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2013 November 12

Long weekend, little accomplished

Filed under: Uncategorized — gasstationwithoutpumps @ 22:47
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I just had a 4-day weekend, in which I got little more accomplished than a usual 2-day weekend.

Much of Saturday was spent trying to use PacBio reads to improve a draft genome of  a V. cholerae strain that  I had built with 454 reads a couple of years ago.  There was no problem getting blasr to map the reads, and I could call variants with “samtools mpileup”, though that took 2 CPU days to complete.  Unfortunately, that did not tell me what I really needed to know, which was whether the orignal assembly was in the right order.  I found a couple of places where the PacBio read mapping indicated problems (either the reads all terminated their mapping at nearly the same point, or they suddenly switched from aligning very well to aligning poorly).  Unfortunately, I’ve not yet figured out a good way to automate this detection, so I’m not sure I can find all the places which might have problems.  Dips in average quality of the mpileup consensus over 50- or 100-base windows pulls out the places where the alignments get bad, but not where they suddenly stop.  Furthermore, once I’ve identified the bad regions, I still need to break the genome apart there, rebuild the bad regions from the PacBio reads that map nearby, and see if I can stitch the genome back together (probably with extra repeats that had not been resolved in the 454 assembly).  I’m considering backing off and building a new genome assembly from just the PacBio reads (after cleaning them up using PacBio2CA and the 454 reads) and the Celera Assembler.  I can then compare the genome built from the PacBio reads and the one built from the 454 reads and resolve any discrepancies. Sigh, this project keeps getting bigger, just as I think I’m almost done.

On Sunday, I did a bunch of small tasks: raked leaves and shredded them, updated the grad alumni web page, announced the Freshman Design Seminar class (which will happen winter quarter, though once again as a “Group Tutorial” to prototype the course before submitting the official paperwork), wrote a letter of recommendation for a student applying to grad schools, scanned in the flyer for “Planet of the Abes” (the recent Dinosaur Prom show), scanned 35-year-old t-shirt of mine so that I can get another copy made, updated my paper list to include the just released PNAS paper, wrote a blog post, and caught up with a lot of my e-mail (though there are still some advising e-mails that I haven’t taken care of).

The flyer,  drawn by Hunter Wallraff, for the Dinosaur Prom Improv show.  Because the edge of the drawing was not reproduced on the flyer, I had to try to add it in by hand to get something usable for the titling of the video.  I did not correct the error in the URL for

The flyer, drawn by Hunter Wallraff who holds the copyright, for the Dinosaur Prom Improv show. Because the edge of the drawing was not reproduced on the flyer, I had to try to finish the S and add an E  in by hand for “Broadway Playhouse” to get something usable for the titling of the video. I did not correct the error in the URL for

On Monday, I did a lot of grading, wrote another blog post, used the Planet of the Abes flyer to make titles for the Dinosaur Prom video, and rendered the video (tying up my laptop all night).  I also cleaned up the scan of the old t-shirt and converted it to SVG so that a new silk screen printing can be done. I’ve tried looking for the copyright holder for the design, but I have no idea how to find him (or her)—Google image searches bring up nothing similar, and there is no signature on the design or the shirt. I started working on my slides for the talk I have to give on Thursday, but did not get much done.

This morning, I responded to more e-mail, wrote another blog post, did more grading, and returned the activity monitor I’ve been wearing for the past 2 weeks to the Sleep Center. In the afternoon, I did more grading at Gayle’s Bakery in Capitola, met with my son’s consultant teacher for a couple of hours, bought the usual weekly load of soy milk (only 2.5 gallons this week), did some other grocery shopping, finished the grading, recorded the grades, cleared the rest of the advising e-mail, and compared results on group theory problems with my son.  We’re a bit behind schedule there—he’s not finished all the Chapter 1 and Chapter 2 problems I assigned, and we’re supposed to be finishing Chapter 3 this week—I’ve not even assigned Chapter 3 problems yet.

