Gas station without pumps

2014 October 22

Banana Slug genome crowd funding

Filed under: Uncategorized — gasstationwithoutpumps @ 21:20
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T-shirt design from the first offering of the class.

T-shirt design from the first offering of the class. (click for high-res image)

A few years ago, I taught a Banana Slug Genomics course, based on some sequencing done for free as a training exercise for new technician.  I’ve mentioned the course occasionally on this blog:

The initial, donated sequencing runs did not produce enough date or high enough quality data to assemble the genome to an annotatable state, though we did get a lot of snippets and a reasonable estimate of the genome size (about 2.3GB total and about 1.2GB unique, so a lot of repeats).  All the class notes are in a wiki at https://banana-slug.soe.ucsc.edu/) and the genome size estimates are at https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish.

I did manage to assemble the mitochondrion after the class ended (notes at https://banana-slug.soe.ucsc.edu/computer_resources:assemblies:mitochondrion), but I now think I made a serious error in doing the assembly, treating variants due to a heterogeneous mitochondrial population as repeats instead.  The mitochondrion was relatively easy, because it is much shorter than the nuclear genome (probably in the range 23kB to 36kB, depending on whether the repeats are real) and has many more copies in the DNA library, so coverage was high enough to assemble it—the hard part was just selecting the relevant reads out of the sea of nuclear reads.

Ariolimax dolichophallus at UCSC

Ariolimax dolichophallus at UCSC, from larger image at http://commons.wikipedia.org/wiki/File:Banana_slug_at_UCSC.jpg

The banana slug genomics class has not been taught since Spring 2011, because there was no new data, and we’d milked the small amount of sequence data we had for all that we could get for it.  I’ve played with the idea of trying to get more sequence data, but Ariolimax dolichophallus is not the sort of organism that funding agencies love: it isn’t a pathogen, it isn’t a crop, it isn’t an agricultural pest, and it isn’t a popular model organism for studying basic biology. Although it has some cool biology (only capable of moving forward, genital opening on the side of its head, penis as long as its body, sex for up to 24 hours, sometimes will gnaw off penis to separate after sex, …), funding agencies just don’t see why anyone should care about the UCSC mascot.

Obviously, if anyone is ever going to determine the genome of this terrestrial mollusk, it will UCSC, and the sequencing will be done because it is a cool thing to do, not for monetary gain.  Of course, there is a lot of teaching value in having new data on an organism that is not closely related to any of the already sequenced organisms—the students will have to do almost everything from scratch, for real, as there is no back-of-the-book to look up answers in.

At one point I considered asking alumni for donations to fund more sequence data, but our dean at the time didn’t like the idea (or perhaps the course) and squelched the plan, not allowing us to send any requests to alumni. When the University started getting interested in crowd funding, I started tentative feelers with development about getting the project going, but the development people I talked with all left the University, so the project fizzled.  I had a full teaching load, so did not push for adding starting a crowd-funding campaign and teaching a course based on it to my workload.

This fall, seemingly out of nowhere (but perhaps prompted by the DNA Day celebrations last spring or by the upcoming 50-year anniversary of UCSC), I was asked what it would take to actually get a complete draft genome of the slug—someone else was interested in pushing it forward!  I talked with other faculty, and we decided that we could make some progress for about $5k–10k, and that for $20k in sequencing we could probably create a draft genome with most of the genes annotated.  This is a lot cheaper than 5 years ago, when we did the first banana slug sequencing.

Although the top tentacles of the banana slug are called eyestalks and are light sensing, they do not have vertebrate-style eyes as shown in this cartoon.  Nor do they stick out quite that much.

Although the top tentacles of the banana slug are called eyestalks and are light sensing, they do not have vertebrate-style eyes as shown in this cartoon. Nor do they stick out quite that much.

