Gas station without pumps

2015 September 2

Another bioinformatics teaching post

Filed under: Uncategorized — gasstationwithoutpumps @ 09:52
Tags: ,

This seems to be a good time of year for posts about teaching bioinformatics:  I just got another post about teaching bioinformatics in my feed reader, Scripting for Biology – Online Virtual Classroom-based Module « – Bioinform:

I am building a number of online virtual classroom-based modules for researchers working on biological data. The description for the first one is attached below, and I will have a beta test starting Sept 14. Please feel free to pass to anyone interested. The beta test is free, and all course materials (including cloud account) will be provided. I currently have only a small number of spots left for this one. If interested, please email pandora at

The post describes an upcoming attempt to build teaching modules for researchers.  The classes will be chat-based and one thing particularly struck me:

We will keep the class size small (~10) so that I can monitor the work done by every student. Each student will be solving problem at his own pace without being impacted by the rest of the class. So, if someone learns fast, he can finish the modules quickly or go on to solve more difficult problems.

A class size of 10 is very good for personal attention—even at the University we rarely get the luxury of such a small class.  I wonder whether the modules are intended to scale to larger classes, or if the plan is always to have 10-student classes.


2015 August 31

Eighth weight progress report (and colonoscopy)

Filed under: Uncategorized — gasstationwithoutpumps @ 19:48
Tags: , , ,

This post continues the series of weight progress reports from the previous one.

My weight went up a little in August:

Weight went up a little, but stayed in my target range (barely).

Weight went up a little, but stayed in my target range (barely).

My exercise was down a bit for the month (only averaging 2.25 miles/day of bicycling, down from 3.48 in July and from my normal year-round average of just over 4 miles/day).  Non-Californians may find this strange, but I bicycle much more in winter (daily commute to campus) than in summer. It hasn’t helped that we had a heat wave at the end of August—I’m no longer used to afternoons with temperatures over 95°F (35°C), and I just stayed in my nice cool bedroom/office all day.

I had really expected to lose some weight this month (despite the less-than-adequate exercise), because  I had a colonoscopy in the first week of August.  With 3.5 days of clear liquids only (about 400 Calories a day) and massive doses of laxatives, I expected my weight to plummet, needing some effort to bring back up.  Look closely at that weight plot—do you see a drop at the beginning of August? Neither did I. Confounding my expectations, I put on weight during the colonoscopy prep—more liquid went in than came out.  My experience should make it very clear that counting on laxatives for weight loss is a really bad idea.

And despite the rather draconian prep protocol I followed, the gastroenterologist pronounced the prep merely adequate, which is still better than the last two times, when a more standard protocol resulted in inadequate prep.

I have a very slow transit time (3–4 days, rather than the usual 1–2 days), so I need to customize the colonoscopy prep protocol. I customized the protocol this time, rather than following the standard one that the gastroenterology office wanted me to follow.  Their protocols had failed twice already, because the protocols were based on an average individual, not customized for me.

The protocol I followed this time was

Day –7:
Discontinued nuts, whole grains, popcorn, fish oil, aspirin.
Continued multivitamins, atorvastatin, and calcium carbonate.
Day –3:
00:00 Discontinued solid food.
11:30 two Bisacodyl tablets (2× 5mg)
17:30 one dose Purelax (17g PEG 3350) in 300ml apple juice
Day –2:
00:00 Stop all alcohol, red, blue, or purple fluids.
10:30 One bottle magnesium citrate solution (17.45g magnesium citrate)
15:45 One bottle magnesium citrate solution (17.45g magnesium citrate)
Day –1:
08:05-09:30 2L PEG-3350 solution in 8 250ml doses, 10 minutes apart (210g PEG 3350, 2.86g sodium bicarbonate, 5.6g sodium chloride, 0.74g potassium chloride)
Day 0:
07:00 2L of PEG-3350 solution (in 8 250ml doses, 10 minutes apart)
10:40 stop all fluid intake
13:40 colonoscopy

The Bisacodyl and Purelax had little effect, but the magnesium citrate was very effective. The PEG-3350 was rather slow-acting—very little of the 2L that I took early in the morning of Day 0 had come out six hours later. Drinking 2L in 75 minutes was very hard on my stomach—the first 1L was easy, but my stomach was painfully distended by the end of 2L.  (I had deliberately selected a 4L protocol, rather than the 2L Moviprep protocol that I used last time, because I thought that the flushing action of more water would increase effectiveness.)

