DIYbio/FAQ/Projects

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= IMPORTANT NOTE =  
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'''Regardless of what you've read in Wired magazine or other publication written by journalists who don't do any fact checking might say, most of the questions regarding building "new living organisms" is currently not possible
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* '''Regardless of whatever article you've read in Wired magazine, or other publication, written by journalists who don't do proper fact checking might sensationalize, most of the questions regarding engineering "new living organisms" or "replacement organs" or what have you, is currently not possible (and won't be for decades).  Sorry to have to point out the obvious. ''' -- Jonathan Cline on the DIYbio google group
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(and won't be for decades).  Sorry to have to point out the obvious. ''' -- Jonathan Cline on the DIYbio google group
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= External Links =
= External Links =

Revision as of 01:53, 24 May 2011

Intro    In The News    Educational    Equipment    Projects    Kits    Methods    DIYbio.org    DIYbio googlegroup    FriendFeed - DIYbio    0.png

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):
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


Contents

IMPORTANT NOTE

  • Regardless of whatever article you've read in Wired magazine, or other publication, written by journalists who don't do proper fact checking might sensationalize, most of the questions regarding engineering "new living organisms" or "replacement organs" or what have you, is currently not possible (and won't be for decades). Sorry to have to point out the obvious. -- Jonathan Cline on the DIYbio google group

External Links

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.

  • Comparing various inexpensive reagents to the purified commercial counterparts; for example, food-grade agar-agars to commercial agaroses.
  • 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 a spin coater (from DC motors or computer drives) - which can be used for building microfluidics, etc
  • Imaging system for Electrophoresis Agarose Gels (or Gel Box that includes the imaging system built-in)
  • Modifying one's own biology through diet, and quantifying medical change by common and/or special medical tests, as compared to prior results and standardized results.
  • Distributed testing foods sold in grocery stores or restaurants by genetic sequencing or low-cost field tests, and publishing results based on geographic region.
  • Distributed Sample collection and sequencing system + protocols, with long-term archival and open source database.


  • add your project ideas here

Technology Platforms (Microcontrollers, etc)

 The following product is from Microchip.  Microchip has grown in
 interesting ways: they now have a cross-platform software development
 environment (Win, Mac, Linux) based on NetBeans (called MPLAB X).  The
 original MPLAB is one of the best microcontroller dev environments,
 especially for the cost (free), though previously limited to Windows.
 They are moving to the GNU compiler for their 32 bit
 microcontrollers.  They have an iPhone dev kit (which requires an
 Apple hardware license, since Apple is closed hardware, which some
 here don't like) and now recently announced an Android dev kit: with
 "Arduino footprint compatible for prototyping", even.  I don't want to
 stir up a big hooplah between microcontroller choice, but I will say
 that Arduino using AVR is a more expensive choice any time I've looked
 at it.  A typical microcontroller + board + periphery should not cost
 more than $60 for wired internet-capable designs and within $10-30 for
 standalone designs.
 This kit below (quite new, so docs still forthcoming) might satisfy
 some people's needs. Who here is designing smartphone-biotech-related
 devices?  Why have a lab device if it can't connect to a smart phone,
 that's my thought.  The smart phone app is the new user interface;
 don't waste $ or time building user interface LCD/touch screen/buttons
 into a lab equipment box (unless there are clean-room restrictions).
  http://www.microchip.com and search for DM240415
 Approach to Develop Android¿ Accessories ($79.99)
 * Buy the PIC24F Accessory Development Starter Kit for Android 
 ($79.99)
 * Download the no-fee, royalty-free licensed software library
 * Contact androidsupp...@microchip.com for additional support
 PIC24F Accessory Development Starter Kit for Android  (DM240415)
 * PIC24F 16-bit PIC® MCU with USB OTG
 * Type A USB connector
 * User interface buttons
 * LEDs and potentiometer
 * Device charger circuitry up to 500mA
 * Arduino footprint compatible for prototyping 
 Perhaps compare to a CUI32 PIC32MX Development Stick ($40):
 http://www.sparkfun.com/products/9645
 or to Ethernet Mini-Web PIC18 Development Board ($42)
 http://www.sparkfun.com/products/7829
 To do that on Arduino, you'd need the main board plus ethernet shield
 board ($30 + $45.00 at Adafruit).
 I've played with a Teensy board (AVR, was $20, but not
 Arduino) and it's cheap and useful as a USB device (not USB
 host).  It is comparable but less scalable than the USB Bit
 Whacker - 18F2553 Development Board ($25),
 http://www.sparkfun.com/products/762 
Jonathan Cline on DIYbio google group
 I was at the Google I/O conference all day yesterday.
 One of the featured talks was about the new Android Open
 Accessory Development Kit, that allows hardware hackers to
 attach microcontrollers to the USB port and controll them with
 the phone:
 http://developer.android.com/guide/topics/usb/adk.html
 I will be connecting my Droid to one of these:
 http://focus.ti.com/docs/toolsw/folders/print/ez430-t2012.html
Simon Quellen Field on DIYbio google group
 Take a look at some low cost boards not Arduino branded by John Luciani.
 http://wiblocks.luciani.org/ZB1/index.html 
John Griessen on DIYbio google group

