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experiments for reassurance

As the last few experiments didn’t really work out, it’s time to replicate some of the originals, and re-think the ones did recently. Starting from square 1:

  • re-grow the bacteria on top of a plate, taken from the cryogenic storage
  • create overnight liquid cultures from single colonies of the regrown bacteria
  • create agar plates with the liquid culture in them
  • perform arabinose experiments with it

Moreover, the UV-light bacteria killing experiment had to be re-done, as most probably the plastic cover of the petri dish itself filters out the harmful UV lights ) So I just did that, and have some plates exposed to UV lights without the petri dish cover, and now waiting in liquid LB to see if they grow out.

In more detail:

day 1: re-grow bacteria

Re-grow the bacteria on top of a plate, taken from the cryogenic storage. I did this on two plates today, one with just ampicillin in it, and the other also with arabinose, to see if it turns fluorescent at all. Easy reassurances create a flow experience )

day 2: create liquid cultures

Take single colonies from the plates that grew overnight, and create liquid cultures from them. Also verify that the plate with the arabinose in it turned fluorescent.

day 3: create agar plates & perform arabinose experiments

Take the liquid culture that grew out and crate agar plates with the bacteria in them. As the plates are a few (at least 3) hours old, drop 5μl droplets of arabinose on them, and leave overnight to develop. Do the experiment in the following three settings:

  • always have the plate in a 37°C incubator
  • always leave the plate at room temperature
  • always put the plate in the fridge

Moreover, have two kinds of plates for each experiment:

  • regular LB-agar plates with bacteria in them
  • ‘top agar’ plates

day 4: verify fluorescent pixels

Take the plates that had the arabinose dropped on them, and verify if any of the drops turned fluorescent, or the whole plate turned fluorescent.

just a tiny little drop, Sir?

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Good news - it seems that the fab@home fabber can indeed create tiny little drops. One has to push the syringe tool about 0.1 - 0.2 units in, and then a little back so that the next drop doesn’t start to form immediately. The drops seem sufficiently small to be used for the installation, so it seems no special pumps are necessary.

The bad news is that the control software doesn’t want to take my simple hand-made STL files to create a lot of these small droplets. But everything in due time…

it can’t always work out

It seems that the experiments performed last week by Vincent van Rixel and Joeri Verasdonck didn’t really work out as expected.

Having exposed bacteria inside LB agar to 254nm UV light for 1, 10 and 100 minute durations - they still live. Whereas they should have died instead.

The other experiment revolved around plates with bacteria inside LB agar, left to grow at room temperature, first at room temperature and then put into the fridge 3 days later, or put in the fridge immediately. After 3 days, I dropped 5μl drops of arabinose on them so as to turn on the GFP-producing gene - but nothing happened.

So now I prepared some new plates, and also had one of the plates under 254nm UV light for an overnight time period. Let’s see if they work out…

edible fabbint at the Happy Chaos

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On Saturday, I demonstrated the fab@home 3D fabber to the participants of the Happy Chaos symposium, using Nutella to print shapes on bread - something inherently sweet ) The idea of using Nutella was actually pioneered by Frank Oxener. Though the material doesn’t allow to draw complex 3D shapes, as it melts away fast, it’s a nice way to raise awareness towards the FabLab itself.

InsideOut: Laboratory Ecologies

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We had Jennifer Willet’s InsideOut: Laboratory Ecologies event at the Museum Volkenkunde in Leiden last Friday, which was culmination of her VivoArts class here at The Arts & Genomics Center. Artists doing bio-related stuff disguised as an outdoor picnic - felt really like being inside a ‘70-ies Miklós Jancsó movie…

experiments still to be done

The following experiments still need to be done:

  • killing the bacteria with UV light (a 2 day experiment)
  • test for different timings for the arabinose drops to have an effect (a 4 day experiment)

These experiments are going to be done mostly by Joeri Verasdonck and Vincent Van Rixel, students at the Leiden University.

Killing the bacteria with UV light

Have some plates that have the bacteria inside the agar, and try to expose the plates to UV light for different durations. we have 4 plates, so I’d recommend doing a logarithmic scale: 1, 10 and 100 minutes, and leave the 4th plate as a control.

then, take the plates exposed to UV light, cut some part out of them, and try to make a liquid culture out of each of them. overnight we should see which grew out, with expeting the control to grow of course.

