DIY Labware review

[bostjan]

Hello everyone!

This is my first post, so let me introduce myself shortly, I'm Boštjan and while a trained Biologist, I'm new in the DIY bio community. I work at IRNAS Institute, where we are setting up an open biolab/biohackspace, which is located in Maribor (Slovenia). Together with my colleagues (who are mainly engineers) we are setting out to develop DIY lab equipment, which will be comparable to the commercial props in terms of functionality, but much more affordable. To not "reinvent warm watter", we started making a review of existing DIY equipment and how it compares to the commercial counterparts, whether it is feasible to make etc. 

You can find it on github: https://github.com/symbiolab/bio-labware/blob/master/000_bio-labware_overview.md

Hopefully we will soon be able to publish some designs of our own. The review is not completely finished yet, but with the development of DIYware, let's hope it never is. In any case, maybe some of you will find it interesting, I know that there are many collections of DIY stuff available already, however, we tried to structure it a little in terms of methodology and add some context. I would very much appreciate any comments and suggestions for improvement, as we probably missed some things and perhaps misrepresented others. I wish you all a very pleasant weekend!

Cheers,

Boštjan

[Jake]

Wow!  Great resource!  Looks like a lot of well spent time and effort went into this.  Thank you.

A couple suggestions... I'd try to make it less confusing to worldwide audiences by using USD instead of Euros and using the decimal point "." as the decimal separator.  Currently it seems to be a bit of a mix.

It's kind of hard to read "usually in sizes for 0,5, 1,5, or 2ml and falcons (conical centrifuge tubes)".

You might suggest overhead stirring as an easier alternative to magnetic stir plates.  It's relatively easy and a lot cheaper to use a regular burner/hot plate with an overhead stirring apparatus.

Another helpful addition might be sections on techniques to get around the use of expensive equipment.  I've actually seen smart people mentally stumped by the lack of, or waste time waiting for, a stir plate.  That might seem silly, but a picture of a stir rod might actually save a few people some effort or expense.

[bostjan]

Hi Jake,

thanks for the feedback and ideas. I will definitely have to go through the text again (or maybe a few times) and make formatting coherent, especially for the decimal point! 

Also adding the overhead stirrer seems a good idea, I will add it to the list. Since I never used it before, do you have experience on how to hande it in combination with other devices? I see how its a major improvement when combined with a hot plate, but I imagine it would be somewhat of a hindrance when used with a pH meter?

Adding simple alternatives is also a great idea, I will work on that. If you have more suggestions, please let me know =)

Best wishes,

Boštjan

Dne ponedeljek, 18. april 2016 01.05.46 UTC+2 je oseba Jake napisala:

[ukitel]

Very interesting resource! Great job!
Keep up with the good work, making a review of all devices available is great. I also had the impression that it is everything a bit messy

[William Beeson]

Hi Bostjan,

Thanks for sharing the work you have done.  Like Jake said, this looks like a lot of work!  As someone who has been obtaining/building DIY lab equipment first hand, I have read a lot of the source materials you linked to.  I have a few suggestions that might help you in your decision making and for others trying to make the same decisions.

First off, one very important consideration for a new piece of DIY equipment is safety for the intended use case.  There are examples of DIY lab equipment that are demonstrably not safe.  Obvious things to look out for are fire risks, electrical shock risks, and cut risks.  

Next, I have a very heavy bias towards repurposing "consumer" equipment that can be purchased from reliable vendors at relatively low cost.  For example, I substituted a commercial water bath incubator with a sous vide cooker I bought on Amazon.  The sous vide has 0.5C accuracy and cost me less than $200 shipped.  The advantage of using mass market consumer products is that they are normally produced at close to the theoretical minimum cost (for the safety/reliability of the item).

Finally, I think you should determine what is the value of your time and factor that into the cost of building a piece of equipment.  If you can buy the pieces for $100 and then it takes 8 hours soldering, painting, cutting, building, etc -- that is a lot of cost in your time.  Obviously if you have fun building things then this isn't a big factor.  

-Will

[Jake]

I've never used overhead stirring with a pH meter.  It's often used for viscous liquids that are too thick to be stirred by magnets.  I wouldn't imagine it would be difficult to set one up on one side of the beaker and the pH meter on the other, but the stirring might be a bit more uneven and you'd probably want them both to be well secured so they don't interfere with each other.  There are a few different types in use.  The type with a rod through a ball joint connected off center to a gear works well to get a wide stir path through a smaller neck vessel, but otherwise is a big pain compared to a simple paddle type.

Here's a thread with a few made from drills or dremel type drives...

http://www.sciencemadness.org/talk/viewthread.php?tid=949&page=23

Another thing I see is the laminar flow hood section.  My advice on that is that laminar flow does not work well for micro.  People use them plenty, but I don't feel like blowing your work directly into your face is really a very good practice.  

Biosafety cabs. are too complicated to DIY IMHO.  I don't think you could really get one working right without an excessive amount of research, work, and testing.  There's nothing special about laminar flow and people waste way too much time trying to achieve it.  

