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2011 January 28

Myro robot programming interface

Filed under: Robotics — gasstationwithoutpumps @ 17:00
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I was just pointed to the Myro robot programming interface, which seems to an API for the IPRE Robot,. They say

The entire robot kit (robot + Fluke add on board) is available for $199.98 at Georgia Robotics.

But that seems to be misleading: there are two pieces, the Parallax Scribbler Robot and the Fluke add-on board, and each piece seems to be $200. Either I misread the Georgia Robotics site or the IPRE website misreported the cost.

IPRE robot kit from Georgia Robotics

The  Myro Reference Manual has a number of functions defined in a Python module, allowing fairly high level control of the robot.  It looks like fun toy for a robotics class (maybe usable by the Robotics Club we’ve started at my son’s high school), but the API (Applications Programming Interface) seems to me to have somewhat too high a level of abstraction for a robotics club (Logo-turtle-like movement commands, for example, with no access to the motors or servos of the robot itself).  It is clearly an API that is useful for only this one robot, not a more general robotics language.

Given the goals of the IPRE project (“applies and evaluates robots as a context for computer science education”), their decision to create a simple low-cost robot and provide a high-level API is not a bad one.  They are not trying to teach robotics, but computer science, and so a higher level or abstraction where many of the interesting robotics problems have been abstracted away may well be appropriate.

I think that embedding an API in Python is an excellent idea though, as Python is powerful and easy-to-use, and so makes a good first or second programming language.  The lack of easy multi-threading (unlike Scratch), is a bit of a limitation, though.

Summer Programs: Listed by Topics of Interest

Filed under: Uncategorized — gasstationwithoutpumps @ 12:07
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The Davidson Institute has collected a nice list of summer programs suitable for gifted students: Summer Programs Listed by Topics of Interest.

Age and level varies from program to program and they include some that are aimed more at slightly above average kids than gifted kids (like the id Tech camps). I was going to say that they omitted the Johns Hopkins camps, but they simply mis-spelled them (as most people do, since “Johns” is such an unusual name and “John” such a common one).

2011 January 27

NAEP Science 2009 Report

Filed under: Uncategorized — gasstationwithoutpumps @ 08:21
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The National Assessment of Educational Progress has a detailed (and depressing) report on the state of science learning in our schools: Science 2009 Grades 4, 8 and 12 Report Viewer. (I found the pdf file for the report easier to read than waiting for each page on the viewer.)

California falls in the bottom 5 states for both 4th grade and  8th grade.

In 4th grade, the private and Catholic schools did better than the public schools at having students get to “proficient” (48–50% vs. 32%) but no better than public schools at getting to “advanced” (1%).  That suggests to me that differences are likely to be form selection bias, rather than from differences in pedagogy.  California has only 23% proficient and above, but the usual 1% advanced.  Only Arizona, Nevada, and Mississippi do worse.  I suspect that the 1% who are advanced have been taught science by parents rather than by schools, which explains why California (which has a lot of engineers) can maintain the 1% advanced kids while getting so few up to proficient.

The picture is similar at 8th grade, with private and Catholic schools getting 42–44% up to proficient, and public schools getting only 29%.  The private schools manage to get 3% up to advanced, while the public schools get only 1%.  Parental education level is the strongest predictor of the fraction above proficient (other than race), suggesting that it is indeed the parents doing the science teaching.  California has only 20% of 8th grade students performing at proficient or above. Only Hawaii, Louisiana, and Mississippi do worse—Alabama ties.

The 12th grade results are not split by state (a much smaller nationwide sample was used), but the national results are terrible, with only 21% at proficient or above and 1% at advanced.  Again race and parental education seem to be the strongest predictors of score, though how many science classes were taken in high school is about as good a predictor as parental education.

The report is profoundly depressing, as the levels defined for “advanced” are not really very advanced, but only 1% of our students are attaining them. We are bringing up a generation with essentially no competence in science.  This might explain in part why so many of the college seniors I see in my class seem to me to have less than a high-school education.

2011 January 25

DNA2.0 tools and student contests

Filed under: Uncategorized — gasstationwithoutpumps @ 16:56
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One of the many companies that does gene synthesis (synthesis of long strands of DNA for expression of proteins in bacterial or eukaryotic cell cultures), DNA 2.0, has a special page of resources for resources for educators and students.  The site includes their bioinformatics tools for design of synthetic genes (they have the best expression optimization I’ve seen published), the support they give for an iGEM synthetic biology team, and a somewhat vague offer of prizes for the best student project submissions.

Another of their pages,Gene Designer 2.0 in the Classroom, has some suggestions for how to use their tool for the design of synthetic genes in a classroom. Of course, their hope is that people will then want to order the synthetic genes from them, so distributing the tool for free is not such a strange idea even for a small company.

2011 January 22

Course redesign for protein informatics

Filed under: Uncategorized — gasstationwithoutpumps @ 16:25
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For several years I have taught a graduate protein informatics course every Spring (2005–2009, skipping last year), which has focused mainly on my research area: protein structure prediction.

I will be teaching it again this Spring, and I’m thinking of doing a major revision to the course.  I’ve asked advice from students, alumni, and colleagues on a choice of two different directions to take the course, and I thought I would ask my blog readers also. Note: I’m on sabbatical next year, so this course won’t be offered again until 2013, if ever.  I’m currently teaching an unsustainable teaching load, and some courses will have to be shed.  I’ve only made fairly minor changes to the other 4 courses I’m teaching this year (partly because 2 of them were ones I designed and taught for the first time last year), so I can afford some time to think about more major changes to this course.

I’ve been thinking of two different ways to do the course:

  • PREDICTION: group project on protein structure prediction, building a full-scale prediction web site that uses a mix of UCSC tools and tools from other groups. This would be replacement for the somewhat dated servers currently being run (which have not been modified since 2008 and really follow the 2006 protocols). Individuals would examine different alternatives for standard steps to the prediction, and the group would try to piece together the best choices. This is much more structured and group-oriented than previous offerings of the course. There are unlikely to be PhD-sized projects coming out of this version.
  • DESIGN: journal club and individual projects to come up with design methods for proteins. This will be even less structured than previous offerings, as we struggle to find doable projects in design. There are unlikely to be projects smaller than PhD size, so the challenge will be to find pieces of projects that are still interesting but doable in a quarter.


Prediction is a well-established field with many researchers, so there are a lot of papers to read and standard methods to teach. Testing methods have been well-developed and there is a wealth of data for both training and testing. Building a web service is a useful skill, even if protein structure prediction is not a field you wish to study. I’ve been working in protein structure prediction for about 15 years, and our group has been one of the top ones for most of that time. On the other hand, I’ve not gotten a grant funded in the field for a long time, and I’ve pretty much given up trying. There are only so many rejections I can take before giving up.  I have heard from alumni who graduated with MS degrees that setting up web services is indeed one of the standard tasks that they are expected to do.

Design is much more speculative than prediction, as we have essentially no way of telling if our designs are any good—there certainly isn’t time within a quarter to design a protein, express or synthesize it, purify it, and characterize it. There are few groups working in the field, so the field is not as crowded. Risk: one of the most famous groups has come under suspicion of fraud (or at least fooling themselves) in the past couple of years—reading the papers of that group and the challenges to those papers could be an interesting study in research ethics.

Some new ideas have come up in discussions with others about the redesign.  One that I had not thought of is adding a wet-lab component to the course.  I don’t do wet-lab research and have no wet-lab skills, so this would certainly require a co-instructor (who may be available, but I don’t know if there would be budget to pay him).  I had thought that our 10-week quarter was far too short to learn protein structure and design tools, do a design, express it, and test it in one quarter.  The advances in gene synthesis, though, make this much more feasible than it used to be, as one local company is promising 2-day turn-around for gene synthesis and delivery in an expression vector.  I don’t know that we’d be able to afford them (no prices on their web site!), but I’ve contacted them to check.  We would not get much past doing solubility checks (and maybe circular dichroism), but solubility is one of the big pitfalls of protein design, so even that would be valuable.

Added info:  the gene-synthesis company responded to my request for info last night (five-hour response to an e-mail request on a Saturday is pretty impressive).  They have $0.75/basepair (<15 business days) to $3/basepair (<5 business days), but for the protein sizes we’re interested in it would be a flat $1000 for a rush order. I suspect that the rush order would be too expensive for us, but we might be able to afford the standard order (which they claim averages 10 business days for the small genes we’d be interested in having synthesized).

I’ll be on sabbatical next year, trying to choose the direction for my research for the next 5–10 years.  The two main contenders are protein design and assembly of genomes from next-generation data.  If I revamp the protein informatics course to do design rather than prediction, then the two courses I’ll be teaching in the Spring would correspond to the two fields.  (The other course is Banana Slug Genomics, which I taught for the first time last year.)

So—I’m looking for advice from my readers: should I keep the course subject in protein structure prediction and move it towards development rather than research, or should I change the subject to protein design with much more open-ended and speculative sorts of homework and projects?  Teaching the course exactly the way I last taught it two years ago is also a theoretical possibility (and certainly would be the least work), but I don’t think I want to do that.

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