DIYbio FAQ v1.0 - copied on 4/7/2009 from heybryan.org...DIYbio_FAQ - update mercilessly

There have been many amazingly useful discussions on the mailing list, but unfortunately we collectively forget what we have talked about because we haven't yet assembled a FAQ to give to new members. Where can they possibly buy supplies? Where can they read up on protocols? What books have been recommended to DIYbio amateurs in the past? And so on. There is a lot of good information. So, how can you help this FAQ? The biggest thing at the moment would be to go through the mailing list and find three of the most insightful and useful topics that you've seen there. It's okay if you started it, or if you were the one who started asking the question, as it's probably something valuable, and just add it to the bottom of the page, or try to fit it into a category or question that others probably have. This way, we can begin to build up this document to a somewhat reasonable state.

What is DIYbio, as an organization?

DIYbio is an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety. This will require mechanisms for amateurs to increase their knowledge and skills, access to a community of experts, the development of a code of ethics, responsible oversight, and leadership on issues that are unique to doing biology outside of traditional professional settings.

DIYbio is a distributed community of amateur biologists. Our activities range across a broad spectrum, from molecular naturalism (sequencing part of your own genome or bacterial populations) to biological engineering (RFP lactobacillus -> melanometer) to building low-cost, open-source alternative lab equipment (Gel Box 2.0).

<html> <div style="float:left;"><object width="560" height="315"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="http://vimeo.com/moogaloop.swf?clip_id=3454392&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=00ADEF&fullscreen=1" /><embed src="http://vimeo.com/moogaloop.swf?clip_id=3454392&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=00ADEF&fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="560" height="315"></embed></object><br /><a href="http://vimeo.com/3454392">The DIYbio Community - Presented at Ignite Boston 5 (2009)</a> from <a href="http://vimeo.com/macowell">mac cowell</a> on <a href="http://vimeo.com">Vimeo</a>.<br /><br /></div> <object width="560" height="340" style="float:left;"><param name="movie" value="http://www.youtube.com/v/-IIWH6Hhcnc&hl=en&fs=1&rel=0"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/-IIWH6Hhcnc&hl=en&fs=1&rel=0" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object> <div style="clear:both"> </div><br /> </html>

What is DIYbio's mission?

Are we moving to a future where everyone performs a little genetic engineering?

How can I get involved?

Many ways! Here's a brief overview:

mailing list (most activity) (note the discussion on the list's standards)
IRC (#diybio on irc.freenode.net)
local groups

So far, we mainly communicate through the mailing list, which is where the majority of people are listening in on the conversations and discussions. Since the volume of discussion can be extreme, there is also a very low volume DIYbio announce mailing list, which occassionally has announcements that the community might be interested in. Also, there are groups for San Francisco, Chicago, New York (city), London, and Boston.

You're welcome to show up on the mailing list- in fact, we encourage it. Just be sure to follow conventional netiquette rules. Historically, the main DIYbio mailing list hasn't really set its foot down regarding top versus bottom posting (or even side posting or diagonal posting), but please do be kind and trim your replies. Reading about netiquette wouldn't be a bad idea.

There are also some forums that nobody uses: biopunk.org, diybioforum.org, ...

Is there a group in my area?

There's probably a group nearby- maybe at least somebody somewhat interested in getting together for lunch or maybe sitting down over a bench and doing serious experiments- at any rate, you can find out about those near you by checking out the map below or diybio.org/local.

<a href="http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&ll=42.358163,0.0&z=2&spn=0,0&msid=117373025318808082442.00045fd549f07830e0465&source=embed">View a larger map, or to add yourself or your group to the map.</a> You'll need to sign into your Google account in order to add a new point. It's a little unclear, so here's a <a href="http://skitch.com/jasonmorrison/bycdy/add-a-point.png-png-image-864x494-pixels-scaled-70">screenshot of adding a new point</a>. </html>

Are there any videos from regional groups?

DIYbio-NYC: Shot glass DNA extraction

DIYbio-SF: Tito's food coloring electrophoresis

DIYbio-boston: diybio visits the fablab

Where can I see an archive of previous DIYbio discussions and questions?

Right over here.

Some of our favorites ("member picks") include discussions on ..

Public perception
your favorite thread here

What is synthetic biology?

Synthetic biology is an attempt to apply the engineering techniques developed over the last century to enable construction and operation of complex systems to biology. Succinctly, Synthetic Biology is the set of technologies that enables the biological engineer to accelerate the engineering cycle, taking less time to iterate through device design to modeling, construction, testing/measurement, and (re)design.

Professor Drew Endy explains that Synthetic Biology techniques are built on top of the foundational technologies of genetic engineering (PCR, oligonucleotides, and DNA sequencing) and are include abstraction, standardization (i.e., biobricks), and automated DNA synthesis. Insulation and Standard Measurement Units (i.e. signal carriers) in biological systems are also significant interests in current synthetic biology research. See also syntheticbiology.org.

Drew Endy - Informal - Broad overview

What are biobricks?

iGEM?

iGEM, the international genetically engineered machine competition, is the premiere undergraduate synthetic biology conference in the world and the main driver of the production of standard biological parts. iGEM teams have been testing and realizing the principles of synthetic biology on a massive scale for the last 5 years and are an existence proof for the viability of garage biotechnology. Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. Check out igem.org or wikipedia for more info.

Videos

See DIYbio/Videos for a collection of DIYbio, iGEM, and Synthetic Biology videos.

Do you recommend any books, guides, periodicals, journals, feeds, blogs, wikis, instructables, .. ?

Safety documentation

This section is for safety documentation from external bodies. DIYbio-related safety information should be found elsewhere.

Laboratory Biosafety Guidelines 2004

Legal issues

Are gray. Email safety@diybio.org to get involved in the discussion.

we need to understand and work on LICENSE COMPATIBILITY for software, hardware, and wetware objects and on a SOCIAL CONTRACT for our community that exhorts innovators to use the "OPEN" licenses.

BioBricks (legal stuff)

What's all this about "open", anyway?

What's all this about "open", anyway? is a long "copy-and-paste" essay about open source as it relates to do-it-yourself biology, biotechnology, science, patents, open source hardware, open wetware, and so on. It was meant to be an introduction to the topics of open source, free software, and how "open source" software communities typically exist. In particular it was written during one of the spikes in new mailing list subscriptions in late 2008.

A note about the ambiguous use of "open source" as a buzzword
other stuff here that time has forgotten (it would be nice to port the entire "what's all this about open, anyway" essay on to this wiki)

What equipment is in a basic biology lab?

.. and how can I make it?

Would you like to contribute to an answer for this question? Run around a lab that you have access to and document all of the equipment that you see, or remember, etc. It's ok if some of the equipment is ridiculous (like 100k+ RPM centrifuges), because we can filter that out later and reduce the lists down to equipment in a basic biology lab.

Using ebay to set up a molecular bio lab for less than $1k USD (see also [1] and [2])

MacGyverisms

Cheap technology for biology
CO-2 rich environment in a ziplock baggie
gel electrophoresis in a straw (keiki gels)
inkjet, laser printer, wax, ice-lithography, sharpie, or other forms of diy microfluidics
5 minute DNA extraction in a shot glass

Where can I find auctions for biotech?

Are there any plans for a DIYbio-friendly file format for protocols, instructions and hardware?

Yes, absolutely. You should consider contacting Bryan Bishop about this. There is also a lot of reading material distributed throughout the web on this topic.

An index of threads related to open manufacturing and standardized packaging of open source hardware projects
Recipe representation
Recipe representation as it concerns DIYbio
More on recipe representation (especially re: an open thermocycler project)
More on protocols and hardware packaging formats (2009-04-15) (see also Meredith's notes)
other links here.

What is open source hardware?

http://p2pfoundation.net/Open_source_hardware

"Open Source Hardware is hardware that keeps its designs available in a way similar to the open source in software." There is no defacto license for open source hardware yet. Some websites (like ponoko, thingiverse, unptnt) put hardware CAD files under a "Creative Commons" license. However, it's still unknown how this is likely to interface with the legal systems around the world (i.e., patents). And it's not necessarily true that putting something directly into the public domain is the best way to go either. So, the future is presently unclear- in terms of legal issues.

DIYbio has many big supporters of standardized packaging formats (like .tar.gz, .deb, .tar, .rpm, etc.) for automatic downloading of hardware components and instructions on how to build the components. There are some sites that almost implement this (but not quite) such as instructables, ponoko, thingiverse, odesigns, unptnt, etc.

other notes here

Slashdot discussions

Has DIYbio been in the news?

Yes.

June 2009 issue of Gourmet magazine [3]
2009-05-18: In attics and closets, "biohackers" prove the spirit of Thomas Edison endures
2009-05-12: In Attics and Closets, 'Biohackers' Discover Their Inner Frankenstein
2009-03-18: The Geneticist in the Garage
2009-01-19: DIY DNA: One Father's Attempt to Hack His Daughter's Genetic Code
2009-01-07: Rise of the garage genome hackers
2008-12-30: Students, Scientists Build Biological Machines (transcript) (Lehrer on PBS) (video)
2008-12-25: Amateurs are trying genetic engineering at home (Slashdot)
2008-12-18: Público: Biohackers: reventar y reinventar la biología desde los garajes
2008-12-11: The Biohacking Hobbyist
2008-09-15: Hackers aim to make biology household practice
many, many other occurences- keep sending them in
- also, there have been many news stories from the pre-DIYbio era which should be in this list

Keiki gels (gels-in-a-straw) MiniFAQ

Do all of the straws run at the same rate?

"I think the key there will be making sure that all the straws are exactly the same length -- each straw behaves like a resistor, so just like any other resistive material, a greater amount of material will mean a higher resistance (and thus lower current at constant voltage)." -- Meredith

How do you strain for DNA in a straw?

"Easiest way to do that would be to use a stain that you add to the warm agarose before pouring, such as SYBR Safe or GR Safe (or ethidium bromide, but the cool kids don't use that anymore). I suppose you could slit the straw open with a razor blade if you wanted to use methylene blue, but that sounds like a huge pain in the ass." -- Meredith

What equipment do I need to perform experiment XYZ?

Just run it through the handy "checktools" program. ((Note: the idea here is that once the pcr.xml file makes a few friends with other protocols, software can then be written to extract a list of tools from the standardized protocol format. But this doesn't exist yet, since we only have "pcr.xml".))

Genetic engineering

DNA synthesis MiniFAQ

Can I order DNA over the internet?

mrgene, e-oligos, geneoracle, etc.

What are oligonucleotides?

Wikipedia sez: "An oligonucleotide is a short nucleic acid polymer, typically with twenty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized by polymerizing individual nucleotide precursors. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases. The length of the oligonucleotide is usually denoted by "mer" (from Greek meros, "part"). For example, a fragment of 25 bases would be called a 25-mer. Because oligonucleotides readily bind to their respective complementary nucleotide, they are often used as probes for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarrays, Southern blots, ASO analysis, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes. Oligonucleotides composed of DNA (deoxyoligonucleotides) are often used in the polymerase chain reaction, a procedure that can greatly amplify almost any small piece of DNA. There, the oligonucleotide is referred to as a primer, allowing DNA polymerase to extend the oligonucleotide and replicate the complementary strand."

How are oligonucleotides synthesized?

Oligonucleotide synthesis is done via a cycle of four chemical reactions that are repeated until all desired bases have been added:

Step 1 - De-blocking (detritylation): The DMT is removed with an acid, such as TCA (get it at Sigma-Aldrich), and washed out, resulting in a free 5' hydroxyl group on the first base.
Step 2 - Base condensation (coupling): A phosphoramidite nucleotide (or a mix) (struct, synthesis of phosphoramidite building blocks [pdf]) is activated by tetrazole (get) which removes the iPr2N group on the phosphate group. After addition, the deprotected 5' OH of the first base and the phosphate of the second base react to join the two bases together in a phosphite linkage. These reactions are not done in water but in tetrahydrofuran (get) or in DMSO (get). Unbound base and by-products are washed out.
Step 3 - Capping: About 1% of the 5' OH groups do not react with the new base and need to be blocked from further reaction to prevent the synthesis of oligonucleotides with an internal base deletion. This is done by adding a protective group in the form of acetic anhydride (get) and 1-methylimidazole (get)which react with the free 5' OH groups via acetylation. Excess reagents are washed out.
Step 4 - Oxidation: The phosphite linkage between the first and second base needs to be stabilized by making the phosphate group pentavalent. This is achieved by adding iodine (go to local store) and water which leads to the oxidation of the phosphite into phosphate. This step can be substituted with a sulphorylation step for thiophosphate nucleotides.

(Note: this might be a good document to see how phosphoramidites can be ordered from suppliers.) Here are some oligo synth protocols in molecbio. Quantifying oligos from phosphoramadite synth. Note that you may not have to actually purchase phosphoramadites to start off with, but instead begin with a purified solution of nucleic acid??

What are the origins of oligonucleotide impurities and errors?

See here.

Microfluidics MiniFAQ

DIY microfluidics for continuous liquid flow using toner transfer (How To)

The following is a run of the example microfluidics T-junction simulation in elmer, an open source CFD/FEM/FEA package. What you see here is the progression of an analyte due to electro-osmotic flow. There are two electric fields, three boundary conditions and a lot of wasted hours playing around with ElmerGUI and ElmerFront.

What are microfluidics?

Wikipedia sez: Microfluidics deals with the behavior, precise control and manipulation of fluids that are geometrically constrained to a small, typically sub-millimeter, scale. Typically, micro means one of the following features: small volumes(nl, pl, fl); small size; low energy consumption; effects of the micro domain (i.e., laminar flows, surface tension, diffusion, Marangoli forces, capillary forces, ...).

What is a lab on a chip (LOC)?

A lab-on-a-chip (LOC) is a device that integrates one or several laboratory functions on a single chip of only millimeters to a few square centimeters in size. LOCs deal with the handling of extremely small fluid volumes down to less than pico liters. Lab-on-a-chip devices are a subset of MEMS devices and often indicated by "Micro Total Analysis Systems" (µTAS) as well. Microfluidics is a broader term that describes also mechanical flow control devices like pumps and valves or sensors like flowmeters and viscometers. However, strictly regarded "Lab-on-a-Chip" indicates generally the scaling of single or multiple lab processes down to chip-format, whereas "µTAS" is dedicated to the integration of the total sequence of lab processes to perform chemical analysis. The term "Lab-on-a-Chip" was introduced later on when it turned out that µTAS technologies were more widely applicable than only for analysis purposes.

Ultimately the idea is to have all of the typical components, procedures and processes of a laboratory available on a "chip", on a single perhaps disposable device, rather than having to build or purchase bulky equipment that sometimes tends to be hard to acquire or learn about.

Appendix 1 - list of Synthetic Biology Companies

DIYbio/FAQ