UCSC BME 123B Winter 2010

Engineering Design Project II

(Last Update: 16:35 PST 26 February 2010 )
link to homework

This course continues BME 123A. For catalog copy and pre-requisites, see the main page for BME123.

Who, When, and Where:

Instructor:

Kevin Karplus ( karplus@soe.ucsc.edu)
http://users.soe.ucsc.edu/~karplus
Office hours: PSB 318, (to be determined)
+1-831-459-4250

Lectures: W 5-6:45 Jack Baskin Engineering 165 (subject to change, if students choose a different time)

In addition to the weekly meeting, I will meet individually with students (or project groups) once a week for about half an hour each. This will be a good time to consult with me on the project, discuss feedback I've given on written reports, and so forth.

Final exam slot: Wed March 17 noon—3p.m.
We may use this exam slot for design presentations.

Online discussion forum: http://seniordesign.soe.ucsc.edu will have project descriptions, student bios, team blogs, and so forth. We may continue to use the SDP site this quarter, particularly for final project reports and presentations. A different mechanism may be used for draft reports.

Texts

There will be no required texts this quarter, but students may need to consult writing and document-design books. I particularly recommend the following books:

Thomas N. Huckin and Leslie A. Olsen.
Technical Writing and Professional Communication for Nonnative Speakers of English.
McGraw-Hill Book Company, New York, 1991.

This text (used in CMPE 185) has some excellent chapters on organizing your writing for readability.

William Strunk Jr. and E. B. White.
The Elements of Style.
Macmillan, New York, third edition, 1979.

Short, easy reading, and generally good advice about making writing readable.

Leslie Lamport
LaTeX, a Document Preparation System.
Addison-Wesley, Reading, Massachusetts, 1994.

LaTeX is the document-preparation system of choice for computer scientists, mathematicians, and physicists. If you need to put math in your writing, nothing else does as well. Not bad for free software. And your documents are still usable 10–20 years later, unlike with proprietary word-processing systems.

Edward R. Tufte
The Visual Display of Quantitative Information.
Graphics Press, Cheshire, Connecticut, 1983.

Excellent advice for including graphics in documents when you really need the graphics to convey information, not just be decorations. Tufte has 3 more recent books in print, which I've heard are as good, though I've only read one of them and don't have copies.

Report drafts and other homework

All students are expected to keep individual lab notebooks of their work, and keep them up to date. Bring these to class each week.

Every two weeks a written progress report is due.

Each report should be a more complete draft of the final report, with additions and corrections since the previous one, plus a cover page listing the main differences.

Every week, each individual or group will be expected to give a 5-minute presentation on their project status. Mostly, these will be informal (no slides) verbal presentations, but in the middle of the term there will be a more formal, 10- to 15-minute presentation with visual aids.

At the end of the quarter, there will be formal presentations on the entire project, probably 15- or 20-minute presentations. Although these are tentatively scheduled for our final-exam slot, we may coordinate with CMPE 123B and EE 123B to get a larger audience.
Due Date (E groups) Due Date (L groups) Assignment
13 Jan 20 Jan Draft 1
27 Jan 3 Feb Draft 2
3 Feb 3 Feb Formal oral progress report
10 Feb 17 Feb Draft 3
24 Feb 3 March Draft 4
17 March17 MarchFinal Report (noon drop-dead deadline—no extensions)
17 March17 MarchFinal exam slot 12–3 (probably unused)
19 March19 MarchFinal Oral presentations 5–10 Engineering Auditorium (or Simularium, if we can't get the auditorium)
E groups: Chan, Eberle, Linderkamp, Rogers
L groups: Cherf, Downey, iRage(Azarnoff, Maitra, Nayak)

Evaluation

Academic Integrity

Anyone caught cheating in the class will be reported to their college provost (see
UCSC policy on academic integrity) and may fail the class. Cheating includes any attempt to claim someone else's work as your own. Plagiarism in any form (including close paraphrasing) will be considered cheating. Use of any source without proper citation will be considered cheating. If you are not certain about citation standards, please ask, as I hate having to fail students because they were improperly taught how to cite sources.

Collaboration without explicit written acknowledgment will be considered cheating. Collaboration on lab assignments with explicit written acknowledgment is encouraged—guidelines for the extent of reasonable collaboration will be given in class.