And now there is a crowd funding campaign at http://proj.at/1rqVNj8 to raise $20k to do the project right!  They even put together this silly video to advertise the project:

Nader Pourmand will supervise students building the DNA library for sequencing during the winter, and Ed Green and I will teach the grad students in the spring how to assemble and annotate the genome.  Ed has much more experience at that than me, having worked with Neanderthal, Denisovan, polar bear, allligator, and other eukaryotic genomes, while I’ve only worked on tiny prokaryotic ones. (He’s also more famous and more photogenic, which is why he is in the advertising video.) We’re both taking on this class as overload this year (it will make my 6th course, in addition to my over-300-student advising load and administrative jobs), because we really like the project. Assuming that we get good data and can assemble the slug genome into big enough pieces to find genes, we’ll put up a genome browser for the slug.

I’m hoping that this time the class can do a better job of the Wiki, so that it is easier to find things on it and there is more background information.  I’d like to make the site be a comprehensive overview of banana-slug facts and research, as well as detailed lab notebook of the process we follow for constructing the genome.

Everyone, watch the video, visit the crowd funding site, read the info there (and as much of the Wiki as you can stomach), and tell your friends about the banana-slug-sequencing effort.  (Oh, and if you feel like donating, we’ll put the money to very good use.)

 

2014 October 19

Summer project 2

Filed under: Uncategorized — gasstationwithoutpumps @ 20:50
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In Summer Project, I introduced the project I’ve been working on all summer: a “kit” for making dimmable LED lamps, consisting of

  • a dimmer board that reads a potentiometer and converts it (non-linearly) to a pulse-width-modulated 9V output signal and
  • LED boards that hook up to the two wires of the PWM input signal, and that can be run in parallel,

and I showed the custom desk lamp I made for my son.  That was a fairly quick build, because it needed to be functional, but did not need to be very pretty—my son likes the exposed-wire look.  I asked him today how the lamp has been working out for the past week—he almost always uses it near the lowest setting, since he is either just filling in some shadows in an already lit room, or he is working at his desk while his roommate is sleeping.  In both cases he doesn’t need or want much light.  I suggested unmounting some of the LED boards, to get more control at the low light levels he needs.  Based on the measurements and calculations from the data sheets I did in LED board I-vs-V curve, he should be getting a range of  10–375 lumens from his desk lamp.  With only 3 LED boards, he would have a range of 6–225 lumens. But he likes having 5 shadows, so he turned down the suggestion. I considered changing the firmware for his lamp, to provide lower levels (has has all the equipment and software needed to reprogram it), but it is hard to get a duty cycle lower than 0.2% from the PWM controller.  If he really wants to go to low light levels, he could replace the 9V power supply with a 5V one, but then he’d have a range of 0.008–0.3 lumens, when what he probably wants is 1–40 lumens, which would need a 5.5V supply (not a standard size).  I think that he’ll sometimes need the 200–375 lumen range for task lighting when he is working with something fiddly late at night, so he is probably best off keeping with a full-power lamp.

The other project I mentioned was making a prototype table lamp for my sister, which needs to look a bit nicer, since she is considering making a series of table lamps using stiffened-silk shade.  I’ve now finished a prototype to send her, pictured below:

Here is the lamp, turned off.  The base is a wooden bowl from the thrift store, sanded so that it sits flat.  The upright is a standard brass lamp pipe, and the shade is just folded out of a 0.5m square of paper (the most common fold for making a paper cup).

Here is the lamp, turned off. The base is a wooden bowl from the thrift store, sanded so that it sits flat. The upright is a standard brass lamp pipe, and the shade is just folded out of a 0.5m square of paper (the most common fold for making a paper cup).

When turned on, the lamp produces a modest downward light and illuminates the shade.

When turned on, the lamp produces a modest downward light and illuminates the shade.

The lamp is done except for a knob for the potentiometer for controlling the dimmer. The only knobs I have are too large and industrial looking—I’ve ordered some smaller metal ones via Amazon, but they are being shipped from China, so I’ll probably have to mail my sister the lamp before the knobs get here. It turns out that if you want decorative, rather than ugly plastic, potentiometer knobs, the best source is companies that provide guitar parts.  The knobs for controls on electric guitars come in a wide variety of styles, some of them quite elegant.  (But guitar parts are also a fairly expensive way to get knobs, so make sure that you really like them!)

