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2015 April 23

Very long couple of days

Yesterday and today have been draining.

Yesterday, I had three classes each 70 minutes long: banana slug genomics, applied electronics for bioengineers, and a guest lecture for another class on protein structure.  I also had my usual 2 hours of office hours, delayed by half an hour because of the guest lecture.

The banana-slug-genomics class is going well.  My co-instructor (Ed Green) has done most of the organizing and has either arranged guest lectures or taught classes himself. This week and part of next we are getting preliminary reports from the 5 student groups on how the assemblies are coming.  No one has done an assembly yet, but there has been a fair amount of data cleanup and prep work (adapter removal, error correction, and estimates of what kmer sizes will work best in the de Bruijn graphs for assembly).  The data is quite clean, and we have about 23-fold coverage currently, which is just a little low for making good contigs.   (See https://banana-slug.soe.ucsc.edu/data_overview for more info about the data.) Most of the data is from a couple of lanes of HiSeq sequencing (2×100 bp) from 2 libraries (insert sizes around 370 and 600) , but some is from an early MySeq run (2×300bp), used to confirm that the libraries were good before the HiSeq run.  In class, we decided to seek a NextSeq run (2×250bp), either with the same libraries or with a new one, so that we could get more data quickly (we can get the data by next week, rather than waiting 2 or 3 weeks for a HiSeq run to piggyback on).  With the new data, we’ll have more than enough shotgun data for making the contigs.  The mate-pair libraries for scaffolding are still not ready (they’ve been failing quality checks and need to be redone), or we would run one of them on the NextSeq run.  We’ll probably also do a transcriptome library (in part to check quality of scaffolding, and in part to annotate the genome), and possibly a small-RNA library (a UCSC special interest).

The applied electronics lecture had a lot to cover, because the material on hysteresis that was not covered on Monday needed to be done before today’s lab, plus I had to show students how to interpret the 74HC15N datasheet for the Schmitt trigger, as we run them at 3.3V, but specs are only given for 2V, 4.5V, and 6V.  I also had to explain how the relaxation oscillator works (see last year’s blog post for the circuit they are using for the capacitance touch sensor).

Before getting to all the stuff on hysteresis, I had to finish up the data analysis for Tuesday’s lab, showing them how to fit models to the measured magnitude of impedance of the loudspeakers using gnuplot.  The fitting is fairly tricky, as the resistor has to be fit in one part of the curve, the inductor in another, and the RLC parameters for the resonance peak in yet another.  Furthermore, the radius of convergence is pretty small for the RLC parameters, so we had to do a lot of guessing reasonable values and seeing if we got convergence.  (See my post of 2 years ago for models that worked for measurements I made then.)

After the overstuffed electronics lecture, I had to move to the next classroom over and give a guest lecture on protein structure.  For this lecture I did some stuff on the chalk board, but mostly worked with 3D Darling models. When I did the guest lecture last year, I prepared a bunch of PDB files of protein structures to show the class, but I didn’t have the time or energy for that this year, so decided to do it all with the physical models.  I told students that the Darling models (which are the best kits I’ve seen for studying protein structure) are available for check out at the library, and that I had instructions for building protein chains with the Darling models plus homework in Spring 2011 with suggestions of things to build.  The protein structure lecture went fairly well, but I’m not sure how much students learned from it (as opposed to just being entertained).  The real learning comes from building the models oneself, but I did not have the luxury of making assignments for the course—nor would I have had time to grade them.

Speaking of grading, right after my 2 hours of office hours (full, as usual, with students wanting waivers for requirements that they had somehow neglected to fulfill), I had a stack of prelab assignments to grade for the hysteresis lab.  The results were not very encouraging, so I rewrote a section of my book to try to clarify the points that gave the students the most difficulty, adding in some scaffolding that I had thought would be unnecessary.  I’ve got too many students who can’t read something (like the derivation of the oscillation frequency for a relaxation oscillator on Wikipedia) and apply the same reasoning to their slightly different relaxation oscillator.  All they could do was copy the equations (which did not quite apply).  I put the updated book on the web site at about 11:30 p.m., emailed the students about it, ordered some more inductors for the power-amp lab, made my lunch for today, and crashed.

