NOT copied) from lab
note/protocol
d. Results and Discussion (35 points):
Describe the diagrams (if any)
Describe the Schematics/illustration (if any)
Describe and discuss the results shown in each Figure and Table
For sensorgram, explain what happens in each step.
Below are examples to describe the presentation formats for Figure and Table

Note: 1) The caption of Figure should be under each Figure. The caption should give
meaningful information what this Figure tries to tell the reader. Be clear what
means for each symbol or curve. Any caption is put on the wrong place will lose
5 points.
2) The description of Table should be on the top of the Table. The Table needs to
be present in three-line style. Any description of Table is put under the Table
will lose 5 points.
3) Be sure each graph, Figure, and Table are described in the text body. Missing
the description of any of these formats will lose 5 points.
4) figure 1 shows and table 1 givesin the text body should be Figure 1
and Table 1. Figure and Table should be capitalized. 2 points will be lost if
lower letter shows in Figure or Table.
4) Sometimes, the Results and Discussion sessions could be separated into two
sessions (Results session and Discussion session). This is optional and not
required in our lab report.
e. Conclusions (10 points):
Knowledge gained
Problems encountered
Solutions to problems
Recommendations (if any)
Other comments (if any)
f. Acknowledgement (optional, if applies)
5

g. References (10 points)


* cite any websites that like Wikipedia.com or Google link will lose 5 points.
* at least two related journal papers are required to be cited with the following
format (full list of authors, title, journal name, year, volume(and/or issue), pages). An
example is given here.
1. OShannessy DO, Brigham-Burke M, Peck K. Immobilization chemistries suitable for use in
the BIAcore surface plasmon resonance detector. Anal Biochem, 1992, 205: 132-136.

*numbering your references and be sure to cite each reference in the text body of
the report. Any incited references or any citation in the text body without be given the
references will lose 5 points.
2. Pages will remain flat and stapled in the upper left hand corner. Do your own writing
(even the experiments are performed by a team work). Exercise your writing skills.
3. Labs will be graded on neatness, completeness, accuracy, spelling, grammar, and
timeliness. Do not tape or glue on graphics from the handouts into your write-up. Note:
any delay in turning in your lab report will result in losing 5-20 points in your final grade
(not this lab report grade!), depending on the circumstances.
4. Any students who make copy and paste any part from other students assignments,
homework, and lab reports, will be graded zero (failed). The related documents will be
reported to BE Dept Head and Deans Office.

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