When I first assembled the lamp, there was a rather nasty flaw in the design, resulting in unintended shadows on the shade:

At first there was an extra shadow in the middle of the shade that I did not like.

At first there was an extra shadow in the middle of the shade that I did not like.

With the shade off, it is easy to see where the extra shadow come from—it is the knurled nut connecting the up-facing LED board to the power wires.

With the shade off, it is easy to see where the extra shadow come from—it is the knurled nut connecting the up-facing LED board to the power wires.

The fix was easy—I just put the screw in from the top of the board, so that there was no large assembly to cast shadows:

Here is a closeup of the top part of the lamp, showing the top LED board facing up with the knurled nut on the back of the board. The two end LED boards face down, again having the knurled nut on the back, along with the heat sink.  I had originally planned to support the shade with the same 10-gauge copper wires that power the boards, but I realized that the cooper would corrode in a humid atmosphere, which might stain the shade, so I made a support out of 1/8" 316L stainless steel welding rod, using a little hot-melt glue to attach pony beads to the ends, so that the rods wouldn't poke holes in the shade.

Here is a closeup of the top part of the lamp, showing the top LED board facing up with the knurled nut on the back of the board. The two end LED boards face down, again having the knurled nut on the back, along with the heat sink.
I had originally planned to support the shade with the same 10-gauge copper wires that power the boards, but I realized that the cooper would corrode in a humid atmosphere, which might stain the shade, so I made a support out of 1/8″ 316L stainless steel welding rod, using a little hot-melt glue to attach pony beads to the ends, so that the rods wouldn’t poke holes in the shade.

The shadows cast by the LEDs with the corrected orientation of the screws is much cleaner than before.

The shadows cast by the LEDs with the corrected orientation of the screws is much cleaner than before.

I still have to write artist-level instructions on how to put together the electronics for a lamp. That will probably require a few more closeups of the lamp (with better lighting), which I’ll take during the week, before shipping the prototype to my sister.

2014 October 18

Tread Lightly with Terra Nova!

Filed under: Uncategorized — gasstationwithoutpumps @ 22:13
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A friend of mine, Ken Foster, has just started an Indiegogo fund-raising campaign, Tread Lightly with Terra Nova!, to raise money to restart the bicycle landscaping service that he ran for over 20 years:

Terra Nova’s Tread Lightly Service

Bicycle Powered Landscaping

In 1991 I started a service I dubbed Tread Lightly. This was a bicycle-powered landscape service that served our Santa Cruz area clients. For over twenty years the community hailed the ‘Tread Lightly’ service as an authentic, profoundly ecological approach to landscape care and as a symbol of innovation and hope. One of the principles of permaculture is “Use Small and Slow Solutions.” Tread Lightly was definitely that! Pedal-Powered Permaculture!

I used the Tread Lightly service for a couple of years, then decided that I did not care enough about the lawn to hire a landscape service—not even a bicycle landscape service from a friend. The service was good when I used it, and I was wondering why I never saw his bike trailers around town any more (I still see Ken riding his recumbent around town). It turned out that the trailers, bikes, and equipment eventually wore out, and the bike service was barely making enough to pay the employees. When the recession hit, it hit the local lawn services pretty hard, and Ken had to downsize his business (still doing landscaping, but with a much smaller team and no bikes).

Now that the local economy has improved, he’d like to bring back the signature bike trailers and hand equipment, but he needs to raise some capital to do it.  Borrowing from banks (a traditional business solution) is not likely to work, as the business plan does not result in a high probability of a large profit to pay off the loans. So he is looking for crowd-funding to help him restart the bike landscaping business, train youngsters in sustainable urban landscaping, and bring back a distinctive Santa Cruz institution.

In the years since I used the Tread Lightly service, I’ve bought an electric mower to mow the front yard about every 2 months, and let the back yard get covered with weeds (thistles, grass, blackberry brambles, ivy, kiwi vines, … ).  It is now difficult even to get to the compost heap, and some of the windows on the house are not openable because of the blackberries covering them.  I’ve been thinking of hiring Ken to clear the back yard for me, though I’ve no intention of actually maintaining the yard—too much work for too little reward.  If I were ever to sell the house, it would probably need over $1000 in landscaping maintenance to look attractive to a buyer, but I’m likely to be living here for the next 25 years, so any investment I make needs to pay off in personal pleasure (or reduced maintenance effort) well before then.