Test for different timings

so far we’ve used plates that were grown in a 37 C incubator for our tests when dropping the arabinose on them. we should test if this works in a more relaxed manner, and only using room temperature and a fridge. this seems to be a 4 day experiment.

day 1

first create a new overnight liquid culture using one that’s on the table - should still be OK - you might also make one to see if the liquid culture grows overnight on room temperature, not in the shaker bath

day 2

create a number of plates with bacteria in them. I’d suggest:

  • leaving a few on the table, to grow in room temperature overnight
  • put some in the fridge right away
  • put some in the fridge the next day, after it has grown overnight

day 3

put some of the plates left on the table in the fridge (see above)

get some plates from the table and from the fridge, and drop some arabinise on them

day 4

see if the plates turn fluorescent where they have arabinose.

leave the rest of the plates where they are, so we can drop arabinose on them next week, and see if they work. I’d suggest making a lot of plates, like 15, so that we can leave a lot in the fridge for next week (say 5-6 of those are put in the fridgge right away, 5-6 after 1 day of growth at room temperature). then next week each day take one plate of each kind, drop arabinose on it, and see the day after if it turned fluorescent.

a Meetup az internethajo Kek Noteszben

Holnap indul utjara az idei internethajo, amelynek ‘Kek Notesz‘-eben megemlitesre kerul a Meetup is, a 25. oldalon. Internetes ize lettunk, szerintuk…

experiences with building a fab@home 3D fabber

By now we’ve sort of succeeded in bringing the fab@home 3D fabber into operational state, thanks to the great help of the Waag FabLab people, especially Jean-Michel Molenaar and Bastiaan Ekeler. The kit we worked with is one that we ordered from KoBa Industries. While the kit is designed wonderfully, we still bumped into a number of challanges.

The fabber kit comes in the form of a white box, a bit too big to transport manually alone, weighs in at about 10kg. It includes almost everything you need for assembly, basically all the custom-made plexiglas parts, motors, cables, etc. The fab@home site provides a list of additional equipment that you need, see here. You can follow the documented assembly process, it’s put together pretty much, though navigating between the assembly pages is quite difficult, as the navigation menu is only provided at the bottom of some of these pages, and it’s not obvious which is the first one. The process is surprisingly easy, but of course you can never get everything right at the first time.

Below I listed some issues we’ve found, and also some improvement suggestions.

Some issues with the kit

We’ve encountered the issues below when trying to get the fabber work.

Some motor orientations were incorrect

Though we’ve followed the wiring color convention suggested in the assembly tips page, at the end it turned out that actually 3 of the 4 motors had opposite orientation then expected. Don’t know how / why this happened. By reversing the cable connections from the motor controller to the motors, this issue got mitigated. We’ve had to reverse the limit switch connections as well accordingly.

We only found out about this issue when we were controlling it from the software, as the 3D representation of the kit and its actual movements contradicted each other. For example, the plate was moving up in reality while moving down in the 3D view. Coincidently, the deposition tool’s motor was also reversed, so it was actually pulling back instead of pushing the material out. No wonder nothing got printed at first :)

The controller support doesn’t hold the controller

It seems that the small parts that are supposed to hold the microcontroller on the fabber chassis were added as an afterthought, and they just don’t lock in properly, and thus they don’t support the controller. Maybe a better design would help in the future, so that the controller is held properly on the side of the fabber box.

A Windows-only solution

It’s not mentioned in the required bill of materials, but actually you need Windows to run the fabber software, or even just to connect to the fabber. Seeing that it’s an open source project, actually I didn’t check in advance, but I supposed it most be running on Linux, and possibly cross-platform - well, it’s not.

What’s even more surprising is that the controller is not a regular USB-Serial device that would be generally recognized by operating systems, so one can’t even just connect it to any OS and play around with it via a serial protocol. It needs a special USB driver that is available for Windows only. This also means that if you’re running Windows from a virtual machine within another OS, you need one that enables for USB pass-through from the host OS to the guest OS. (For example, the closed source version of VirtualBox does this, but not the open source version.)