Human Biology Projects

"The Experimental Man" and similar ideas are based on the recent availability and affordability of personalized medical tests which expose and quantify one's own health factors. Some biohackers are monitoring these themselves, far beyond the scope of traditional modern medicine. Based on quantitative measurements, these biohackers are modifying their own biology using diet, vitamins, etc.

These related topics, especially diet, are highly controversial and it is generally not a good idea to attempt to convince others that you're "on to something."

Personal Medical Monitoring

 If I want to completely measure my biology, this is the list of
 everything I can think of which can be measured (non-invasively), on a
 daily basis, for uploading to a PC with a smart measurement device and
 tracking/logging. Are there others?  Listed in no particular order..
 * Body mass - with typical weight scale
 * Body temperature - probably using ear thermometer
 * Body fat - this would use calipers; not sure if there's an
 electronic method.
 * Height - though this shouldn't change normally
 * Blood pressure
 * Heart rate
 * Cholesterol test - LDL, HDL, triglycerides, uses pin prick (also
 quite pricey, and painful, for every day testing).  If pin prick is
 done for this, then should test ketone levels at the same time.
 * Walking cadence / Pedometer
 * Standing weight distribution - using smart body weight scale,
 similar to Wii Fit module, detect center of gravity from standing on
 the sensor, to detect structural imbalances
 * Hearing - with simple audio test
 * Blood glucose - more important for diabetics, of course
 * Breath analysis - chemical sensing: read ketones for diet
 monitoring.  Read nitric oxide to detect inflammation (I haven't
 checked if this test is low-cost-able, these are very expensive
 units).
 Other detectors are summarized here:
 http://www.chestnet.org/accp/pccsu/medical-applications-exhaled-breat...
 * Respiration - breathing flow, with a peak flow meter
 * Mental ability - a while back the experiment used simple math
 problems with a timed computer quiz, with the same math questions
 every time, to judge some aspect of mental ability.
 * Brain activity - SoCal DIYbio is actively doing this with EEG.  Not
 sure what kind of "daily health metric" might be possible to generate.
 * Sympathetic nervous system state - from galvanic response (as I
 posted previously, and FYI, Cornell has a great project write-up with
 software here, although the "professor's preference" of using Begin
 and End statements in C is something from outer space:
 http://instruct1.cit.cornell.edu/courses/ee476/FinalProjects/s2006/hm...
 * Voice recording - Although simple to record voice, I'm not sure
 there's any information which can be extracted from this. 
-- Jonathan Cline on DIYbio google group

Others:

pH
typing ability
blood oxygen saturation level via a cheap Pulse Oximeter 
(which uses a cool/clever optical sensing mechanism); 
http://en.wikipedia.org/wiki/Pulse_oximeter 
For vision, intraocular pressure: 
http://en.wikipedia.org/wiki/Tonometer 
Use GE's InBody Unit. It measures percent body fat using 
electrical impedance ... tells you the fat, muscle, and water 
composition of your torso and each limb. 
Grip strength ; well correlated with all sorts of things: 
http://www.fightaging.org/archives/2010/12/age-accumulation-correlates-with-a-common-measure-of-frailty.php

Brain Wave Measurement

"DIY electrophysiology Brain Recording Kits" http://www.backyardbrains.com/


Diet and Food

 Please contribute to this section.
  • See Calorie Restriction below.

