UCSC BME 123B Winter 2011

Engineering Design Project II

(Last Update: 15:34 PST 28 February 2011 )
link to homework
Rogues' Gallery

This course continues BME 123A. For catalog copy and pre-requisites, see the main page for BME123. This year, bioengineering students doing senior theses will take BME 123B (without BME 123A) for feedback on the writing of their theses.

Who, When, and Where:

Instructor:

Kevin Karplus ( karplus@soe.ucsc.edu)
http://users.soe.ucsc.edu/~karplus
Office hours: PSB 318, MF 11-11:30
+1-831-459-4250

Lectures: W 5-6:45 PSB 305 (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: Thurs March 17 7:30—10:30p.m.
We may use this exam slot for design presentations, depending on coordination with the CMPE 123B class.

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 will 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 (which used to be used in CMPE 185) has some excellent chapters on organizing your writing for readability. Also, several students in the class have grammatical problems that are well addressed in the chapters for non-native speakers.

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 got a copy of one of the more recent ones.

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 and to each individual meeting.

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. Don't forget to date every draft.

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 will probably coordinate with CMPE 123B to get a larger audience.
Due Date (E groups) Due Date (L groups) Assignment
12 Jan 19 Jan Draft 1
19 Jan 19 Jan LaTeX assignment Starter hw1.bib file
26 Jan 2 Feb Draft 2
2 Feb 2 Feb Formal oral progress report
2 Feb 2 Feb gnuplot and rdb assignment
9 Feb 16 Feb Draft 3
23 Feb 2 March Draft 4
7 March 7 March CITRIS White Paper competition
17 March17 MarchFinal Report (noon drop-dead deadline—no extensions)
17 March17 MarchFinal exam slot 7:30–10:30 p.m.
E groups:
L groups:

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

E groups
Circuits Team

Derek Chang

Jessica Borja
Individuals

Asis Lopez

Jimmy Perrott

Laci Hampton
L groups
Reverse Electro-Dialysis (RED) team

Alexandra Eastes

Chirag Sharma

Danny Tate

Dylan Hingey

Ulysses Morales
Individuals

Regina Lam

Ziah Dean

Schedule of activities

5 JanAdministrivia and LaTeX
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.
BibTeX
BibTeX is a free bibliography formatting tool for use with LaTeX (it comes with the LaTex distributions). It has been around a lot longer than commercial tools like EndNote and is likely to outlive them, as there is no commercial impetus to keep changing the product to force people to buy newer versions.
http://www.soe.ucsc.edu/~you/notes/ucthesis-ucsc/
I recommend using LaTeX for thesis proposals and theses. The ucthesis style file seems to be a good style to use.
DeTeXify
There is a cool tool for guessing the LaTeX code for hand-drawn symbols at http://detexify.kirelabs.org/classify.html Personally, I find it faster to scan a list of symbols (particularly since drawing with a touch pad on a laptop is tough), but others may find this drawing approach useful.
12 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.
19 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 '< column 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.

26 JanResumes 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: there is a second edition, c2006.

2 FebFormal oral progress report (videorecorded)
9 FebFeedback on videos
16 FebPoster design
23 FebPeer editing
2 Mar????
9 Mar????
17 Mar Poster session 4:30–6:30 p.m. (see http://intranet.soe.ucsc.edu/lab-support#PosterPrinting for instructions)
17 MarFinal exam slot 7:30–10:30 p.m


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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 http://seniordesign.soe.ucsc.edu
T0599 model 1
Karplus's lab page
UCSC Bioinformatics research

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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