Classroom Accommodations for Disabilities

If you qualify for classroom accommodations because of a disability, please submit your Accommodation Authorization from the Disability Resource Center (DRC) to me during my office hours in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY).

Rogues' Gallery


Scott Azarnoff

Chuck Chan

Gerald (Max) Cherf

Samantha Downey

Melissa Eberle

Bert Linderkamp

Raj Maitra

Sahil Nayak

Adam Rogers

Schedule of activities

6 JanAdministrivia
13 JanGnuplot and graphing resources:
http://t16web.lanl.gov/Kawano/gnuplot/index-e.html
Gnuplot tutorial and tips
http://www.gnuplot.info/faq/faq.html
Official Gnuplot FAQ, including download information.
map_trim11_log
An example data file to use for gnuplot examples.
map_trim11-wrong.hist10000
An example data file to use for gnuplot examples. This one is the output of histogram-from-rdb, but the rdb file is 109Mbytes, so I did not want to put the full data set on the web.
fit-wrong.gnuplot
An example gnuplot script, illustrating fitting a complicated function.
cullpdb-phi-psi.2d
An example data file (output by histogram2-from-rdb), for illustrating contours and heat maps.
phi-psi-hist.gnuplot
An example gnuplot script, illustrating contours.
20 Jan

RDB is a collection of perl scripts that use files with tab-separated columns as a relational database. Rdb is very handy for handling modest amounts of data, where the effort of setting up a real database is not justified. It is very easy to read and write RDB files with almost any programming language, so this is a handy format for the output of analyses,

http://compbio.soe.ucsc.edu/rdb
Documentation for the standard scripts
http://compbio.soe.ucsc.edu/rdb/rdb2.6c+sort-patch.tar.gz
Finding old unix tools like RDB is sometimes difficult. It is included with some Linux installations, but if you need it on another machine, you can download our copy and untar it.
rdb2gnuplot
rdb2gnuplot is a locally-produced script to strip the rdb header off a file, to avoid confusing gnuplot. A typical use in gnuplot is
	  
plot '< row independent dependent < dummy-data.rdb | rdb2gnuplot' with lines
histogram-from-rdb
histogram-from-rdb is a locally-produced script for getting the histogram of a column in an rdb file. There are various options for adjusting how the bin sizes are set. The only documentation is in comments at the beginning of the script.
histogram2-from-rdb
histogram2-from-rdb is a locally-produced script for 2-d histograms from 2 columns of an rdb file. The only documentation is in comments at the beginning of the script.
correlate-rdb
correlate-rdb is a locally-produced script for computing the correlation between two columns of an rdb file.
smooth-rdb
smooth-rdb is a locally-produced script for producing a smoothed curve of one column as a function of another, by averaging over overlapping windows. The only documentation is in comments at the beginning of the script.

27 JanLaTeX and BibTeX.
example.tex
A simple example LaTeX file.
example.pdf
PDF file output for example.tex
Makefile
An example Makefile, showing one of many ways to produce a pdf file from a LaTeX file. You may wish to use Preview on the Mac, or freeware like ps2pdf to create the pdf file. (pdflatex has trouble with included .eps graphics, so I don't recommend it)
Simple on-line tutorial for LaTeX
The Art of Problem Solving website provides a LaTeX tutorial for high-school and middle-school students taking their on-line courses.
XyMTeX
A LaTeX package for drawing chemicals. A little hard to learn, but quite powerful, and supposedly easy to use once you've gotten past the initial hump. I've not used it myself (haven't needed chemical drawings in any of my papers), but one of my grad students has just learned it and likes it.
3 FebFormal oral progress report
10 FebResumes and Tufte's polemic against PowerPoint, which is in the McHenry Library Reserves:
The cognitive style of PowerPoint / Edward R. Tufte
Cheshire, Conn. : Graphics Press, c2003
McH Reserves P93.5 .T848 2003

Note: the copy I was waving around was the second edition, c2006.

17 FebPoster design
24 FebPeer editing
3 Mar
10 MarPoster session (see http://intranet.soe.ucsc.edu/lab-support#PosterPrinting for instructions)
17 MarFinal exam slot 12-3


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SoE home
sketch of Kevin Karplus by Abe
Kevin Karplus's home page
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Biomolecular Engineering Department
BME 123 home page CMPE 123A forum http://seniordesign.soe.ucsc.edu

Questions about page content should be directed to Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
318 Physical Sciences Building

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