The "Portable Laminar Flow Hood by antoniraj" in your guide will rather obviously not achieve laminar flow.  The filter must be the entire size of the workspace to get that.  The border around the filter on your pics will create a pocket of still air behind it and turbulize the air from there on out.  If you drilled pegs into the dados to have the front partly open during work it should still work fine, but isn't "laminar flow".  The plenum also doesn't seem well designed.  You need a plenum because you can't blow air directly on the filter or you will get an uneven pressure across the filter and again have turbulence and hence no laminar flow.

The design here is also not well done...

http://fradnai.free.fr/docs/doc23.pdf

This design has a few errors.  The pre-filter should be on the exhaust side of the blower.  Blowers are designed to push air, not suck it.  And you loose the utility of the pre-filter to smooth the air and prevent it from blowing directly on the HEPA filter.  The only time you should have a prefilter on the intake side is to reduce the flow of oversized blowers, and this is usually done by blocking off part of the intake rather than filtering it since filter flow changes over the life of the filter as it becomes plugged.  The design also has the blower blowing directly against a wall perpendicular to the filter, again this will cause uneven static pressure across the HEPA.  This design looks like it also has a filter smaller than the work area. Perhaps the worst part is that the blower is enclosed inside a box, which could be a fire hazard if the blower is overdriven or the prefilter clogs up.

The FreshCap design looks similar to what a lot of mycologists build, but I've never understood the focus on laminar flow.  It's extra work and there's a lot more potential problems and pitfalls. If you put sides and a sliding front on the unit you don't need laminar flow and can use much cheaper and much smaller HEPA filters.

The design I use is made just like a fume hood in reverse.  There's a furnace blower on the top pointed down, bolted to a piece of plywood.  Between the plywood and the plenum I have a layer of bedroll foam, and inset in the top of the plenum is a standard furnace filter.  The plenum is stuffed with polyfil (polypropylene pillow stuffing).  Beneath the plenum there is another layer of bedroll foam.  Two small HEPA filters are recessed into the top of the hood body about 3/4 of the way to the back and caulked into place.  They are evenly spaced side to side.  Two dados from top to bottom near the front of the work area hold a piece of plexiglass which is reinforced top and bottom with a strip of 90 degree angle aluminum running full length, minus the dado depth.  In the dados are holes every few inches that I insert a shelf peg or pin into to set the height of the plexiglass front.

The idea with the bedroll foam is to insulate the hood from blower vibrations.  None of the parts are bolted together and rely on the weight of the blower to maintain a seal between them without requiring a direct link that would transmit vibration.  The plenum only needs to be large enough to cover the HEPAs and support the blower.  Not being bolted on also makes for easy access to the filters and polyfil.  The purpose of the polyfil is both as prefilter and to smooth the airflow to the HEPAs.  You use the unit just like a fume hood with just enough handspace open in the front as is needed.

This design works well for me... inside a room in dusty warehouse.  I've verified it a number of times by exposing petri dishes of PDA in the four corners. With 5-8 min exposures I occasionally (~25%) get 1 CFU (out of  the 4 dishes).  I think this is pretty good since I'd imagine that's near the efficiency of the HEPA filter given the exposure time, amount of airflow, surface area, and input air quality.

I used to keep track of contam rate, but it was insignificant enough that I stopped.  I switched to a method where I expose a dish over the course of one block of hood work.  That way I can estimate the air quality for each batch of work.  I keep the dish while the work grows out to make sure there's no problem.

You can use a standalone HEPA filter to help clean the room air, but it also works well to just run the hood for awhile before beginning work.

I wrote a little also in this post...

https://groups.google.com/forum/#!topic/diybio/w2Fonkyangc

Not sure if you have UV in the DIY guide, but I mention the tubes I use there.

[Ilya Levantis]

Hi Bostjan,

This looks like a great resource. I have been working on a table which details very similar (but less detailed) information to your review. I will try and put what I can in your format and add it to the review.

One thing that I think would be worth noting is that sometimes multiple DIY options for the same piece of equipment can be categorised into two groups: 1) cheap and easy to make and often works just well enough to get by with; 2) more involved to build but gives much better results.

Both types of DIY equipment are valuable - sometimes you only need a piece of equipment once, sometimes a lab may not have enough time / money to build the more involved version. My own notes have attempted to capture both the minimum el-cheapo version and more solid DIY version for each piece of kit and give recommendations as to which option is best depending on how much budget is available. I shall attempt to integrate this into your review.

Additionally, my experience from London Biohackspace is that the best option for hardware is often cheaply bought / donated (free) 2nd hand commercial lab equipment or repurposed catering/medical/tattooing equipment. This sort of equipment has the benefit of not having to be built from scratch - thus making setting up a working lab much quicker and in the  case of free donations even cheaper than DIY equipment. The reason this is so effective is that, although wetlab biology has evolved over the past 20 years, it's mainly the reagents which have changed and not the machinery - new centrifuges do the same thing as a 30 year old model, hot water baths still just heat water, the important parts of a PCR machine haven't changed much since the 90s. The only major difference between new equipment and equipment that is 10 years old which university labs are often willing to donate for free is the absence of touch screens!