Measure Food Effects or Quality

Edibles and Medicines

 Kitchen only -> play with yeast.  Make bread by hand.  Make
 cheese by hand.  Make beer (with a simple kit).  Make kimchi.
 Easily doable and is the basis for microbial biology.  Exotic
 stuff such as tempeh is simple as well.  Kombucha is also
 interesting.  I haven't found red yeast for purple pork, still
 looking for it.  The anti-bacterial effects of some of these
 foods is under scientific investigation and also they're very
 tasty.  Studies of chinese medicine were prominently featured
 at the last synthetic biology conference in Hong Kong.
 By the way, if you brew your own beer or Kombucha, you will
 suddenly find that you have a lot of friends.  That's more of
 a sociology experiment at that point.  :-D 
-- Jonathan Cline on the DIYbio google group
 Kombucha is interesting stuff, definitely an acquired taste.
 Big thing to bear in mind though is that Kombucha *needs* that
 30C growth temperature, moreso than most cultures. If you have
 pure yeast, perhaps they'll be ok at cooler temperatures and
 just grow more slowly. But Kombucha is a mix of up to 7
 species, and if the temperature is wrong some species will
 dominate more than normal, making for a bizarre and
 potentially disgusting brew.
 Interesting tidbit: I was researching Gluconacetobacter
 xylinum, the species that produces the most prodigious amounts
 of microbial cellulose in culture, and found that the highest
 quality cellulose to be isolated so far appears to have been
 from a strain of G.xylinum isolated from... Kombucha. Because,
 Kombucha has been selected for boyant, homogenous "SCOBY"
 pancakes of cellulose for generations, so we've effectively
 domesticated the strain to make the perfect cellulose. I
 imagine if you were to play with the mix of yeasts and
 G.xylinum, and feed them a bland sugar-nutrient mix to avoid
 colours, you could make some great premium paper! :) 
-- Cathal Garvey on the DIYbio google group

Longevity

 Please contribute to this section.


DIYbio - Growing movement takes on aging: http://hplusmagazine.com/articles/bio/diy-bio-growing-movement-takes-aging
Add Years to Your Life: What the anti-aging experts are doing now to live longer, better http://www.methuselahfoundation.org/files/newsletters/february2010/topstory.html Please note this is controversial research not yet quantitatively proven.

Longevity Research

 The Campaign Against Aging is interested in condensing and simplifying
 the vast amount of information that exists about the biology of aging
 and the work being done to combat age related damage.
 Below is a list of books that we think may be useful.  If you can add
 to the list, please do.  http://www.campaignagainstaging.org/
 Aging at the Molecular Level (Biology of Aging and its Modulation)
 Modulating Aging and Longevity (Biology of Aging and its Modulation)
 Aging of Cells In and Outside the Body (Biology of Aging and its
 Modulation)
 Aging of the Organs and Systems (Biology of Aging and its Modulation)
 Molecular Biology of Aging, Guarente
 Cellular Aging and Cell Death (Modern Cell Biology)
 Biology of Aging: Observations and Principles, Arking
 Biogerontology:  Mechanisms and Interventions 
-- Anonymous Poster on DIYbio google group


 Open Cures, a volunteer initiative to build a bridge between laboratory
 biotechnologies demonstrated to slow or repair aspects of aging and the
 developers who can bring this new medicine to the clinic. You can read about
 our aims at the Open Cures website: overview, background, and roadmap for
 future development: https://www.opencures.org 
-- Reason on DIYbio google group

Calorie Restriction

Plants, Fungi

Grow plants and fungi for fun.

Fungi

  • The Glow Fungi Project. Panellus stipticus is a non edible bioluminescent fungus, naturally occurring in Europe and North America. http://www.glowfungi.com/


Microscopes, Colorimeters, Spectrophotometers, "Cheaposcopes"

Spectrophotometers


Cheaposcope

Laser Projection Microscope

"Basically, they are just pointing a laser through a drop of water suspended from the tip of a syringe."