In five years, when I’m scheduled for the next colonoscopy, I’ll modify the protocol further, discontinuing solid food 12 hours earlier, replacing the Bisacodyl and Purelax with an earlier bottle of magnesium citrate (1 on day –3, 2 on day –2),  and doing 3L of the PEG-3350 on Day –1 in 3 1L sessions (8:00, 12:00, 16:00), with only 1L early in the morning of the day of the procedure.

2015 August 30

Ask better questions

Filed under: Uncategorized — gasstationwithoutpumps @ 15:29
Tags: ,

There is a new blog, intended for K–12 math teachers, that is dedicated to “trying to get a little bit better at questioning”:

I read a number of math-teacher blogs, even though I’ve not taught a math course since Spring 2003 (Honors Applied Discrete Math), because a lot of the teaching discussion is relevant to what I do teach. I also read some physics teacher blogs, for the same reason.

It would be nice if there were blogs discussing precisely the same courses and teaching challenges that I face, but I don’t know if there is anyone else in the world who teaches the same eclectic mix of courses that I do. Last year I taught a first-year grad course on bioinformatics, a how-to-be-a-grad-student course, a freshman design seminar for bioengineers, a senior thesis writing course, a grad course on assembling the banana-slug genome (co-taught with another faculty member), and a lecture/lab course on applied electronics.  Over the decades I’ve been a professor, I’ve created and taught courses on an even wider range than that, including bicycle transportation engineering, desktop publishing, VLSI design, technical writing, digital synthesis of music, and most of the core computer engineering courses. At the moment, I don’t see myself creating any more new courses before I retire, unless I can hand off some of the existing courses to younger faculty.

The “better at questioning” theme of is an interesting one for a teacher blog, as it focuses on one rather narrow aspect of teaching, but is open to a diversity of different subjects, different age ranges for the students, and different teaching styles.  I’ve considered joining that blog as a contributor (it is open to any teacher, I believe), but I’m not sure how much I have to say about asking questions that is relevant to the math teachers who are the main audience.

I have much less time with students than K–12 teachers do (35 hours for a standard course, 95 for my intense Applied Electronics lecture+lab course), so I don’t have the luxury of slowly developing a classroom culture—I fully expect some students to still be uncomfortable with the way I teach even at the end of the course, though I attempt to get them to buy into the main purposes of the course within the first few hours of class time.

My goal in lecture classes is not to ask questions, but to get students to ask me questions—I’d rather that they figured out what they needed to know, rather than me trying to guess what holes they have based on what they get wrong on questions. I’m also not very interested in what students can do in 30 seconds—I want to know what they can do if they have adequate time to think and to look things up, so in-class questions don’t tell me much about what students need.  I rely on week-long homework and papers to do that.

I mainly use in-class questions to keep students engaged in the class—asking for the next step in a derivation, for example—rather than to test their knowledge or understanding. Since engagement is my goal, I don’t generally ask students who raise their hands, but do cold calling—selecting students randomly after asking the question.

Questions in the lab are a different matter. There I’m either trying to understand what the student is attempting (“What is the corner frequency you were trying to get?”) or prompting them to learn to do debugging (“Where is your circuit schematic?” “Have you compared your wiring to your schematic?” “What voltage did you expect to see there?”).


2015 August 28

New Stem Cell Assistant Professor position

Filed under: Uncategorized — gasstationwithoutpumps @ 22:07
Tags: , ,

UCSC has just announced a new Assistant Professor position in Stem Cell Genomics in the Biomolecular Engineering Department.  The job description and application is at, and the key line is probably

The successful candidate will be expected to establish a wet lab operation focused on stem cell genomics research, to develop a vigorous, externally funded research program, contribute significantly to undergraduate and graduate education, and perform university and professional service.

We are defining stem-cell genomics fairly broadly, particularly the “genomics” part—the stem-cell part is an absolute requirement, as the available lab space is dedicated to stem-cell research.  The “genomics” is there because that is where the department has critical mass—it will be easier to integrate a genomics person into the department than someone who is further afield.  That said, we always look for the best available candidate using a broad definition of what the position calls for.

Personally, I am hoping that we get someone in stem-cell engineering, as we are an engineering department, not an extension of the Molecular, Cell, and Developmental Biology department.  I’m not on the search committee, though, and I don’t know whether they share my view of the importance of strengthening the engineering and design components of our curriculum and teaching—they may not even distinguish between science and engineering.

