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2019 July 17

3D slugs in gold

Filed under: Uncategorized — gasstationwithoutpumps @ 21:42
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In 3D slug printing, I described the design for a 3D slug pendant and said that I had ordered two different gold filaments: Hatchbox Gold, which is what the IEEE slug was printed with, and CC3D Silk Gold, which should be shinier.  I also ordered some hardware for attaching the slug to the purse (split rings and lobster hook).

The package from Amazon arrived today, and checked that the hardware worked with the ring—the size was just right for the lobster-claw hook, so I did not need to modify the design.

I tried printing the slug in both Hatchbox Gold and theCC3D Silk Gold.  Both printed fine, with only a little stringing on the eyestalks, which was easily trimmed off with flush-cut wire cutters.

Here are the 3 slugs I’ve printed, in Monoprice green PLA, Hatchbox gold PLA, and CC3D Silk Gold PLA (from left to right).

The Hatchbox gold is a very close match to the color of my wife’s Michael Kors purse, which is what she wanted it for

The Michael Kors purse was a shopgoodwill.com find—they sometimes have good stuff at reasonable prices, but the auction prices sometimes get high, if people realize what the value of the item is.

The CC3D Silk slug is much shinier and also works well with the purse, but is a less subtle accent.

You can tell I’m not a professional photographer or graphic designer, as I made no attempt to make the three photos in this post be color matched.  On my laptop, the middle photo (of the Hatchbx Gold slug on the purse) is the closest to the real colors.

I released the model as https://www.thingiverse.com/thing:3735186

2019 July 7

3D slug heart

Filed under: Uncategorized — gasstationwithoutpumps @ 18:34
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Earlier today I posted about adding a ring to scanlime‘s banana-slug design on Thingiverse by merging two STL files in Cura.  Today, I tried using the “include” command of OpenSCAD to get a properly merged STL file that I can post to Thingiverse.

The OpenSCAD code is quite simple:

module torus(big_radius=3, small_radius=1, big_fn=100, small_fn=30)
{   rotate_extrude($fn=big_fn)
    translate([big_radius,0,0])
    circle(r=small_radius, $fn=small_fn);
}

union()
{
    import("slug-fixup.stl",convexity=5);
    translate([-15,27,0])
        intersection()
        {   translate([0,0,1]) torus(big_radius=3.6, small_radius=2);
            translate([0,0,50]) cube(size=[100,100,100], center=true);
        }
}

I decided to go one step further and make a “slug heart” as suggested by my wife—it would be good for IEEE to sell at Valentine’s Day next year:

module torus(big_radius=3, small_radius=1, big_fn=100, small_fn=30)
{   rotate_extrude($fn=big_fn)
    translate([big_radius,0,0])
    circle(r=small_radius, $fn=small_fn);
}

module slug()
{    translate([-18,0,0]) rotate(a=[0,0,-12]) import("slug-fixup.stl",convexity=5);
}
union()
{
    slug();
    mirror([1,0,0]) slug();
    translate([0,25,0])
        intersection()
        {   translate([0,0,1]) torus(big_radius=3.6, small_radius=2);
            translate([0,0,50]) cube(size=[100,100,100], center=true);
        }
}
slug heart jewelry

View of the heart showing the ring for hanging it. This was printed at “draft” resolution (0.2mm/layer)—the jewelry will look better with 0.1mm/layer

slug heart jewelry

View of the heart showing the interior heart shape. I still only have green filament, but the slug will look much better in gold.

The slug-heart pendant weighs 13.46 grams in draft mode—I suspect it will be a similar weight for the final printing when I get the gold filament.

UPDATE 2019 July 7: I released the design as https://www.thingiverse.com/thing:3735198

3D slug printing

Filed under: Uncategorized — gasstationwithoutpumps @ 14:39
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I used my Monoprice Delta Mini 3D printer again yesterday, after a long break since the last usage.  My wife wanted a banana-slug charm to hang on her new mustard-yellow purse—she liked the color and size of the 3D-printed slug I had bought her from the UCSC IEEE chapter, but it did not have any easy way to attach it to the purse.

I found the design on Thingiverse by  scanlime, and checked the licensing (CC by 3.0), which only requires attribution, even for commercial uses.

I wanted to add a ring to the slug, so that it could be attached to a keyring.  Unfortunately, the design is only available as an STL file, and I’ve been using OpenSCAD, and I forgot that OpenSCAD has an import option for importing STL files, so I did a crude hack instead:  I made a ring in OpenSCAD, exported it as STL, then placed it in Cura overlapping the slug STL file.  When I sliced the models, the two files were merged producing a single gcode file, that printed as a single object. I think I want to see if I can also use the “include” command and get a properly merged STL file that I can post to Thingiverse.

I printed the model with 0.1mm resolution (finer than the resolution used for the IEEE printing, but I was not trying to produce slugs in sufficient quantity to sell them, so a slower printing to get a smoother surface was fine for me).

The gold slug is the one I bought from the IEEE student chapter, and the green one is the one I printed with the added ring.

The green color is obviously not suitable for banana slugs, but I’ve ordered some gold filament to print the slug properly.

One interesting side effect of slicing two overlapping models is that the exterior wall of each model was preserved, so that there were interior lines in the finished slicing corresponding to the original exterior walls.  This is an interesting, if somewhat awkward, way to get Cura to create specific interior structure, in addition to the generic interior fill patterns that it uses.

I have ordered two different gold filaments: Hatchbox Gold, which is what the IEEE slug was printed with, and CC3D Silk Gold, which should be shinier.  I’ve also ordered some hardware for attaching the slug to the purse (split rings and lobster hook).  I’ll have enough filament to do hundreds of slugs, since it only weighs 6.51g (not that I plan to make more than a handful—one in each color for my wife, and maybe another one for my backpack). The extra shiny gold filament can be used to make costume jewelry for WEST Performing Arts perhaps.  The filament costs a little over 1¢/gram, so the only real cost is the design and printing time.

Incidentally, the photographs were taken using another recent acquisition: a large Shibusa Photo Studio in a Bag, which I got from American Science and Surplus.  I think that the reason they were marked down is that the sides are so warped that they unsnap under the weight of the top.  I managed to make the thing work by using binder clips to insert some MDF pieces to stiffen the sides.  I think that I want to cut a couple of permanent MDF pieces that are exactly the right size and shape to support the top cleanly.  It would probably be best to use a laser cutter, but I’ll probably just use my scroll saw.

UPDATE 2019 July 7: I released the model as https://www.thingiverse.com/thing:3735186

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

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.

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