Microscope Heater

Objective heater. http://www.instructables.com/id/Objective-heater/

Microfluidics, Controller Boards, building Related Equipment

Introduction to Microfluidics

Using Jell-O for Hands-On Microfluidics chips

 Yes, store-bought Jello.  "Lemon-flavored Jell-O jelly powder was used
 because it
 produced chips with the best optical transparency."
 Yes, microfluidics.
 Yes, a good DIYbio introductory-to-microfluidics project.
 Open access article!   http://pubs.acs.org/doi/full/10.1021/ac902926x
 Anal. Chem., 2010, 82 (13), pp 5408¿5414
 DOI: 10.1021/ac902926x
 Cheng Wei T. Yang, Eric Ouellet and Eric T. Lagally
 University of British Columbia (Canada)
 Publication Date (Web): May 25, 2010
 Copyright © 2010 American Chemical Society
 "Using the Jell-O fabrication technique, microfluidics may be more
 easily demonstrated in a hands-on approach to convey current research
 topics to younger students and the general public. Our experience is
 that when students learn about science at a young age, they will
 become more attracted to pursuing an engineering or science degree in
 their post-secondary education. To encourage this process, three types
 of Jell-O chips have been fabricated: a ¿JELLO¿ chip, a Y-channel
 chip, and a pH sensor chip. Using these demonstrations, elementary and
 high school students, as well as the general public can learn about
 how microfluidic chips are made; learn microfluidics concepts,
 including dimensionless scaling factors, diffusion coefficients, and
 pH sensing; make the connection to current microfluidics research; and
 become excited about scientific research.
 The fabrication method is fast, simple, and inexpensive, allowing Jell-
 O chip demonstrations to enter a wide variety of learning environments
 not accessible to current microfluidics methods. Other types of chips
 (including bubble and droplet generators, not shown) can also be
 fabricated, suggesting that this technique possesses an enormous
 educational potential. Experiments with other naturally-occurring gels
 also indicate that this method could be extended to developing regions
 of the world to provide microfluidic technology both for education and
 diagnostics. Finally, we are also currently developing fabrication
 techniques for bonded and functional multilayer Jell-O chips to
 further extend the applications of this fabrication method. We hope
 that this work will serve as a model for future educational endeavors
 in science."
 Figure 1. Scheme for producing Jell-O chips using soft lithography.
 (A) A negative mold is made with desired features. (B) Liquid chip
 material is poured onto the mold. (C) Mold with liquid material is
 cured. (D) Solidified chip is peeled off and (E) placed on a rigid
 substrate for experiments.
 Figure 2. General workflow for producing Jell-O chips using soft
 lithography approach. (A) Foam plate and wooden coffee stirrers are
 starting materials for making the mold. (B) A negative mold is made
 with desired features using double-sided tape. (C) Jell-O and gelatin
 liquid mixture is poured onto the mold. (D) The molds with liquid
 material are left to cure in a 4 °C refrigerator. Solidified chips are
 peeled off and placed on aluminum pans for experiments at room
 temperature.
 Figure 4. (A) A Jell-O Y-channel chip with a Reynolds number of 30.
 The injection of colored water to one inlet and clear water to the
 second results in the classic laminar flow profile, in which both
 streams remain separate and mix solely by diffusion along the length
 of the channel. (B) Diagram of laminar flow diffusive mixing occurring
 at the interface between two different fluids along the channel
 length. This phenomenon is governed by the Pclet number (adapted from
 Kamholz).(25)
 Figure 5. Dual Jell-O chip pH sensor. (A) Two different pH sensing
 regions per channel can be used to detect different solutions. (B) The
 addition of either acidic or basic solutions to each channel results
 in a distinct pattern of color change visible to the naked eye. (C) pH
 indicator chart for reference (adapted from EM-Reagents).
 "SUPPORTING INFORMATION
 Detailed Chip Fabrication Protocol
 List of Materials Required for Jell-O® Chip Fabrication
 * Two 85g boxes of lemon-flavored Jell-O jelly powder (Kraft Canada)
 * One pouch (7g) of unflavoured (the Original) Knox Gelatine
 (Associated Brands
 LP)
 * 2 beakers of 120mL of purified water for dissolving Jell-O® and Knox
 Gelatine
 * Six 6¿ foam plates, round (Safeway Limited Canada)
 * One drinking straw, round (Safeway Limited Canada)
 * PAM® Original no-stick cooking spray (ConAgra Foods Canada Inc.)
 * Several 7¿ wooden coffee stirrers (Starbucks Coffee Company Canada)
 * Food-grade colour dye, green (McCormick Canada)
 * Single- and double-sided tape (3M Canada)
 * Six 5¿ aluminum weighing pan (Cat No. 12175-001, VWR International)
 Sources of Chemicals and Materials
 Lemon-flavored Jell-O Jelly Powder, unflavoured gelatin, round foam
 plates (6),
 drinking straws, no-stick cooking spray, wooden coffee stirrers (7),
 food-grade colour
 dyes, and single- and double-sided tape were obtained from local
 convenience stores."


