Gas station without pumps

2014 August 19

Two papers submitted

I got two papers with a co-author finished and submitted today.

One of them is based on the segmenter algorithms that I wrote up in this blog (with some improved parameterization): Segmenting noisy signals from nanopores, Segmenting filtered signals, and Segmenting noisy signals revisited.

The other one is an HMM paper that uses the automatic segmentation and an HMM that models the DNA motor behavior to do the same analysis that was done by hand in an earlier paper “Error Rates for Nanopore Discrimination Among Cytosine, Methylcytosine, and Hydroxymethylcytosine Along Individual DNA Strands” in PNAS.  The automatic HMM method was more accurate than the hand curation and feature extraction followed by sophisticated machine learning methods like support vector machines and random forests—I think that we were limited before by the biases of the hand curation and feature extraction.

Unfortunately, we were not able to do side-by-side comparison on exactly the same data, as the original data for the PNAS paper was lost in a 2-drive failure on a RAID that had not been properly backed up.

The paper writing did not take much of my time this summer, as my co-author did a lot of the writing and kept me from procrastinating too much.

I’ve also been working on my book, tentatively titled Applied Electronics for Bioengineers, but without a co-author to keep me honest, I’ve been doing a lot of procrastinating.  Yesterday I had planned to show the waveform of the gate signal on a nFET being used for pulse-width modulation, to show the “flat spot” that results from feedback through the gate-drain capacitance.  I fussed with that for quite a while, but never got a recording I liked the looks of—so ended up getting nothing written on the book.  I’ll probably try again tomorrow, but with a backup plan of working on a different section if that one gets too frustrating, or of writing some of the text that will go around the figure, once I get a figure I can use.

The book is currently 215 pages, but that includes the front matter and back matter.  The core of the book is only about 188 pages, with 74 figures.  I probably need a bunch more figures (schematics, graphs, photos, …), but those are what take the longest to produce.  There’s a little over a month left until classes start, but I don’t see myself finishing by then.

2014 August 17

New bedroom furniture

Filed under: Uncategorized — gasstationwithoutpumps @ 12:58
Tags: , , , ,

I’ve added some new furniture to the bedroom:

My new 42" rolling cabinet tool box.

My new 42″ rolling cabinet tool box. The plastic tool box on the top is my son’s.

For several years I’ve been planning to clean up the garage, put up shelving, and get all the “stuff” in the garage organized. It has been a firm commitment each summer, and each summer nothing happens (well, one year I got some nasty old shelving taken down and everything put into boxes, but that was sort of negative progress, as I never got new shelves put up).

Part of the plan was to get all (or most) of my tools into a rolling tool box, so that I could have easier access to them. I’ve often ended up buying a new hand tool because I couldn’t find what I was looking for in the garage. This summer I finally bought a 42″ rolling tool box from Harbor Freight for $370, after giving up on finding anything locally. The shipping from southern California added another $97 to the price (shipping weight is 289 pounds). Because most of the tools get used in the house, not the garage, I decided to keep the toolbox in the house. I’m planning to clear my son’s stuff out of the living room and into his bedroom when he leaves for college (so the robotics table, scroll saw, and drill press would move out of the living room, restoring it to a more livable space), so I didn’t want to put the tool box in the living room. Since I want the tools to be readily available when I’m working on electronics stuff, I ended up putting the tool box in my bedroom, which has gradually been becoming my workshop for computer and electronics stuff.

My wife has been patient with the gradual conversion of our bedroom into a workshop, but I think that we could make the room more comfortable by rearranging the furniture. I hope to get the floor of the bedroom mostly cleared of junk before school starts, though that may require getting some shelving that fits under the window to tidy up the junk that has accumulated while still leaving it mostly accessible. I’ll probably have to buy the new bed she wants, though this will require some careful selection, as there won’t be room for bedside tables and our current bedside lamps are not tall enough to work with a conventional bed.

I spent some time yesterday getting the tool box into the house—the delivery service wouldn’t even put it on the porch, so I had to uncrate it on the driveway, remove all the drawers, then get my son and my wife to help me put it up the front steps. While I had all the drawers out, I lubricated the slides with paraffin (the T9 lubricant I use on my bike chain). I then spent most of the afternoon unearthing tools in my garage and organizing them in the tool box. I couldn’t get all the hand tools into the toolbox, but most of them fit.

At the end of the day, I had my son go through his tool box and mine, selecting what he would take to college. He ended up with a somewhat smaller set of tools than the rather large list I had put together, rejecting the socket wrench set and the screwdriver security bit set as too big.