This morning, I got up around 6:30 a.m. (as I’ve been doing all quarter, though I am emphatically not a morning person), to make a thermos of tea, and process my half-day’s backlog of email (I get 50–100 messages a day, many of them needing immediate attention). I cycled up to work in time to open the lab at 10 a.m., then was there supervising students until after 7:30 pm. I had sort of expected that this time, as I knew that this lab was a long one (see Hysteresis lab too long from last year, and that was when the hysteresis lab was a two-day lab, not just one day).  Still, it made for a very long day.

I probably should be grading redone assignments today (I have a pile that were turned in Monday), but I don’t have the mental energy needed for grading tonight.  Tomorrow will be busy again, as I have banana-slug genomics, a visiting collaborator from UW, the electronics lecture (which needs to be about electrodes, and I’m not an expert on electrochemistry), and the grad research symposium all afternoon. I’ll also be getting another stack of design reports (14 of them, about 5 pages each) for this week’s lab, to fill up my weekend with grading. Plus I need to update a couple more chapters of the book before students get to them.

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

2013 February 26

UCSC tiptoes around crowd funding for science

Filed under: Uncategorized — gasstationwithoutpumps @ 09:56
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UCSC is beginning to look seriously into crowd funding for small science and engineering projects (like student senior projects, which typically have budgets around $2k–3k and have very short timelines for finding donors).

I attended an information session (Fund your research through the crowd! – Jack Baskin School of Engineering – UC Santa Cruz) by Microrysa yesterday, which is a small startup specifically interested in crowdfunding science projects for universities.  They are doing some things right, but their choice of name (which Google wants to correct to mycorrhizae) indicates a certain naivete about search engine optimization, which is disturbing in a company that is about helping researchers get their research funded by outreach to the public.  It also means that people will have a hard time finding their site to make donations, even if they are looking for it.

One thing that Microrysa does right is working with the University so that the funding can go directly into a research account, rather than into a personal bank account where it would be taxable.  They also have taken the approach that what science donors want is to be kept up to date on the project, so the “rewards” of donation are progress reports (on the Microrysa website and by e-mail), rather than the T-shirts, coffee mugs, and other junk that SciFund seems to encourage.

I have a project that could use some micro funding.  To run the banana slug genomics course again, we’d need some more sequence data: preferably mate-pairs with a moderate insert size (like 1k bases).  Estimates for creating and sequencing such a library are around $5k.  With that data, plus what we already have, we should be able to assemble the banana slug genome into larger fragments than we currently can—maybe even big enough to do some gene-finding.

Crowdfunding has relatively low overhead (credit-card companies get 3%, the crowd-funding company gets 5%, and UCSC charges a gift tax of 6% to keep their development bureaucrats paid, even if they do none of the work of raising the funds), so researchers would get about 86–87% of the donated funds.  Given that Microrysa would be doing most of the work of setting up the web site and collecting the funds, I think that UCSC should forego the gift tax for crowdfunded projects, perhaps getting a contact list of donors instead.

2012 March 20

Petridish, another science crowd-funder

Filed under: Uncategorized — gasstationwithoutpumps @ 11:08
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Thanks to a post on the New Zealand blog misc.ience (Petridish – the new kid on the science crowdfunding block), I’ve found out about another crowd-funding service, in addition to SciFund, that I blogged about before. Petridish was created specifically for science funding, and I’m not yet sure what its advantages and disadvantages are compared to SciFund.

As with any funding source, the important questions include

  • How much money can be raised?
  • What is the probability of getting the funding?
  • How much effort is involved in trying to get that funding?
  • What strings are attached to the funding?

SciFund charges 4% and 4% for credit-card processing—I believe that they are also a for-profit company, since they don’t mention tax deduction anywhere.

Petridish is a for-profit company, and they take 5% of all donations (the research projects are also responsible for credit-card fees, which I believe run another 3–5% depending on the card used, and can be much higher for tiny transactions, due to fixed minimum fees). Petridish is looking into ways to make (part of) donations tax-deductible, but they are unlikely to be successful at that.

SciFund is a keep-it-all funder—the person requesting the funding gets everything that is raised (minus fees), whether or not they reach their funding goal.  This allows setting a higher goal, though there are some incentives in place for keeping the goals realistic. Many projects reach their funding deadline without coming close to their initial funding goals and some go well over—funding amounts seem to be in the range $10–$10000 ($300–$3000 if you remove a few outliers), almost independent of what the funder requested, with a median of about $1000.