I’m not in stem cells myself, so I’m not up-to-date on what is going on in the labs.  As I understand it, current research is mainly with mice (particularly hematopoietic stem cells), but there are a number of new induced pluripotent stem cell lines being established for various primates.  (A couple of the senior theses that I read several times as part of senior thesis writing courses dealt with establishing iPSC lines from orangutan fibroblasts.)

This faculty slot is the last wet-lab person the department will be able to hire for some time (until the campus rationalizes their currently dysfunctional way of allocating space—we are desperately short of wet-lab space while other departments are trying to figure out what to do with all their unused wet-lab space), so we want to get someone good who’ll stay with us for a long time.

It is an assistant-professor-only slot (tenure-track, but arriving with tenure)—the department has wasted way too much time on failed senior recruitments (generally forced on us by higher administrators—the School of Engineering has done much better growing our own faculty from promising assistant professor candidates).


2015 August 26

Few Santa Cruz businesses on bike league list

Filed under: Uncategorized — gasstationwithoutpumps @ 10:23
Tags: , ,

Every year the League of American Bicyclists publishes a list of “bicycle-friendly businesses”, which employers (including governments and non-profits) can apply to be on.

I was surprised at how few Santa Cruz employers were on the list:

  • Ecology Action (silver)
  • County of Santa Cruz (bronze)
  • Santa Cruz Seaside Company (bronze)

The League also has listings for communities, universities, and states.  The City of Santa Cruz has a silver listing, as does UCSC. UCD is platinum; UCSB is gold; UCB and UCI are also silver; UCLA and UCSD are bronze.  UCSB and UCD are also listed as businesses (their bike-friendliness towards employees, rather than towards students), with the same ratings.

UCSC does do a fair amount for bicycle commuters. I know of free showers in at least 4 buildings on Science Hill, and there are probably others. Most buildings allow people with offices to bring their bikes into their offices and there are card-operated bike lockers next to some of the more popular buildings.  Bike posts and other low-security bike parking are provided in adequate quantity (though the quality is not aways the best).  There are free tool stands at several places on campus and an on-campus bike shop (the Bike Co-op, which is not a full-service bike shop).  All the campus buses and the SCMTD buses that serve campus have racks for 3 bikes, and UCSC runs an uphill-only shuttle with a trailer for a dozen bikes from the Westside several times an hour.

Having seen what UCSB does, it looks like the main differences in bike friendliness come from UCSB’s campus being flat and compact, while UCSC’s is sloped at 4% and spread out.  The ravines and hills on the UCSC campus make it very expensive to provide additional roads and bike paths, and the 4% climb for a mile from the entrance to campus to Science Hill is daunting for many beginning bicyclists.

UCSC could do more to promote bicycling to campus, but there is a point where even large investments result in only small increases in bicycling—UCSC has invested much more heavily in transit options than in bicycling, as they expect that to make larger changes in student and employee behavior.  (And it seems to be working—UCSC has tripled in size in the last 30 years, with only modest increases in motor vehicle traffic.)

I don’t know whether Santa Cruz has been slipping as a bike-friendly place, whether other places have overtaken Santa Cruz, or whether businesses and governments in Santa Cruz simply can’t be bothered with the bureaucratic process of the League’s classification scheme.

What is the return to the community if more businesses were listed as bike friendly, or the community rating were higher? The listing is primarily a marketing tool—from a bicyclist perspective, what matters is what the infrastructure and policies are, not whether the LAB knows about them. And marketing is not that valuable to the community right now. It isn’t as if Santa Cruz were trying to lure more people to move here—we already have a serious housing crunch, particularly for the rental market. (Prices are high also: studio apartments are about $1600 a month, 2-bedroom about $2200 a month, I think.)  I do think that Santa Cruz would benefit from more ecotourism marketing—getting tourists to bicycle around town rather than clog the streets with their bad driving would be an improvement.

What Santa Cruz is trying to do is to lure more tech companies to Santa Cruz, to take advantage of the highly educated people already here and reduce the long-distance commuting to high-paying jobs in Silicon Valley. It is not clear whether getting a better bike-friendly community rating would help with that effort or not, though one of the big attractions for tech workers in Santa Cruz is not having to do the Highway 17 commute.  Being able to bike to work is a big attractor for engineers, particularly in software businesses (it is often our only source of exercise).  Whether it is an attractor for tech companies is a somewhat different question.

Next Page »

The Rubric Theme. Create a free website or blog at


Get every new post delivered to your Inbox.

Join 321 other followers

%d bloggers like this: