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DIYbio FAQ v1.5: "The biohacker's FAQ"

This FAQ for DIYbio is actively maintained by it's editors, and by you! Edit your contributions directly or email updates to the DIYbio email list, diybio@googlegroups.com.

Major contributors (in alphabetical order):

• Bryan Bishop <kanzure@gmail.com>
• Jonathan Cline <jcline@ieee.org>

The contents of this FAQ are copyright under the OpenWetWare Copyright policy (Creative Commons Attribution-ShareAlike 3.0 Unported). When quoting any content of this FAQ elsewhere, include a full hypertext link back to the main FAQ page.

This topic DIYBio Projects is part of the DIYBio FAQ

This FAQ for DIYbio is actively maintained by Jonathan Cline.

You may edit it directly, or send questions/comments to jcline@ieee.org -- please note that while mistakes in this FAQ may exist, it is the hope that it continually improves over time. If you make improvements, feel free to add an attribution under the new content for yourself as well.

The contents of this FAQ are copyright under the OpenWetWare Copyright policy (Creative Commons Attribution-ShareAlike 3.0 Unported). When quoting any content of this FAQ elsewhere, include a link back to this main FAQ page.

External Links

• OpenWetWare DIYBio main topic Projects section
• DIYbio web page, selected project summaries
• add your external project link here

Project Ideas

The following are project ideas (brainstorming) which have been discussed on DIYbio google group. Research papers or existing products similar to these ideas can be found, with the DIYbio aspect of lowering the cost, open sourcing the design, and allowing latest technology (such as USB or network, for electronics devices) to be added as enhancements.

• Using LEDs as spectrophotometer, colorimeter, etc. Some projects already exist around the web.

• Using USB/networkable microcontrollers for thermocyclers.

• Fabricating microfluidic devices and using USB microcontrollers for microfluidics (pump/valve/syringe) control.

• Printing, patterning, synthesizing various substances or microbes with inkjet printers. Modifying gene expression with inkjet dispensing.
  • Several other fields are also very engaged in modifying inkjet printers: for making electronics circuit boards (inkjet PCB); for making physical objects (inkjet fabrication), for printing on objects (inkjet handhelds). Check these projects for how to modify inkjet printers for Bio projects as well.

• Making Taq

• Imaging system for Electrophoresis Agarose Gels (or Gel Box that includes the imaging system built-in)

• add your project ideas here

Microscopes, Colorimeters, Spectrophotometers, "Cheaposcopes"

Spectrophotometers

• Open Spectrophotometer Project. To provide a open source hardware LED-based spectrophotometer. http://openwetware.org/wiki/Citizen_Science/Open_Spectrophotometer_Project

Cheaposcope

• The cheaposcope: development of a low cost fluorescence microscope for teaching. We've exploited recent developments in LED technology, optical filters and cameras in an attempt to construct cheaper instruments for fluorescence microscopy and detection. http://www.plantsci.cam.ac.uk/Haseloff/imaging/cheaposcope/cheaposcope.htm

Microfluidics and Controller Boards

Continuous Flow Microfluidics

Microfluidic Flow Device

http://thebigone.stanford.edu/foundry/technology/index_clip_image002_0000.jpg

• ""Soft Lithography is a microfabrication process in which a soft polymer (such as polydimethylsiloxane (PDMS) ) is cast onto a mold that contains a microfabricated relief or engraved pattern. Using this technique, membrane microvalves can be produced. To design your own microfluidic device, please follow the Basic Design Rules and Mask Design Rules and make use of all the design information and reference articles provided on our website. "" http://thebigone.stanford.edu/foundry/services/designyourown.html

Controllers

• USB 24-Valve Controller Assembly Guide, Rafael Gómez-Sjöberg, QuakeLab–Stanford University. ""This document briefly describes the assembly of a USB-based controller for 24 solenoid pneumatic valves that can be used to drive a microfluidic chip fabricated by Multilayer Soft Lithography. You can build a computer-based electronic valve controller to allow you to control the opening and closing of valves and pressure in the flow lines of your chip. The controller is comprised of 1) an electronic controller box and 2) a set of electronic valves. "" Project at http://thebigone.stanford.edu/foundry/testing/own_controller.html and main page at http://thebigone.stanford.edu

Fermentors, Bioreactors, Photo Bioreactors

• An automated home-built low-cost fermenter suitable for large-scale bacterial expression of proteins in Escherichia coli. We have developed an automated fermentation system for cost-efficient upscaling of protein expression in bacteria. The system, built for use by nonbiotechnologists, can be assembled mostly from standard laboratory equipment and allows a largely unattended growth of bacteria to OD 25 (at 600 nm) in a 12 L vessel. http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=6660&itool=Abstract-def&uid=18687068&nlmid=8306785&db=pubmed&url=http://www.biotechniques.com/article/000112830

For Yeast

• DIY CO2 Injection: The Yeast Method. This article gives instructions for a cheap Do-It-Yourself CO2 injection system. The CO2 is produced by a mixture of sugar, yeast and water, and the setup is constructed entirely from cheap and readily available materials. http://www.thekrib.com/Plants/CO2/co2-narten.html

For Algae

• A Photo Bio Reactor (PBR) is a system that provides an artificial environment for photosynthetic organisms (Algae) to perform a chemical conversion. Scientists and engineers have been developing several types of photo-bio reactors (PBR’s) over the past fifty years to grow microorganisms that are used in a wide variety of applications. Cultivated algae cultures can be used to produce human food, animal feed, health food, therapeutics, chemicals, fuel, hormones, and fertilizer. A prototype PBR was built at SDSU in 1998 that had a reactor capacity of 1 gallon. The prototype was inoculated with algae obtain from Argonne National Laboratory and produced an algae biomass in excess of 25g. The success of the prototype led to the decision to scale up the prototype PBR to capacity of 500 gallons. The 500 gallon PBR is large enough to study the feasibility of commercial production algae. In the summer of 2000 research was initiated to evaluate the feasibility of scaling up the prototype PBR. Research revealed that little is known quantitatively about how the different subsystems interact and affect algal biomass production in PBR. The scaled up PBR design was then modified to allow for the testing of the effect the different subsystems have on algal biomass production independently as well as interactions of the subsystems. Test variables may be light type (wavelength), intensity of light, mixing intensity, nutrient requirements, control strategies, etc. http://abe.sdstate.edu/faculty/garyanderson/website/pbr_home.html

• An Algae Bioreactor from Recycled Water Bottles. In this instructable, we describe how to build a photo-bioreactor that uses algae to convert carbon dioxide and sunlight into energy. The energy that is produced is in the form of algae biomass. The photo-bioreactor is built from plastic recycled water bottles. By designing the apparatus to be compartmentalized, we are able to do many experiments in parallel. http://www.instructables.com/id/An_Algae_Bioreactor_from_Recycled_Water_Bottles/

• How To Make an Algae Test Photo Bioreactor...Part One. This gives a step-by-step instructions on making an algae test photo bioreactor. This can be used in any application that calls for testing and/or growing algae, to determine maximum growth rates, best nutrients, etc., such as... Making algae biodiesel, Animal feed, Organic fertilizer, Cosmetics, Health food supplements and many more. http://www.instructables.com/id/How-To-Make-an-Algae-Photo-BioreactorPart-One/

• Inventgeek Photo Bio Reactor Array V.1 http://inventgeek.com/Projects/photo-bio-reactor/overview.aspx

• Inventgeek Photo Bio Reactor V.2 This design has many improvements that make it far more sustainable and practical for long-term use. I really focused on making it highly modular and insuring it was rugged for prolonged outdoor use that is easier to fill and harvest from. While the array is smaller for this project it can be scaled to any size or requirement.http://inventgeek.com/Projects/Photo-Bio-reactor-V2/overview.aspx

• I got interested in the idea of growing Spirulina at home after I obtained a breeding pair of Bristlenose Pleco’s. What better food source than fresh Spirulina, I thought to myself. I wondered around Google for days, which turned into weeks, then months. No where could I find a single source that could easily explain how to grow Spirulina at home. If you are interested in growing Spirulina at home, I hope you find this method useful. I’ll give you a quick run down of my version of “Growing Tubes”, both in expensive and easy to build in a day. I went to Home Depot.... http://gpasi.org/forums/index.php?topic=64.0