Continuous Flow Microfluidics

Microfluidic Flow Device

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

DIY Spin Coater

 On Dec 3, 1:06 am, Nathan McCorkle <nmz...@gmail.com> wrote:
 > I want to make a spin coater using a highly UNMODIFIED cd or dvd rom.
 > Meaning I want to keep the laser mechanisms in place, and try to keep all
 > the moving parts as free from nasty buildup and grime.
 The electronics will have to be replaced or bypassed, for sure.  The
 couple times I've seen spin coaters used, the dispensing didn't seem
 critical (i.e. scoop polymer onto disc during spin up) and the
 rotation seemed to even everything out.  Does your protocol require
 baking the result, if so, better add some heat to the device right?
 References:
 Spin-Coating of Polystyrene Thin Films as an Advanced Undergraduate
 Experiment
 http://www.jce.divched.org/Journal/Issues/2003/Jul/abs806.html
 Abstract
 A simpler version of the well-established technique of spin-coating
 thin polymer films on glass slides is described. Starting with simple
 instrumentation and using an ordinary, commercially available cooling
 fan (a "CPU cooler"), a method of spin-coating an expanded polystyrene
 foam on glass slides is described. Making thin films of commercially
 available polystyrene on glass slides is also included for comparison.
 An interferometric technique is used to measure the film thickness
 employing a UV¿vis spectrophotometer. FTIR spectroscopy is used to
 verify the identity of the polymer on the glass slide. Using the Beer¿
 Lambert law of absorbance, the film thickness is also calculated from
 the FTIR spectra of films. A comparison is made between the
 interferometric and FTIR methods for thickness measurements. An
 organic dye is doped into a film and a UV¿vis spectrum is used to
 identify the dye.
 http://nathan.instras.com/projects/spin-coater/index.html
 Spin Coater System
 This was my attempt to build a low cost spin-coater system that does
 both horizontal and vertical spin coating.  For about $70.00 dollars
 in parts and some ingenuity, I was able to put together the system
 shown below.  Ironically, we latter purchased a commercial spin-coater
 for $5000.00, but I saw little difference in the sample prepared using
 the one I built and it.  In my opinion, the only reason to even buy
 one of those things is to get better control of the overall spinning
 process.  However, most people just need something that goes around
 fast. As you can see, it's basically just an aluminum base that holds
 two small DC motors (RadioShack).  Power is supplied by a 1-10V DC
 power supply.  CDR cases serve as the spin chamber.
 http://dx.doi.org/10.1016/j.porgcoat.2006.05.004
 Spin coater based on brushless dc motor of hard disk drivers
 Abstract
 We have developed a novel programmable, low cost, spin coater to be
 used for applications where flat substrates are coated with an uniform
 thin layer of a desirable material. The equipment is built with dc
 brushless motor present in most of the hard disk drivers (HDDs). The
 system offers manual control, wide speed range (from 0 to 10,000 rpm),
 spin speed stability and compact size. The paper also describes the
 use of such equipment for the fabrication of thin poly(o-
 methoxyaniline) (POMA) films, which are of particular interest for
 design organic electronic devices, such as diodes, transistor, sensors
 and displays.
 http://www.chemistry-blog.com/2007/01/13/pimp-my-spin-coater/
 Pimp My Spin Coater
 If you're going to start making your own lab equipment you might as
 well trick out the new hardware. In that spirit, my spin coater has 3
 light emitting diodes: a green one, a red one, and a blue one. I can
 vary the revolution per minute from ~500rpm to ~2500rpm by varying the
 voltage I supply to the spin coater. The sample is mounted in the
 center and is stuck to the spin coater by Velcro, this can be more
 easily seen in the next photo. As can also be seen in the photo, my
 spin coater is just a regular pc fan I bought at CompUSA this past
 Wednesday. I monitor the speed of the spin coater with a laser mounted
 above the spin-coater that shines through the fan's blades and strikes
 one of our group's alpha detectors. The nice thing about the alpha
 detector is that I don't even have to supply any power to it. There is
 enough current generated, I presume by the photoelectric effect, to
 carry a signal to an oscilloscope which I can use to monitor the fan's
 speed. A picture of the laser, which is my boss's laser pointer he
 uses for talks, is seen in the next photo at the top of our group's
 only non-radioactive chemistry hood. It took me 2 days to build my
 spin coater, Wednesday and Thursday, and one more day to make sure it
 calibrates properly, Friday. The total amount in extra costs was $20
 for the spin-coater(pc fan) all the rest of the equipment we had lying
 around.
 http://docs.google.com/viewer?a=v&q=cache:R929V8Bup34J:www.ccmr.corne...
 Title: Engineering Organic Light-Emitting Devices
 Appropriate Level: High School Regents Chemistry, or any advanced high
 school
 Chemistry course
 Using a spin coater is the ideal method for applying this ruthenium
 layer.  A simple
 device can be made using an 80mm fan and simple circuitry.  If a spin
 coater is not
 available, Q-tips and a heat gun can work to a certain degree:
 Use a Q-tip to apply some of the Ruthenium-tris(2,2¿-bipyridyl)
 tetrafluoroborate to the glass slide and then dry with a heat gun for
 3-5 minutes. 
-- Jonathan Cline, on DIYbio google group

Fermentors, Bioreactors, Photo Bioreactors

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 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)


Stirrer, Hot Plate

"DIY Stirrer/Hot Plate". http://www.instructables.com/id/DIY-StirrerHot-Plate with video http://www.youtube.com/watch?v=YKWimlx2_44



Incubator, Shaking Incubator



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.

shake1.gif

Figure 2: Additional Parts for the Shaking Incubator.

shake2.gif

Figure 3: Portrait of the Final Product.

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

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

Thermocycler / PCR

Light Bulb PCR - http://vimeo.com/18827627


Laser Tools

Inexpensive laser shutters using common electronics!
"DIY Laser Shutter" http://www.instructables.com/id/DIY-Laser-Shutter/
Pranav's air freshener laser shutter. http://openwetware.org/wiki/User:Pranav_Rathi/Notebook/OT/2010/10/31/Laser_Shutter_.1
Laser Tweezer Enclosure
http://openwetware.org/wiki/User:Anthony_Salvagno/Notebook/Research/2010/09/17/Tweezer_Enclosure_Creation

Gene Gun

 You can make your own gene gun using either a modified pellet
 gun, or by turning a diaphragm valve on a lathe and pulsing a
 low-density high-pressure gas to a small aperture, or by
 shooting a prepped wall of a vacuum chamber to disperse a
 prepared nug of DNA coated fine metal particles with a small
 arm (don't do this).
 Here's a video that'll give you a good idea of how they can be
 used, they're good for transforming most things.
 Also be aware the video contains a rat brain being autopsied.
 http://www.jove.com/details.php?id=675 
 The manufacture of the ammunition is the tricky part, it
 involves engineering the DNA payload and binding it to very
 small tungsten or gold particles. The process is outlined in
 the video, note the part where the plastic tube is filled with
 dried metal-bound dna and cut up to make bullets. 

-- Forrest Flanagan on the DIYbio google group

Homebrew Centrifuge

Warning: Building a high speed device is dangerous. Take appropriate measures to ensure safety.

Physics

Jonathan Cline: A basic equation of physics, for those out there building their own centrifuges: What are RPM, RCF, and g force and how do I convert between them? The magnitude of the radial force generated in a centrifuge is expressed relative to the earth’s gravitational force (g force) and known as the RCF (relative centrifugal field). RCF values are denoted by a numerical number in “g” (ex. 1,000 x g). It is dependent on the speed of the rotor in revolutions per minute (RPM) and the radius of rotation. Most centrifuges are set to display RPM but have the option to change the readout to RCF. To convert between the two by hand, use the following equation: RCF = 11.18 (rcm) (rpm/1000)^2 Where rcm = the radius of the rotor in centimeters. http://88proof.com/synthetic_biology/blog/archives/380

Dremelfuge

Cathal Garvey has designed a simple centrifuge using open source hardware technology, and you can order one yourself! Dremelfuge is a rotor designed to fit standard lab microcentrifuge tubes and miniprep/purification columns, to be spun by either a powerdrill or other chuck-loading machine or by a popular rotary tool. Dremelfuge features an easy click-in loading system which holds tubes parallel to the plane of rotation for optimum pelleting and delivery of force. Intended basic applications of Dremelfuge include column purification (tested to work with miniprep columns) and bacterial/cell debris pelleting (under testing). With standard microcentrifuge tubes, the average rotary distance is 4cms. Results are shown with the Dremelfuge used to pellet E. Coli samples. Dremelfuge is open-source hardware. Source files are available on Thingiverse, linked from the items on Shapeways. The Creative Commons license used entitles copying, sharing and remixing for any non commercial purpose. Please consider that professional printing services qualify as commercial use.

Two editions of Dremelfuge are available for purchase at http://www.shapeways.com/shops/labsfromfabs

Open Source Gel Boxes

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


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
Personal tools