  • metric Allen wrenches (from a set from Harbor Freight, I’ll keep the English and star bits)
  • screwdrivers (he already had a handle and bit set)
  • claw hammer (he already had one)
  • mini hammer with screwdrivers
  • mini level (which comes with a warning for people with pacemakers, which is pretty silly considering how weak the magnet on it is)
  • adjustable wrench (an 8″ one with a 1″ jaw opening, the second smallest of the set of laser-marked ones from Harbor Freight)
  • measuring tape (he’s only taking one of the two 25′ ones he already had)
  • razor knives
  • Leatherman pocket tool (which he already had)
  • zip ties
  • velcro cable straps
  • needle nose pliers (2, which he already had)
  • diagonal cutters (which he already had)
  • end nippers (which he already had)
  • self-adjusting wire strippers
  • electrical tape
  • multimeter (from his chemistry lab kit)

There were also several leftovers from my first prototype run of the circuits course:

We still have some things not added to his tool box, which is already full:

  • bike patch kit
  • stainless steel bike tire levers
  • needles and thread
  • tweezers
  • Arduino and Freedom KL25Z boards
  • power supply for Arduino boards?
  • Ethernet cable
  • USB cables
  • soldering iron and stand (my old Unger iron, or perhaps he’ll take the one bought for his company)
  • Power strip with surge protector
  • solder
  • 22-gauge wire for breadboarding
  • first aid kit: band aids, larger gauze pads, antibacterial ointment, paper tape, medic scissors, thermometer, ibuprofen, antacid, simethicone

We’ll have to go over the previous list to check for other things he might need, but I think this list has most of the things I’m responsible for.  We might make a trip to Home Depot on move-in day to pick up a few other things.

 

 

Oregon Shakespeare Festival

I’m a little envious of my son—he’s gotten to go to Ashland twice this year to see plays at the Oregon Shakespeare Festival.  He’s seen nine different plays there this year, two of them twice.

For the first trip this year he went with Alternative Family Education, as part of their Dramatic Literature course in spring semester.  They teach the course each year around the plays that they’ll be seeing in Ashland—he’s taken the course three times and enjoyed it each time (except for some of the written assignments).  The first time he went, I was on sabbatical, so took the time to travel with the group as a “chaperone”—we’d had to fly to Ashland separately, rather than travel with them on the bus, because the trip left the day of the state science fair, though we both rode the bus home.  Since then he’s been able to travel both ways with the school group, but I’ve always had a heavy teaching load in the spring, and couldn’t justify skipping class for a pleasure trip to Ashland.

Last week, he traveled with a group from West Performing Arts.  This is the first time that WEST has done an Ashland trip, and it was planned at the last minute, so they were not able to get enough tickets or transportation for parents to accompany the group. It was a smaller group than the AFE—only ten teens and two adults. They were originally planning to see five plays, but while they were in Ashland they managed to get the last twelve standing-room tickets to Into the Woods, so they ended up seeing six plays—a pretty intense schedule with only three hotel nights!  They didn’t do as many workshops as the AFE group, but a lot of the workshops are aimed at general school groups, not at kids who had as much theater training as this group.  I don’t think that the teens minded not having a lot of workshops—most of them had just finished a two-week intensive Shakespeare conservatory, and all of them had done at least one of the Shakespeare conservatories (either this year or in a previous year).  It was an older group than the AFE trip also, as three of the teens were 18 or older and had graduated from high school.

I had some time this summer and could have gone myself, but arranging my own transportation and lodging at the last minute did not appeal to me, and my wife was not particularly interested in going there. She would travel to see world-class opera, particularly if the destination also had great art museums, but not for theater—the local productions are high enough quality for her and not much trouble to attend.  We had season tickets for Santa Cruz Shakespeare this year (as we did for Shakespeare Santa Cruz most previous years), and we’ve got season tickets for next year’s Jewel Theatre season.  We’ll also go to 8 tens at 8, an annual production of 8 new (or fairly new) ten-minute one-acts, and probably the best of the rest, a staged reading of another 8 from the pool considered for 8 tens at 8.  We also usually see the Shakespeare To Go performance, though not together—my wife sees it when they tour to her school, and I see the last performance they do, up on the UCSC campus. We’ll probably also go to the WEST Ensemble Players performances and the summer teen show by WEST. Though our son won’t be in them any more, we still know a number of the actors and they kids usually do a good job (tickets are cheap also).  If Santa Cruz Shakespeare puts on a holiday pantomime this year, we’ll probably go to that to, and possibly go to see the long-form improv group Freefall at one of their shows.