I enjoyed doing some gardening as a child, and thought I would enjoy it as an adult when I bought the house, but it turns out that I never have the time or energy to do any gardening. There is always something more interesting or more urgent to do. Even the tall raised beds that I built and that I had Ken build have gotten covered with weeds. It would be nice to have an herb and vegetable garden in them again, but I know I’ll never get around to planting and weeding, much less the incessant watering that is needed to have anything less hardy than thistles survive around here.  (I put in a drip irrigation system once, but such systems need annual maintenance, which I never got around to doing, so it disintegrated years ago.)

 

2014 October 15

LED board I-vs-V curve

Filed under: Data acquisition — gasstationwithoutpumps @ 21:27
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I earlier did simple go/no-go testing for a bunch of the LED boards that I designed for lighting fixtures (see Summer project), but I thought it would be interesting to characterize at least one of the boards more thoroughly. So last night I wired up a little circuit to control the current through board to plot an I-vs-V curve:

The transistor is a 1W transistor with a DC current gain of about  120, so this circuit can sink up to about 300mA with Vss=9v.

The transistor is a 1W transistor with a DC current gain of about 120, so this circuit can sink up to about 300mA with Vss=9v (as long as the voltage drop across the LED board keeps the collector voltage down low enough).

I measured the voltage across the board and the current through it with multimeters (using the better multimeter for the current measurement). I was expecting a constant current when the voltage was high enough, then a linear decrease in current as the voltage was lowered down to a cutoff threshold. That is pretty much what I got:

The constant current was set at about 118mA (I had intended 130mA), and the linear region corresponded to 10.6Ω.

The constant current was set at about 118mA (I had intended 130mA), and the linear region corresponded to 10.6Ω. (Click to embiggen)

The constant-current region was not as crisply defined as I had expected, and the current was lower than I had intended.  The 10.6Ω impedance in the linear region initially came as a bit of surprise, but when I added together the resistance of my current sense resistor and the dynamic resistance of the LED in the relevant region it seems about right.

The measurements were hard to make, because the current did not remain constant, but tended to drop as I was measuring, particularly in the high-current regime. I believe that this droop is due to thermal effects—the current drops as the board warms up, and I did not wait for the board to reach equilibrium temperature.  The lower-than-expected  constant current is probably also due to thermal effects, since it was based on scaling up tests done at low currents, where there would have been no significant heating.

To test this hypothesis, I set up a different experiment this morning, connecting the board in series with  a 20Ω resistor and connecting both to a 12V power supply, monitoring the voltage across the resistor (and hence the current through the board) using PteroDAQ on the FRDM KL25Z board.

The initial current was close to the 130mA I had expected, based on scaling up of experiments I had done with a similar circuit that had provided 13mA.  But as teh board warmed up, the current dropped substantially, down to around 116mA.

The initial current was close to the 130mA I had expected, based on scaling up of experiments I had done with a similar circuit that had provided 13mA. But as the board warmed up, the current dropped substantially, down to around 116mA.

So my “constant-current” circuit isn’t really constant current—it is very temperature dependent. The change in brightness is about the same as I would get from a 13° change in the position of the control potentiometer for my dimmer. I can live with that in the design, but it is a much bigger temperature dependence than I had expected.

According to my infrared thermometer, the heatsink got up to about 60°C at the end of the run, with 9.75V across the board and 0.116A through it, for a power dissipation of about 1.13W. If the room was at about 20°C, that means a temperature gain of about 35.4°C/W.