Things I wanted to do this weekend but didn’t:

  • Get the slides done for Thursday’s talk
  • Get the Program Learning Objectives written for bioinformatics
  • Get assessment plans defined and written for the Program Learning Objectives for both bioengineering and bioinformatics.
  • Create a draft of a revised curriculum for the third track in bioengineering (which also needs a new name and a clearer focus).
  • Rewrite the handout for the next programming assignment in the Bioinformatics: Models and Algorithms courss.
  • Write code for looking for regions of the Helicobacter pylori genome that are possibly swapped in the current assembly and test for which rearrangement is most consistent with our data.
  • Start testing the BitScope differential input device they sent me.
  • Start working on Chapter 3 problems in group theory.
  • Start writing a paper on the segmenter that I described in my blog 3 months ago.
  • Clear the leaves off the roof before the rains start, since the leaves form dams that keep the rain from running off into the gutters properly.

There were probably other things, but I forget what they were now.  Once the to-do list gets longer than my piece of paper can hold, things fall off it.


2013 April 27

Dinosaur Prom Improv, Spring 2013 shows

Filed under: Uncategorized — gasstationwithoutpumps @ 10:56
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The teen improv group my son is in has two shows coming up: one this weekend and one in May as part of the Santa Cruz Improv Fest, a month-long showcase of Santa Cruz’s improv troupes.

Dinosaur Prom logo

This Town Ain’t Big Enough for the Ten of Us

The Broadway Playhouse

526 Broadway St, Santa Cruz, CA

Sunday, April 28, 2013, 7:00 pm.


Santa Cruz Improv Fest Performance

The Broadway Playhouse

526 Broadway St, Santa Cruz, CA

Sunday, May 12, 2013, 7:00 pm.


Information about their shows can usually be found at Upcoming Shows | Dinosaur Prom Improv.

Although I may be biased as a parent of a cast member, I find their shows to be pretty funny, and the laughter from the audience suggests that I am not alone in this assessment.

2012 December 4

Reflections on teen improv

Filed under: Uncategorized — gasstationwithoutpumps @ 22:46
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Dinosaur Prom logo

logo by Hunter Wallraff

On Sunday, 2012 Dec 2,  I went to see two different teen improv troupes: Water the Weeds in the afternoon, and Dinosaur Prom in the evening (I announced those shows here previously).

The Water the Weeds troupe had about 16 members, roughly equally divided between male and female, while Dinosaur Prom has 10 (7 male and 3 female).  I found the two shows quite different, though they played some of the same improv games (both played the Good, the Bad, and the Ugly advice show game, for example).

Both troupes have shows every few months (maybe 3 times a year) and both troupes have an adult coach.  Both troupes practice about once a week, for similar amounts of time. The Water the Weeds troupe has been around since at least 2006 (when it was a younger kids troupe), while Dinosaur Prom started in the fall of 2011, and did their first show Jan 2012. Most of the players have been with the troupe for about a year. I don’t know how many of the Water the Weeds troupe are new players and how many have been with the troupe for years.

One might expect the longer-running troupe to be more polished, but the opposite was true—Water the Weeds came across a lot like a school play with earnest students trying hard, but not quite getting things to work.  There were a couple of players in Water the Weeds who seemed to know what they were doing, but they were often partnered with weaker players so that the ensemble as a whole rarely kept the action moving.  It was not a bad show for a class, but it was clearly a for-parents-and-friends-only production.  The adult coach stepped in several times to announce things and keep the show moving.

Dinosaur Prom, on the other hand, kept the audience laughing practically their whole show.  Several of the players had excellent comedic timing and came up with good material, and even the weakest players could at least keep straight lines coming for the others to work with. The adult coaches for Dinosaur Prom were not visible during the show (one was in the audience, the other in the tech booth)—the teens took care of all introductions, game announcements, explanations, and transitions themselves.

The biggest problem with the Dinosaur Prom show was that it was too short, at under 45 minutes.  I believe that they had planned to have a show that was over an hour long, but they ran through their playlist faster than they expected. The troupe also did one long-form game that may not have lasted as long as they had planned on. Part of the short running time was because they knew when a game had run dry and moved quickly on to the next one without awkward pauses (except at the very end, when their set ended rather abruptly). There may have been some directorial influence, in that the lighting was generally lowered between games—it may have been the adult coach in the tech booth recognizing when it was time to move on to the next game, rather than the teens themselves, but if so, the signaling was subtly done.

For future shows, I think that they need to plan enough games for a 2-hour show and have someone checking the time before each game to see if they are over an hour.  Once they hit the hour mark (or 1:10 or whatever they are aiming for), they can jump forward in their playlist to whatever they planned for their finale (or ask the audience for advice about what to do next).