It would be nicer to have the controller as a generally recognized USB-Serial device that is picked up by all major operating systems. It would be even nicer if the whole solution would run on a range of operating systems, especially Linux, so that one can create a complete fabber solution running on nothing but open source software.

Possible improvements

The following would improve the kit building experience.

Include more of the easy-to-break parts

While I know that professionals never make mistakes - me as an amateur, I sure do. And as more and more people try to get into 3D fabbing, more amateurs are entering the scene. It would be nice thus to include more of the easy-to-brake-but-cheap parts in the kit. This is especially true since internationally some are very difficult to replenish, just because of the different markets around.

For example, I ruined all limit switch connectors when putting them together, and took me about 3 days to find replacements. Unfortunately the kind of connectors used are not available here in the Netherlands, so I had to buy replacement limit switches. Fair enough - but these are actually of different shape (the connectors on it are not on the side but on the bottom of the switch), which means they don’t fit into all the locations they are supposed to on the fabber. We worked around it by creating adapters for them using a laser cutter at the Waag FabLab - but not a lot of people have this luxury.

All this could have been prevented by supplying say twice the amount of the small white connectors and the crimp contacts used, which I guess would have cost about $5 more at most, less than 0.2% of the kits overall price. And would have saved me 3 days.

Use fewer kinds of screws

It’s not apparent on the assembly tools page, but putting the fabber together requires a huge range of different screwdrivers. Moreover, it requires both metric and imperial scale screwdrivers. Thus no one is having a good time: actually you have to buy sets of different norms, it’s not enough to have everything from one norm. It’s also annoying to always look for the other screwdriver as the one in your hand is just not the one from the six kinds used.

I’m sure this all stands to reason, but maybe lowering the number of different screws in the construction would make for easier assembly and maintenance.

Provide a JTAG adapter with the kit

A JTAG adapter for the board used in the kit is not easy to get internationally. Took me about 2.5 weeks to finally get one shipped here in the Netherlands, and about €85 including shipping, even though the list price is about half at that at $55. This being about 1.9% of the overall price of the fabber kit, it might be wise just to include the JTAG adapter in it.

Of course one can argue that this is generic, re-usable equipment. But it never hurts to have one, and amateur enthusiasts are not going to have this specific adapter anyway. And yes, you’ll want to have one to upgrade the firmware, even though KoBa Industries sent the controller already flashed with some version of it.

Provide easier adjustment for the Z-top limit switch

One has to adjust the Z axis top limit switch quite often, so as to accommodate the size of the syringe nozzle in the deposition tool. This has to be done by loosening a hexagonal screw, which is opposed by a nut on the other side. Unfortunately the nut is very hard to reach because of the vertical support rods of the plate. It would make life easier if one could loosen and tighten these screws easier.

As a workaround, we glued the nuts to the limit switch, so that they oppose the screws movements without having to manually hold on to them.

our fabber to be shown at Happy Chaos

If all goes well, we’ll show our fabber at the Happy Chaos event this Saturday at the Pakhuis de Zwijger. Because of legal reasons, unfortunately we can’t bring the bacteria along, so we’ll be just showing the fabber as it is, creating nice 3D form out of Nutella, unto toast that has some imagery burned into it by a lasser cutter at the Waag FabLab.

Bon apetit!

more fiddling with the fabber

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Today we’ve done some more fiddling with the fabber, after exchaning some e-mails with Frank Oxener from the Texel FabLab. First the tip of the syringe hat to be clean of dried-up Nutella. Frank’s suggestion was to use a lower pressure for pushing out the Nutella, so that the plug will not push through it. Using a video link to FabLab Norway, we also found out that they were using chocolate to do some fabbing themselves. I also thought - if one can create a syringe that one can keep at constant temperature, one could really use well tempered chocolate for fabbing.

So, we tried again, but it didn’t work. After some annoyance and investigation, it seemed that the 3D representation of the fabber inside the fabber software was quite contradictory. After some investigation, it turned out that 3 of the 4 axes were connected in reverse - even though we followed the documentation properly. Well, anyway, after connecting the stepper motor cables to the control electronics, at least the 3D representation seems to be OK.

And them editing and playing about with the tool description file, and it seems to be working…

Though the thing is, that the fabber stops in between the process, ‘waiting’ for something. Well, I guess there’s still some stuff to figure out…