The LEDs get derated to about 93% of their room-temperature efficiency at 60°C, so when combined with the current drop to 116mA, I expect about 75 lumens for each board when it is fully on. Maximum efficiency would be at the knee of the I-vs-V plot, where the voltage is about 6.67V, getting 75 lumens for 0.77W, or 97 lumen/W.  (The temperature may not get as high at that voltage, since the power dissipation is less—the terminal temperature would probably be only about 48°C, which means the current would drop less and efficiency would be slightly higher.)  At my design voltage of 9V, the efficiency is only about 72 lumens/W.  The LED boards seem to be able to run at 12V, where the power dissipation would be 1.4W/board and the efficiency only 54 lumens/W.

One surprise for me in the testing was how low a current would still produce light. I observed dim light down to about 4µA, giving the LED boards a dynamic range of about 32000 in brightness (4.5 decades), while my PWM circuit only has a dynamic range of about 43 (1.6 decades).  The range on the dimmer is adequate, since even a night light produces about 15 lumens, and my dimmer goes down to about 2 lumens. But it is clear that one could design for a much wider dynamic range.

Redoing the I-vs-V plot to have a logarithmic scale for the current, we can see the whole dynamic range.

Like many semiconductor devices and circuits, the boards have an exponential characteristic for subthreshold conduction.

Like many semiconductor devices and circuits, the boards have an exponential characteristic for subthreshold conduction.

The LED boards could be operated at as low as 5V, but the brightness is very low at that voltage (about 0.15 lumens)—not suitable for a room light or even a night light. A 7.4V Li-ion battery pack would be a good match to the LED boards.  A $14, 2200mAh battery should be able to power the LED board at full brightness for about 10 hours, and at reduced brightness for another 8–10 hours. I’m not currently planning any battery-operated lights, but it is nice to know that they are doable.

Top 50 Colleges for Hispanic Students

UCSC recently got some good news, being top-ranked in BestColleges.com’s list of the Top 50 Colleges for Hispanic Students:

In 2012, 49% of Hispanic high school graduates enrolled at a postsecondary, public institution. This percentage surpassed that of white students for the first time, and Hispanic enrollment in colleges and universities, which has increased 240% since 1996, is expected to continue to grow. Many Hispanic students are the first in their families to attend college, so it is important for them to find a support system that will help them navigate degrees, financial aid, and their school and social obligations.

To make the transition from high school to college, many students may be looking for “Hispanic-friendly” schools. These are schools with a high concentration of Hispanic students already in attendance, or they have a cultural center that focuses on Latino/a, Chicano/a or Hispanic heritages.

Students may also look for a school that will protect their rights and ensure they receive the same quality education as non-Hispanic students. The Hispanic Association of Colleges and Universities (HACU) is an organization that strives to protect the educational rights of Hispanic students. It was instrumental in increasing funding from Title V of the Higher Education Act for Hispanic-Serving Institutions (HSIs). For the 2014 academic year, HACU convinced Congress to give $98 million to HSI undergraduate programs.

To create our rankings, we relied upon our normal methodology to find schools that rank well for academics. Our team then compared that list to the 242 HACU member schools in the U.S. to find the best schools for Hispanic, Latino/a and Chicano/a students. We included the percentage of Hispanic students currently enrolled at each college, along with in- and out-of-state tuitions to add more weight to our rankings. Each school on our list boasts a cultural center, degree programs, or scholarships dedicated to enhancing the experiences of Hispanic students.