PetriDish is a all-or-nothing funder: “Projects will only be funded if they reach their goal before the deadline set by the researcher.”  That means that researchers have to guess how successful the crowd-funding will be when setting their goals, despite having no access to information about how many people visit the site, nor what the success rate is for other projects. (That information may become available, once PetriDish has some history to share.)

Researchers who guess wrong are unlikely to get a second chance: “We hand select the most interesting and meaningful projects we find to be featured on our site and then allow you to get involved.”  So not only do researchers have to guess at the tastes of the general public, but they also have to guess at the tastes of an unknown review panel.  The panel may be easier to please than a typical funding agency panel, though, as PetriDish is not risking any money by accepting a proposal—just a little bit of credibility if the project is bad.

I think that the keep-it-all funding of SciFund makes more sense for science funding.   Crowd-funding will rarely pay for a complete project—it will almost always be a small add-on that will enable doing a little more, not making or breaking a project.  Forcing the scientists to gamble on how much to ask for seems silly in that context.

What strings are attached?  Projects must offer rewards to the individuals funding the project, just like SciFund:

Every reward is unique to its project. Some rewards offered on Petridish include:

  • Souvenirs from the field, like a rock from the highest peak in Madagascar or a vial of water from 400 feet below the surface.
  • Talks or dinners with famous researchers
  • Limited edition photographs or artistic renditions of the subject matter
  • Acknowledgements in journals
  • Naming rights for new discoveries, like new species
  • In person participation in a field project

In my earlier post about SciFund, I discussed the possibility of using it to get some funding for banana slug genomics—a project that has some potential for being achievable with only about $5000 or $10000 in funds (as long as no one is paid from the funds—even one quarter of grad student funding costs too much).  The expensive part of scientific research is nearly always the personnel, and I don’t see any way that crowd-funding will make the slightest dent in that cost.

I see SciFund and Petridish as more an opportunity for outreach and publicity for cool projects than as serious sources of funding for science. In that context, I’m seriously tempted to put together a funding request for banana slug genomics, which has a “coolness” factor that few of my other projects have.  What’s stopping me is mainly my fear of the University bureaucracy, who will prohibit me from attempting crowd-funding, soak up any money that comes in as “overhead”, or just make it so difficult to use the money that it would be less painful to fund things out of my retirement savings.

2011 November 3

SciFund crowd-sourcing science funding

Filed under: Uncategorized — gasstationwithoutpumps @ 02:25
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For those science projects that don’t need a lot of money, but you can’t get Federal funding agencies interested in (or for which the time and effort it would take to write a proposal and get it funded are out of proportion to the money needed), there is now an alternative: crowd-funding.

Here’s how it works at SciFund (part of RocketHub):

A “creative” proposes a project, describing it with text, pictures, and/or videos.  There are 3 required components: a funding goal, a deadline, and rewards for the “fuelers” who donate money.  The rewards can be anything legal, except investment opportunities, lotteries, revenue share, or equity.  They can be tangible (like t-shirts, copies of artistic works, … ) or experiences (like seminars, opportunities to participate in research, … ).

RocketHub collects a percentage of all donations (4% if you make your target goal, 8% if you don’t) and passes on shares of credit-card fees (for another 4%), thus keeping 8–12% of money collected, which is not a bad overhead (according to Charity Navigator, the median for charities is about 10%).

Ariolimax dolichophallus at UCSC

Ariolimax dolichophallus at UCSC. Image via Wikipedia

I’ve been wondering it it would be worthwhile to put together a funding request for reagents for finishing the banana slug sequencing.  I think that we need between $5000 and $10000 for that, which may be in the range of crowd funding.  I’d have to pin down the amount better and get commitments from volunteers to do the sequencing if the money comes through.  Rewards could be banana-slug genomics t-shirts or coffee mugs (though the donations would have to be big enough to pay for the extra cost of the rewards).   We could also offer a webinar about the banana slug and its sequencing for any level of donation.

Of course, one problem with this idea is that the most likely people to contribute to a crowd-funding campaign for sequencing Ariolimax dolichophallusare UCSC alumni who are proud of the unusual mascot, but the dean of the School of Engineering has told faculty not to contact alumni about the silly idea of sequencing the banana slug (or at least, I’ve heard rumors to that effect—I’m sure that the development office wants to keep a tight handle on the reins of any fund-raising).

We’d have to come up with a way to convince people that sequencing the banana slug is really cool, as the competition for “fuelers” is pretty stiff, and some of the projects on SciFund sound pretty cool.

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