• In-Home Photosynthetic Bioreactor - 1997-98. Invented by Lee Robinson, the founder of the British biotechnological company Biotechna, the Biocoil is a "photosynthetic bioreactor that provides an environment for biological organism to grow in a controlled manner." The frame is built and clear PVC tubing is wrapped around it to form a circular model so that it is easier for photosynthesis to occur. Sunlight or artificial light is then put in at an angle to shine on the tubing while the algae flows through. Chlorella algae was used in the Sewage Sister Biocoil to remove nutrients from the sewage flowing along with the algae. The tubing of the Biocoil consists of several sections of tubing rather than one piece wrapped all of the way around. Compressed air pumps are used to push the algae and water through the Biocoil and to prevent anoxic conditions in the water. http://web.archive.org/web/20071009122237/http://advbio.cascadeschools.org/97-98/minicoil.html

The Biocoil Operations Manual (The Trip From the Algae's Point of View). The Biocoil is a tertiary sewage treatment system which utilizes light and algae to remove phosphates and nitrates from secondary effluent. The Biocoil is a round unit eight feet tall and six of those feet are surrounded by 1600 feet of clear one inch inside diameter food grade tubing. This tubing is exposed to light 24 hours a day, either by natural sunlight or artificial light. The inside of the Biocoil is composed of three tanks, the contact, holding, and settling tank. The manifold which distributes water from the tanks to the tubes is also located inside the Biocoil. http://web.archive.org/web/20070520071350/advbio.cascadeschools.org/95-96/biomanual.html

The Biocoil Project - 1994-95 http://web.archive.org/web/20080330070953/advbio.cascadeschools.org/94-95/biocoil.html

The Biocoil Project - 1996-97 http://web.archive.org/web/20080314163104/advbio.cascadeschools.org/96-97/biocoil.html

The Biocoil Project - 1997-98 http://web.archive.org/web/20080216032605/advbio.cascadeschools.org/97-98/biocoil.html

Images http://web.archive.org/web/20070207033743/advbio.cascadeschools.org/97-98/images/morepic2.html

Basics of Growing Algae

"How to get started growing algae at home."

Needed:

• a space that can be easily heated or cooled depending on the weather.
• cool white flourescent lights 35-40 watts.
• aquarium aereation pump. tubing, and airstones... tees(all this from walmart.)
• shelves depending on how many cultures you want to grow
• glass jars one quart, and one gallon for as many cultures as you plan to grow
• aquarium sea salts (Instant ocean) I cup per gallon of distilled water.
• dial thermometers
• graduated measuring cups
• Ph. papers
• Nutrient solution
• algae cultures( often come in 50 ml tubes )
• growing instructions come with the cultures.

Setup:

• when you receive the culture add the contents of the tube to 250 ml of water (salt or fresh)
• keep lights on 24/7
• keep aereation on 24/7
• once the 250 ml turns green add another 250 ml and so on untill you have a liter of green algae
• take the green liter and add it to a gallonglass jar,
• once you have a gallon you can seed a ten gallon aquarium or you can add the gallon to larger tanks or to a closed loop ecosystem
• and in two weeks, voila! youll have algae growing.
• unenclosed ponds are unstable and prone to contamination by outside influences such as acid rain, water fowl that carry wild algae on thier feathers , animals , temperature variations.windbourne pollutants. night time temperature variations.etc

The above is from http://www.ecogenicsresearchcenter.org/biodiesel.htm (lots of pictures there)

Incubator, Shaking Incubator

• BUILD YOUR OWN INCUBATOR. Here's how to turn your flock's extra eggs into a whole new generation of omelet providers, including detailed diagrams, temperature, humidity, movement and ten tips. http://www.motherearthnews.com/Do-It-Yourself/1982-03-01/Build-Your-Own-Incubator.aspx

Bob Horton's Shaking Incubator

Note the date on this project.

• Bob Horton horto005 at maroon.tc.umn.edu
• Wed Mar 6 11:06:24 EST 1996

Bob's Homemade Shaking Incubator Design

---

This is my design for an easy-to-build and inexpensive laboratory shaker/shaking incubator. It will undoubtedly remind many readers of something they may have built for the Science Fair in the 5th grade, but as far as I know, the use of record-player power and the hanging platform are original. And, hey, you can't argue with the price.

Three figures are attached. The attachments are MIME-encoded, and should be decodable with any MIME-compliant newsreader, including the one built into NetScape 2.0. The figures are small, black and white drawings in GIF format, and should be viewable from any web browser, once they are decoded.