I’ve been trying to figure out what makes the difference between the two troupes.  Is it just a random difference about who joined which troupe?  Is it a difference in coaching and rehearsal style? Is it a difference in selection process for troupe members?  Is it a difference in the intensity of the rehearsals because of the difference in troupe sizes?

I don’t know what makes for the difference in the performances, but I have some conjectures.  First, I think that Water the Weeds puts all their students in the performance, whether they are ready or not, while Dinosaur Prom is the performing troupe that students graduate to from an improv class—not all the class members perform with Dinosaur Prom. Second, I believe that 16 is too large a troupe to really get enough practice playing against other members of the troupe.  The pairings go up quadratically with the troupe size, so just increasing the practice time linearly with the number of players is probably not enough. Third, I think that coaching styles are different, with the Dinosaur Prom coaches inspiring the teens to higher levels of performance—but I’ve not observed either troupe in practice, so I don’t know what the differences are. Fourth, I think that Dinosaur Prom got lucky with a couple of very creative improv players who push the others to improve.

I believe that both troupes will be participating in the Santa Cruz Improv Fest next May.  I think that Dinosaur Prom will be as good as some of the adult and college troupes who are the mainstay of the Improv Fest.

More details about Dinosaur Prom can be found at their temporary web site, which will move to a more permanent location after it is completed.  Disclaimer: My son is part of the Dinosaur Prom troupe (see my post Dinosaur Prom improv), and so I may be unduly biased in their favor.


2012 November 17

Teen improv Dec 2

Filed under: Uncategorized — gasstationwithoutpumps @ 12:01
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Dinosaur Prom logo

logo by Hunter Wallraff

On Sunday, 2012 Dec 2, two different teen improv troupes will be presenting shows in Santa Cruz:

  • Water the Weeds, 2:00–3:30 p.m., Tannery World Dance & Cultural Center, 1060 River St Studio #111, Santa Cruz
    Adults $5, kids and teens free.
  • Dinosaur Prom, 7:00–8:30 p.m., Broadway Playhouse, 526 Broadway St, Santa Cruz
    The Dinosaur Prom show is titled “Creature from the Marine” and is free.
    More details about Dinosaur Prom can be found at their temporary web site, which will move to a more permanent location after it is completed.

Both troupes have shows every few months (maybe 3 times a year).  I believe that both troupes will be participating in the Santa Cruz Improv Fest (along with several adult improv troupes) next May.

My son is part of the Dinosaur Prom troupe (see my post Dinosaur Prom improv), and so I’ve seen several of their shows. Like any improv troupe, not everything they try works, but they’re usually pretty good.

I’ve seen fewer shows by Water the Weeds—it’s a larger troupe with a wider range of abilities and I have no predictions about how good this particular show will be.  It will be interesting to see both troupes on the same day, to contrast the styles.


2012 May 12

No coordination in our school district

Filed under: Uncategorized — gasstationwithoutpumps @ 20:28
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Three high schools in the same school district have all scheduled their Spring musicals at the same time: Big weekend for theatrical productions.  We managed to get to none of them, as we had the MATE underwater ROV contest today, and so were too busy packing up stuff last night and too fried this evening.  Had they been spread out over three weekends, we probably could have made at least one of them.

You’d think that the three theater teachers in a small school district would get together to coordinate the scheduling of their shows, so that they would not steal audience from each other, and so that their students could see the shows that their friends are putting on at other schools.  Many of the theater kids at each school know one another from theater camps and evening theater classes and have been socialized that it is polite to see each other’s shows.

One of the three shows continues next weekend, and we may get to see it, though we already have tickets for a Pinocchio performance Friday night, Saturday afternoon is a teen improv show (not my son’s troupe), Saturday night is one of the Improv Festival shows, and Sunday we’ll be at Maker Faire.

My son’s improv troupe (Dinosaur Prom) will be giving a short performance at the Museum of Art and History’s third Friday event on Friday 18 May 2012.  I just hope that they schedule the improv show at a time before we have to go to the Pinocchio performance!  The Pinocchio show is being put on by the same organization as the improv troupe (WEST performing arts), so I hope that they can avoid conflicts. Unfortunately, MAH has not been very good about releasing detailed schedules for their events, so we won’t know until the staff at WEST pass on the information.

My son is planning to create a web site for the improv troupe he is in when he gets some time (probably after his presentation in Spanish class on Wednesday).  I’ll announce the site here when it goes live.

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