[bostjan]

Hey everyone, thanks for all the great feedback!

William, I agree that if there are commercial household/hobby alternatives available, they will probably make a better/cheaper alternative than a DIY device and I invite you to add such items to the review if you find some. I will also try to add a few my self. Also considering safety, that is a good point! I think we could add that to the review, however, it will take some time =)

Jake, thanks for the input on the laminar flow hoods/clean benches, I know what you mean...actually I was wondering whether it was worth it to make a DIY build that was nearer to the commercial devices. At the moment, I just work around a bunsen-burner when I have to transfect some samples in a "near sterile" environment, which is ok if it can be "quick and dirty", but it's not a long term solution if you have multiple samples...

Ilya, I agree and you are very welcome to contribute to the Github reivew.

[Jake]

I've built 3 flow hoods, and refined the design a little each time.  My main desire was to have a large workspace, which I couldn't really get with most designs out there.  I've had two large commercial units I bought at auction for next to nothing.  But I never ended up using either of them.  Replacing the filter would have been way too expensive, and I didn't like the open front designs of them.  For me it is important to have a full window on the front.  I open it, use it, then shut it afterward.  The inside stays clean and I often leave cultures in there since it's a nice clean space.

I'll try to dig up some pics or take some new ones for you.

One thing I found was that blowers always vibrate, and if they're directly attached, or the hood is not fairly heavy, it vibrates your work surface a bit.  This makes some things a lot harder than they should be.

The first super-cheap design I used was the same as this...

https://files.shroomery.org/files/04-06/621223049-glovebox5.jpg

I turned the filter unit upside down and glued or screwed it directly to the bottom of the bin.  That avoids the goofy plastic duct on the back and makes a more solid unit.  I also caulked the filter into the unit, including the edges of the filter.  Then I taped over the seams and switches on the unit to make sure the body was airtight.

I don't remember doing any dish tests on it, but I don't recall having any problems with contamination using it.

[bostjan]

Thanks for the info, some pictures would be great!

[Pieter]

Hi Bostjan,

Excellent collection indeed! For the biohack academy we made a collection of open source lab devices. Hood, centrifuge, thermocycler, pumps, spectrometers, microscopes, etc. All designs, source files, wiring and bill of materials can be found here:

https://github.com/biohackacademy

I've attached a picture with an overview. Also on www.vimeo.com/channels/bha3 you can watch video lectures, some dedicated to the devices.

There are also other catalogs out there that you might want to take into consideration:

http://collections.plos.org/open-source-toolkit-hardware

http://www.appropedia.org/Open-source_Lab

In a month or so we have a meetup in Belgrade. Perhaps you would like to join in? http://fabelgrade.io

All the best,

Pieter

Waag Society's Open Wetlab

[bostjan]

Hey Pieter,

thanks for the thumbs up! This looks great, I even have some of the BHA designs in the review, but not all of them. I will definitely include the missing ones as well. About the meeting in Belgrade, yes, i will try to be there, so perhaps we can exchange some ideas in person. =)

[Marc Dusseiller]

Full dober!!!

amazing work, thanks a lot for putting so much effort.

i guess there is loads of little contributions, more examples, photos (pimp it up!) that we all could contribute.

we once started to put organize some of our content on the hackteria wiki, but for from well documented as you growing repo.

http://hackteria.org/wiki/Generic_Lab_Equipment

it got some nice little articles to read though.

and urs recently put some stuff together here:

http://bio.academany.org/2015/labs/luzern/final_project.html

keep up the great work and also looking forward to meet you in belgrade!

m

[bostjan]

Hehe, hvala lepa Marc =)

Thanks for the nice words and the resources! I'm familiar with the work you did at Hackteria and GaudiLabs, great stuff as well! You are of course welcome to contribute to the repo. =) See you in Belgrade!

Best wishes,
Boštjan

[William Beeson]

Hey Pieter,

That looks awesome. Great work. Any thoughts that instead of using the cut pieces for all the instrument housing that we could come up with 3d printed substitutes? 3d printers are becoming so much cheaper and more mainstream.

Overall the quality and branding in the picture are really excellent.

[Pieter]

Hi William,

Actually I try to avoid the use of 3D printers as much as possible. We have a wide range of DIY 3D printers here in the Fablab Amsterdam (same place as the Open Wetlab), but none is plug and play. Under/over extrusion, wrapping, not sticking to the bed, wacky support structures, holes that are just a little too big or too small, taking hours to get big pieces, etc, etc, countless hours wasted with those machines. So whenever I make something, I ask myself: can I cut it, mill it or mold/cast it? If yes, go for that. Only in case I believe there is no other way, I'd go for 3D printing. 

The only part in the biohack academy kit that is 3D printed is the rotor of the centrifuge

Picture by Waag Society (CC-BY-SA 4.0)

But than last time Ali from the biohack group in Tehran proved my wrong by milling that part too:

Picture by Ali Amirali - BioHack Academy Tehran (CC-BY-NC 4.0)

And when it comes to the housing of the devices, I am actually looking into using general purpose boxes. Because every time I lasercut a box I kind of feel stupid. There are already so many boxes out there :)