Figure 1: Parts for the Home-Made Shaker.

http://iubio.bio.indiana.edu/bionet/mm/methods/attachments/19960306/73d4d331/shake1.gif

Figure 2: Additional Parts for the Shaking Incubator.

http://iubio.bio.indiana.edu/bionet/mm/methods/attachments/19960306/73d4d331/shake2.gif

Figure 3: Portrait of the Final Product.

http://iubio.bio.indiana.edu/bionet/mm/methods/attachments/19960306/73d4d331/shake3.gif

---

The shaking platform is cut from a particleboard sheet the same size as the top of the box; the rest of the sheet is used to reinforce the top of the box. The platform is suspended from the edge of the top opening with strings. Slipknots are used in the strings to make them easy to adjust until the platform is more-or-less level. Then the knots are secured in place with tape. The strings and holes are arranged so that the strings hang as vertically (i.e., parallel to one another) as possible. This way the platform will remain essentially level as it swings around in a circle.

A bolt is mounted on the turntable, and passed through a hole in the platform, so that when the turntable spins, the shaker moves in an orbital motion. Note that it takes very little work on the part of the record palyer motor to move the platform in a horizontal circle, even if it carries significant weight.

The heat source (light bulb), fan, and thermostat are mounted on a particleboard base, and wired so that the fan is always on, but the light bulb is turned on and off by the thermostat in classic Jr. High School Science Fair fashion. The whole heat-control unit is placed in the incubator box, and a thermometer is used to calibrate the thermostat. The thermostat I use keeps the box somewhere 35 and 38 degrees centigrade. I think a regular home thermostat would work better, but the bugs don't seem to mind.

The fan blows air around fast enough that air in the whole box is very close to the same temperature. But I put the thermostat probe behind the fan so it would not detect radiant heat, and the light is below the platform so it doesn't shine right on the cultures.

I covered the areas of the cardboard walls and the portion of the bottom of the platform that come close to the light bulb with foil, to reflect some heat so they wouldn't be quite as likely to catch fire. If you fold several thicknesses of slightly wrinkled foil together, they make a nice shield against radiant heating (this was the suggestion of Mike Herron, from the lab across the hall).

The box is sealed with masking tape, except for the top opening. A lid (not shown) is made of an additional cardboard sheet, edged with soft foam weather stripping. This type of flat lid limits the height of culture flasks to the distance between the shaking platform and the top of the box; alternatively, a raised lid made of a second box would allow more room.

This shaker has three speeds; 33, 45, and 78 rpm. The fastest setting is still somewhat slower than typical bacterial culture conditions, but it works OK if you leave plenty of air in your flasks. A faster motor could be substituted for the record player, but it wouldn't be as cute.

The heating unit and the record player can both be plugged into a power strip, so a single convenient switch can be used to turn the whole thing on and off.

The tools required are fairly simple:

• wrench, pliers, screwdriver, etc. to remove any parts of the record

player that stick up too high.

• drill to mount the bolt on the turntable, and make holes for the

strings.

• knife to cut cardboard and strip insulation on the wires.

• jigsaw to cut the platform from the particleboard.

My estimate of the cost of materials is as follows:

• cardboard box, string, tape, etc.: $0.00

• record player: $0.75 (yes, I can get them in Minneapolis for 75 cents

at the "Digger's Delight" behind Goodwill on Como Avenue near Highway 280. Otherwise they may run you 5 bucks apiece at a garage sale).

• thermostat: $3.50 from AxMan surplus, University Ave., St. Paul. At a

hardware store, these cost about $12.

• fan: $7.50. I used a 120V AC box fan, about 4 inches in diameter

(AxMan Surplus). I couldn't find one the right size at Digger's, but keep your eyes peeled.

• light socket: $0.85 (hardware store)

• weather stripping: ~$3

• power strip: ~$3.50 (only used for the Shaker Deluxe).

• thermometer: $1.19

• I scrounged the light bulb and the particleboard. (Retail ~$3?)

So I have over $20 invested in my shaking incubator, and it could easily cost over $23 if you had to buy particleboard and stuff. Old record players also make great sample rotators, if you set them at a steep angle, or they can be used to wash gels and blots, if you put your pan on the turntable and slightly raise one end of the record player. The only shaking incubator I have in my current lab is of this design (serial number 00000001). I have used it to grow 50 ml E. coli cultures in LB, in regular 500ml Erlenmeyers, and 1.5ml cultures in TB in 15 ml snap-cap tubes. I have recently used this incubator to clone a cDNA sequence for a novel human neurotransmitter receptor subunit. But I'll try not to let Real Science interfere too much with inventin' stuff. :)

Happy shakin'!

