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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.)

Update 30 Oct 2014: UCSC has put out a press release about the project.

Update 31 Oct 2014: It looks like they’ve made a better URL for the crowd-funding project: http://crowdfund.ucsc.edu/sluggenome

2014 October 15

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.

2014 September 9

First-generation students

Filed under: Uncategorized — gasstationwithoutpumps @ 14:27
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There were a couple of blog posts by in The Academe Blog in August 2014 pointing to articles about first-generation college students: students whose parents did not graduate from college with 4-year degrees.  This is a particularly important topic for University of California campuses, as UC admissions puts a high premium on being a first-generation student, resulting in large numbers of first-generation students.  (In Fall 2013, 44% of the freshmen at UCSC were first-generation students.)

In the first post First Generation Students Part I: Difference-Education, Walter Breau quotes from an  interview published in the Stanford Report:

“Closing the Social-Class Achievement Gap,” offers a new approach to help [first-generation students] advance in college: discuss class differences rather than ignore them. The research showed that when incoming first-generation students saw and heard stories from junior and senior students with different social-class backgrounds tell stories about their struggles and successes in college, they gained a framework to understand how their backgrounds shaped their own experiences and how to see this as an asset,”

(How’s that for 4 levels of indirection: me quoting Breau quoting an interview with Hamidani about a paper by Hamidani, Stephens, and Westin.)

The abstract of the paper itself sums up the research fairly well:

College students who do not have parents with 4-year degrees (first-generation students) earn lower grades and encounter more obstacles to success than do students who have at least one parent with a 4-year degree (continuing-generation students). In the study reported here, we tested a novel intervention designed to reduce this social-class achievement gap with a randomized controlled trial (N = 168). Using senior college students’ real-life stories, we conducted a difference-education intervention with incoming students about how their diverse backgrounds can shape what they experience in college. Compared with a standard intervention that provided similar stories of college adjustment without highlighting students’ different backgrounds, the difference-education intervention eliminated the social-class achievement gap by increasing first-generation students’ tendency to seek out college resources (e.g., meeting with professors) and, in turn, improving their end-of-year grade point averages. The difference-education intervention also improved the college transition for all students on numerous psychosocial outcomes (e.g., mental health and engagement).

The do not identify the private university at which they did the study, and I believe that the details of the university make a huge difference.  The adjustments needed when first-generation students are an insignificant minority (as they are at most elite private colleges) and when they are 44% of the incoming class are likely quite different, and so the interventions needed may differ not just in scale but in kind.  Since all the authors are at private research universities (Stanford and Northwestern), they likely did their study at either Stanford or Northwestern, neither of which has many first-generation students, and both of which have large numbers of rather wealthy students.  I question somewhat how well the results of studies on such campuses generalizes to the public universities which may soon be majority first-generation students (or already are in some cases), and where social class is not so skewed toward the wealthy.

In First Generation Students Part II: Cultural Fit, Walter Breau points to an article about cultural fit:

“Unseen Disadvantage: How American Universities’ Focus on Independence Undermines the Academic Performance of First-Generation College Students,” published in 2012 in the Journal of Personality and Social Psychology, concluded:

“That the seemingly positive middle-and upper-class cultural norms that pervade traditional American universities—norms that emphasize independent values such as ‘do your own thing,’ ‘pave your own path,’ and ‘express yourself’—can undermine the academic performance of first-generation students.”

The distinction that the article makes between “middle-class” and “working-class” values is independence vs. interdependence.  They found that college administrators at top-ranked colleges valued independent decision making much more than they valued interdependence, but that there were not significant differences between responses to questions about about independent vs. collaborative work.  Lower ranked colleges had less of a skew toward valuing independent decision making, but were otherwise fairly similar.

The study looked at a modest sample of student surveys and grades (245 first-generation, 1179 continuing-generation) to see whether independent/interdependent motive predicted cumulative GPA at the end of 2 years.  The effect sizes they saw were tiny—only coming out larger than race because they lumped all non-white race categories together, which makes some sense for looking at independent/interdependent, but not for looking at GPA, since Asian student typically perform quite differently from black and Latino students.  SAT scores alone were a much better predictor of grades than any of the sociological variables they looked at, and the only really good predictor of 2-year GPA was the 1-year GPA. So, while their results were statistically significant, it is not clear that they were really large enough to justify any conclusions about whether the “American Universities’ Focus on Independence Undermines the Academic Performance of First-Generation College Students”.  I certainly would not want to base policy decisions on such small effects.

Their study was done at schools with only about 17% first-generation students (based on the participant numbers in their study), which may be typical of US colleges as a whole, but is nothing like the UC system.  Even UCB, with the lowest ratio of first-generation students of any UC campus, had 23% first-generation students in 2010 (the latest for which I could find UC-wide data), and some campus were majority first-generation even in 2010 (Merced and Riverside).

Although it is important for UC to figure out how to help first-generation college students succeed, it is not clear to me that either of the studies that Breau reported on have much relevance for UC.

 

2012 May 7

Kids on Campus

Filed under: Robotics — gasstationwithoutpumps @ 12:25
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Our local community college each year has a number of programs for kids (some for kids as young as 10 years old:  Kids on Campus – Cabrillo College Extension.

My son has outgrown these courses, and his 4 weeks of theater summer camp will make it difficult for him to register for any of the regular Cabrillo college courses.  He did take one of them several years ago: a Lego Robotics course using Logo and the old Lego Dacta serial interface board.  The same course appears to be offered this summer, with the same teacher.  Neither he nor I can remember now whether he had one week or two of using the serial interface—he does not even remember programming in Logo for controlling Lego motors.  I thought at the time that it was a pretty good course, and a nice variant on the mainly visual programming languages then available for Lego robotics.  (He has used a couple of those languages and NQC for programming Lego robots, though now he does most of his robotics programming in C++ on the Arduino, with Python and PySerial to communicate from a laptop.)

So far as I know, UCSC has not attempted to do much with education for children, other than the Seymour Center at the Long Marine Lab and the COSMOS program for high schoolers (which I discussed in a blog post about improving the science fair participation by high schoolers).  There are a lot of summer camps for kids on the UCSC campus, but most of these are from 3rd-party providers (like most campuses, they try to get money out of the dorms on a year-round basis).

2012 March 10

Mechatronics demo at UCSC

Filed under: Robotics — gasstationwithoutpumps @ 21:15
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I just got the announcement for one of the fun events for this time of year:

Come see tired and haggard engineering students who have not slept or showered in weeks! (Oh yeah, and their robots.)

What: CMPE118 Mechatronics Public Presentation
Where: Baskin Engineering 101 (Auditorium), UCSC
When: Wednesday, 14-Mar-2012, 7:00 PM – 9:00 PM

The Mechatronics class is having their public demonstration of their final design lab, Slugs of the Caribbean 2012, Wednesday 14-Mar-2012 at 7:00 PM in Baskin Engineering 101.

The task requires the ‘droids to navigate a field to get to the enemy’s island and return to their own, while shooting at the enemy with ping pong balls. The ‘droids will run against each other on the field. We will run the competition in a round robin format to see which robot reigns supreme.

The public is invited (you might have to duck a few ping-pong balls) and the teams will be on hand to explain their designs to one and all. Come see what these students have accomplished in 10 weeks and cheer on the competition.

The flyer
The project specs

Feel free to forward this to any and all that might be interested, children (future engineers) especially welcome.

I got to the mechatronics demo almost every year.  My son won’t be able to go this year, since it conflicts with his theater class, but I encourage others whose schedules permit to come.

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