The Schools

  1. University of California-Santa Cruz – Santa Cruz, CA
    Hispanic Students as Percent of Total Enrollees: 26%
    Graduation Rate: 91%
    Retention Rate: 74%
    Admissions Rate: 60%
    Tuition and Fees: $13,398 (in-state) and $36,276 (out-of-state)This public research university, located alongside the redwood forests and just under 10 miles from the coast [actually under 2½ miles from the campus entrance to the beach], offers 60 majors in 30 fields. Because of the network of UC campuses, students have a wealth of opportunities that extend beyond UC Santa Cruz. For Hispanic students, the Chicano Latino Resource Center, more commonly known as El Centro, offers a number of programs and resources to support and bolster the on-campus Hispanic community, including academic support, scholarships and financial guidance and social events geared towards unification and integration.
  2. San Diego State University – San Diego, CA
  3. University of California-Riverside – Riverside, CA
  4. Whittier College – Whittier, CA
  5. St. Edward’s University – Austin, TX
  6. California State Polytechnic University-Pomona – Pomona, CA
  7. University of La Verne – La Verne, CA
  8. University of Houston – Houston, TX
  9. Florida International University – Miami, FL
  10. California State University-Long Beach – Long Beach, CA
  11. University of California-Merced – Merced, CA
  12. University of St. Thomas – Houston, TX
  13. Woodbury University – Burbank, CA
  14. California State University-Fullerton – Fullerton, CA
  15. St. Mary’s University – San Antonio, TX
  16. University of New Mexico-Main Campus – Albuquerque, NM
  17. Texas State University – San Marcos, TX
  18. Fresno Pacific University – Fresno, CA
  19. California State University-Channel Islands – Camarillo, CA
  20. California State University-San Marcos – San Marcos, CA
  21. Cuny City College – New York, NY
  22. Mount St. Mary’s College – Los Angeles, CA
  23. California State University-Fresno – Fresno, CA
  24. Texas Lutheran University – Seguin, TX
  25. California State University-Stanislaus – Turlock, CA
  26. La Sierra University – Riverside, CA
  27. California State University-Monterey Bay – Seaside, CA
  28. New Mexico State University – Las Cruces, NM
  29. College of Mount Saint Vincent – Riverdale, NY
  30. California State University-Northridge – Northridge, CA
  31. California State University-San Bernardino – San Bernardino, CA
  32. Schreiner University – Kerrville, TX
  33. Cuny Lehman College – Bronx, NY
  34. Saint Peter’s University – Jersey City, NJ
  35. University of Texas-Pan American – Edinburg, TX
  36. University Of Texas-San Antonio – San Antonio, TX
  37. Texas A&M University-Corpus Christi – Corpus Christi, TX
  38. California State University-Bakersfield – Bakersfield, CA
  39. California State University-Los Angeles – Los Angeles, CA
  40. University of Texas at El Paso – El Paso, TX
  41. Texas A&M International University – Laredo, TX
  42. Eastern New Mexico University – Portales, NM
  43. St. Thomas University – Miami Gardens, FL
  44. Angelo State University – San Angelo, TX
  45. California State University-Dominguez Hills – Carson, CA
  46. Adams State University – Alamosa, CO
  47. Texas A&M University-Kingsville – Kingsville, TX
  48. The University of Texas Health Science Center at San Antonio – San Antonio, TX
  49. Boricua College – New York, NY
  50. Our Lady of the Lake University – San Antonio, TX

I’ve not included the information for the colleges other than UCSC—you’ll have to click through to the original web page to get that information. I note that 23 of the 50 colleges are in California, and 17 of them are public universities. The next biggest group is 16 colleges from Texas. The “name” universities (UCB, UCLA, Stanford,…) don’t appear on the list, because too few of their students are Hispanic—they serve mainly white and Asian students.  UCSC has been aggressively recruiting Hispanic students and has only recently gotten over the 25% enrollment threshold to become an official Hispanic-serving institution (officially given HSI status in 2013), but the figures here are a little old, as we were up to 30% Hispanic by Fall 2013, and are probably above 31% now (Fall 2014 figures aren’t available yet).

Correction 2014 Oct 15: UCSC is not officially an HCI by the US government definition—according to http://officeofresearch.ucsc.edu/broader-impacts/resources/diversity/index.html:

  • The Hispanic Association of Colleges and Universities (HACU) designated UCSC as a HSI member in 2013 because UCSC has >25% Latino undergraduate enrollment). [Of UC campuses] Only UC Merced, UC Riverside, and UC Santa Cruz are members of HACU, as listed on the HACU website.  
  • UCSC is planning to submit a Title V Part A (Developing HSI) grant application in 2015. This is one of EVC Galloway’s “Five by 2015” priorities. We are now conducting an in-depth self-study in preparation for the application—the steering committee in charge of this self-study includes top administrators and senior faculty at UCSC as this is very much a UCSC priority. Once we receive a Title V Part A grant, we will be officially an HSI according to the Dept of Education.
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