Bob Horton

DNA Extraction

Simple DNA Extraction

Extract DNA from your Halloween pumpkin! http://sci-toys.com/scitoys/scitoys/biology/pumpkin_dna/halloween.html

HOW TO EXTRACT DNA FROM ANYTHING LIVING! http://learn.genetics.utah.edu/content/labs/extraction/howto/

How to Extract DNA From Human Cheek Cells! http://biology.about.com/c/ht/00/07/How_Extract_DNA_Human0962932481.htm

Open Source Gel Boxes

• Hosted on OpenWetWare, Open Gel Box 2.0 is now available to buy; includes transilluminator. Contact Tito.

• DIY $25 Gel Box. We constructed a functional Gel Electrophoresis Chamber in a span of a day using [...] http://hackteria.org/wiki/index.php/DIY_$25_Gel_Box

Electrophoresis Gel Box Power Supply

• See Open Gel Box 2.0 Power Supply on OpenWetWare. Working unit has been constructed.

3D Printed Gel Boat and Comb Set

To: DIYBio google group
From: Cathal <cathalgar...@gmail.com>
Date: Sep 17, 10:07 am

I've just published my first designs on Shapeways, for a $100 Gel Boat
and Comb set.
Sit these into a plastic container with some graphite electrodes at
either end, and you have a complete gel electrophoresis kit.
I intend to make more designs and share them both on this shop and
with the open-source community in the near future!

http://www.shapeways.com/shops/labsfromfabs

The designs are open source, and are available on Thingiverse.com for
those with access to a 3D printer.. just be sure and let me know the
results please! I'm awaiting my own 3D printer right now so I'm
itching to see results.

Note: Because of the opaque nature of the printed plastic, UV
visualisation will have to be Top-down.

Gel Box from Tupperware or other

• THE MACGYVER PROJECT: GENOMIC DNA EXTRACTION AND GEL ELECTROPHORESIS EXPERIMENTS USING EVERYDAY MATERIALS. By Yas Shirazu, Donna Lee, and Esther Abd-Elmessih. DNA extraction and separation by agarose gel electrophoresis is a simple and exciting process that anyone can perform. However, the high cost of specialized equipment and chemicals often hinder such an experiment from being carried by members of the high school community. Here, we describe a cost effective way of extracting and electrophoresing DNA under a prescribed MacGyver limitation – that is using only materials available from a grocery store or shopping mall. http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/

• add your gel box project here

Inkjet Printer Hacking for Bio Projects

Many papers over the years involve using either EPSON inkjet printers (piezoelectric print head) or HP/etc inkjet printers (thermal print head) to dispense very small amounts of biomaterial or biochemicals.

EPSON Printers

Epson is the only brand which uses piezoelectric print heads. Epson printers also have CD-printing, which provides a mechanical method to feed larger objects into the printer.

• Epson R280
  • Open Access research paper: "This paper presents a low-cost inkjet dosing system capable of continuous, two-dimensional spatiotemporal regulation of gene expression via delivery of diffusible regulators to a custom-mounted gel culture of E. coli. A consumer-grade, inkjet printer was adapted for chemical printing; E. coli cultures were grown on 750 µm thick agar embedded in micro-wells machined into commercial compact discs. Spatio-temporal regulation of the lac operon was demonstrated via the printing of patterns of lactose and glucose directly into the cultures; X-Gal blue patterns were used for visual feedback. We demonstrate how the bistable nature of the lac operon's feedback, when perturbed by patterning lactose (inducer) and glucose (inhibitor), can lead to coordination of cell expression patterns across a field in ways that mimic motifs seen in developmental biology."

Cohen DJ, Morfino RC, Maharbiz MM, 2009 A Modified Consumer Inkjet for Spatiotemporal Control of Gene Expression. PLoS ONE 4(9): e7086. doi:10.1371/journal.pone.0007086 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007086

As discussed on the DIYbio google group: http://groups.google.com/group/diybio/browse_thread/thread/8d3462454d81611e/96541b1fde01225d?lnk=gst&q=DIY-bioprinting

HP, Canon, .... Printers

• Add inkjet printer projects here