We’ll be going to one more WEST Performing Arts performance this year—a fund-raiser for their scholarship program this Friday.  This is not a rehearsed production—they’ve just requested a number of their more reliable actors to do monologues or sketches.  So my son will have one last chance to perform at West End Studio Theatre, though he hasn’t decided what he’ll do yet.

So with 14 or 15 theater events a year, and more available if we wanted them (UCSC stages several plays every quarter, but we rarely go to any of them), it isn’t as if I was starving for theater. My wife doesn’t get to anywhere near that number of operas (a few in San Jose and a few in San Francisco) and has to make do with broadcasts in the movie theater—and I wasn’t counting the broadcasts of National Theatre London that we see at the movie house, so I shouldn’t count opera broadcasts either. I’ve no cause for complaint.

Still, the Oregon Shakespeare Festival has a bigger budget than anything in Santa Cruz and produces some pretty impressive shows—I would like to see them again. Maybe next year.

2014 August 14

ScratchJr

Filed under: Uncategorized — gasstationwithoutpumps @ 11:42
Tags: , , ,

If you’ve been wanting to teach your child to program, but found Scratch too complicated for your 5-year-old, there is a new option: ScratchJr.

On the  ScratchJr – About page, the developers say

What is ScratchJr?

ScratchJr is an introductory programming language that enables young children (ages 5-7) to create their own interactive stories and games. Children snap together graphical programming blocks to make characters move, jump, dance, and sing. Children can modify characters in the paint editor, add their own voices and sounds, even insert photos of themselves—then use the programming blocks to make their characters come to life.

ScratchJr was inspired by the popular Scratch programming language (http://scratch.mit.edu), used by millions of young people (ages 8 and up) around the world. In creating ScratchJr, we redesigned the interface and programming language to make them developmentally appropriate for younger children, carefully designing features to match young children’s cognitive, personal, social, and emotional development.

ScratchJr is now available as a free iPad app. We expect to release an Android version later in 2014 and a web-based version in 2015.

Unfortunately, I can’t give you a review of the program, as I don’t have an iPad to check it out on (nor do I have easy access to 5-year-olds, now that my son has grown up).  They did a great job on Scratch, though, so I would hope that ScratchJr has extended the concepts to a lower age group appropriately.

2014 August 13

Junk mail from UCSB organizations

Filed under: Uncategorized — gasstationwithoutpumps @ 15:04
Tags: , ,

I was expecting my son to get junk mail from UCSB, but I’m surprised at how much is addressed to the “Parents/Guardians of …”.  Today we got two pieces:

  • From the UCSB Alumni Association, suggesting we  buy him a lifetime membership in the Alumni Association (they’ll throw in a beach cruiser bike and a class T-shirt).  Now I’m aware that alumni associations are pretty aggressive about trying to get alumni to sign up, but I had not previously heard of them recruiting students who hadn’t even started yet.  I guess they are worried about losing the 20% of students who don’t graduate from UCSB even after 6 years.  If those students sign up for life membership in the alumni association while they are still students, they can be marketed to forever, even if they never become alumni in the traditional sense.

    Giving a bicycle as a premium for joining the Alumni Association is not a bad idea, but it is a single-speed beach cruiser, probably of the cheapest possible variety, without racks or lights.  If it had been a 3-speed with brakes on both wheels and a rear rack for panniers, it might have been worth joining the Alumni Association for the bike.

  • From the Residence Halls Association, suggesting that we buy him a “Welcome to UCSB Care Package” consisting of a sports bag, an aluminum sport bottle, a frisbee, a mini football, pens, and “tons of great snacks”—all with the RHA logo on them (except, perhaps, the snacks).  None of those items are ones my son is likely to need more of.  They also sell a couple of care packages for finals, including one with a stainless steel tumbler, a roll-up picnic blanket, sunglasses, coffee/tea packets, snacks, and a “travel stick and flag notebook”.  Their birthday package includes a water bottle, a teddy bear, and balloons “as well as many delicious snacks”.  This is apparently not the first year they’ve done this, so they must have gotten a lot of suckers customers in past years.

    Now, I think that sending care packages from home with favorite snacks is a great idea, and we may even do it a few times, but the selection of stuff in the RHA care packages seems not at all suited to our son, and sticking the RHA logo on everything is practically a guarantee that the resulting objects have no “coolness” factor at college.  Probably they put a water bottle in every care package because students go out of their way to lose the RHA bottles.

Next Page »

The Rubric Theme. Create a free website or blog at WordPress.com.

Follow

Get every new post delivered to your Inbox.

Join 267 other followers

%d bloggers like this: