DIYbio/FAQ: Difference between revisions

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* 1.0 - copied on 4/7/2009 from [http://heybryan.org/mediawiki/index.php/DIYbio_FAQ heybryan.org...DIYbio_FAQ]
* 1.0 - copied on 4/7/2009 from [http://heybryan.org/mediawiki/index.php/DIYbio_FAQ heybryan.org...DIYbio_FAQ]
* 1.1 - some updates to clarify original version
* 1.1 - some updates to clarify original version
* 1.2 - new sections, + sections about agar DOI:10.1007/BF00152620 --'''[[User:Jonathan Cline|jcline@ieee.org]] 12:28, 16 September 2009 (EDT)'''
* 1.2 - new sections, reorg, + sections about DIY agar DOI:10.1007/BF00152620 --'''[[User:Jonathan Cline|jcline@ieee.org]]'''


= What is DIYbio, as an organization? =
= What is DIYbio, as an organization? =
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= What are some educational resources for DIYBio and Biology? What are all these terms and technologies DIYBio keeps discussing? =
= What are some educational resources for DIYBio and Biology? What are all these terms and technologies DIYBio keeps discussing? =


(This section to be split off into [http://openwetware.org/wiki/DIYbio/FAQ/Educational_Resources].)
See [http://openwetware.org/wiki/DIYbio/FAQ/Educational DIYBio FAQ: Education & Resources]
 
There are many biology and science resources on the net, especially with universities providing "open course ware" for viewing or download.  Here are a few university-sponsored educational resources which apply to biohacking.
 
* MIT OpenCourseWare (also on iTunes)
* UC Berkeley educational webcasts: Biology, Chemistry, Chemical Engineering, etc.
* Many universities are hosting classes (such as Biology) on YouTube
 
Here are a few industry-sponsored or non-profit-sponsored educational resources which apply to biohacking.
 
* A SHORT COURSE ON SYNTHETIC GENOMICS, Edge Master Class 2009, George Church & J. Craig Venter.  http://www.edge.org/documents/archive/edge296.html
 
 
== Do you recommend any feeds, blogs, wikis, instructables, .. ? ==
 
== Safety documentation ==
This section is for safety documentation from external bodies. DIYbio-related safety information should be found elsewhere.
 
* [http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/ Laboratory Biosafety Guidelines 2004]
 
 
== What is synthetic biology and related technology? Does DIYBio do Genetic Engineering? ==
 
: Synthetic Biology: A Definition <sup>[From Davidson College's Synthetic Biology Seminar in the Fall of 2007]</sup>
:: [[Synthetic biology]] refers to the design and construction of novel biological systems. Applying an engineering approach to biology, this emerging field provides an opportunity to: 1) develop new organisms that are capable of performing useful functions and 2) test our understanding how complex biological systems work.
:: In 1978, the Nobel Prize in Medicine went to Werner Arber, Daniel Nathans, and Hamilton O. Smith for the discovery of restriction enzymes. This discovery marked the beginning of recombinant DNA technology and genetic engineering. Researchers now had the ability to modify the genomes of organisms by cutting and pasting segments of their DNA. For years, genetic engineers have made slight genome modifications in organisms, either by the insertion or deletion of one or two genes, in order to observe phenotypic changes. More recently, as our knowledge of biological systems has grown, the new field of synthetic biology has begun to steal the spotlight. This field builds on the principles of genetic engineering, but attempts to modify genomes on a much larger scale. Instead of inserting or deleting one or two genes, synthetic biologists use recombinant DNA technology and, increasingly, artificial DNA synthesis to introduce whole gene networks into organisms. Because of its complex nature, synthetic biology brings together many different disciplines such as biology, math, engineering and chemistry to try to engineer genomes using preexisting and new biological systems and components. Mathematical modeling enhances the design of synthetic systems before implementation in the wet lab. The possible areas of influence for such biological devices are seemingly infinite, ranging from the production of reusable biofuels to the treatment of some or all cancers. The ultimate goal of synthetic biology is to both build novel (new) biological systems and to create a better understanding of existing ones.
 
: Also see http://syntheticbiology.org/FAQ.html
 
 
=== Drew Endy - Informal - Broad overview ===
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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., [http://biobricks.org/ 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 [http://syntheticbiology.org/ syntheticbiology.org].
 
=== What are BioBricks? ===
 
BioBricks can be described as Lego blocks for building biological systems.  However they are in "alpha" state and do not yet work for building arbitrary biological systems.  Research needs to be completed and this research will take at least another decade <sup>[1st hand quote from personal conversation with BioBricks founders -- jcline]</sup>.  As of 2009, less than five Biobrick parts have been characterized with reliable and quantifiable behavior.
 
* http://biobricks.org/
* http://partsregistry.org/
 
=== What is iGEM? ===
iGEM, the international genetically engineered machine competition, is the premiere undergraduate synthetic biology conference in the world using and developing Biobricks.  iGEM teams have been testing and realizing the principles of synthetic biology on a massive scale for the last 5 years, illustrating 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 [http://igem.org igem.org] or [http://wikipedia.org/en/wiki/iGEM wikipedia] for more info.
 
== See also ==
* [http://syntheticbiology.org Syntheticbiology.org] Join this mailing list (it's worth it).
* [http://parts2.mit.edu/wiki/index.php/Main_Page Internationally Genetically Engineered Machines Competition] (see [[iGEM]])
* [http://biobricks.org/ The BioBricks Foundation] (see [[biobricks]])
* [http://parts.mit.edu/ Registry of Standard Biological Parts]
* [http://arep.med.harvard.edu/SBP/ List of synthetic biology projects]
 
== Videos ==
See [[DIYbio/Videos]] for a collection of DIYbio, iGEM, and Synthetic Biology videos. For background history on the free software movement, GNU, Richard Stallman, Linus Torvalds, and others, consider watching the freely available video, "[http://video.google.com/videoplay?docid=7707585592627775409 Revolution OS]" ([http://www.revolution-os.com/ official site]). [http://en.wikipedia.org/wiki/Revolution_OS Wikipedia says]: "Directed by [http://en.wikipedia.org/wiki/J._T._S._Moore J. T. S. Moore], the film features interviews with prominent [http://en.wikipedia.org/wiki/hacker_(free_and_open_source_software) hackers] and [http://en.wikipedia.org/wiki/entrepreneurs entrepreneurs] including [http://en.wikipedia.org/wiki/Richard_Stallman Richard Stallman], [http://en.wikipedia.org/wiki/Michael_Tiemann Michael Tiemann], [http://en.wikipedia.org/wiki/Linus_Torvalds Linus Torvalds], [http://en.wikipedia.org/wiki/Larry_Augustin Larry Augustin], [http://en.wikipedia.org/wiki/Eric_S._Raymond Eric S. Raymond], [http://en.wikipedia.org/wiki/Bruce_Perens Bruce Perens], [http://en.wikipedia.org/wiki/Frank_Hecker Frank Hecker] and [http://en.wikipedia.org/wiki/Brian_Behlendorf Brian Behlendorf]."
 
== Legal Discussions ==
 
Legal discussions include both patent issues and safety-regulatory issues.
Email safety@diybio.org to get involved in the discussions of safety.
 
* [http://groups.google.com/group/diybio/msg/0816447f7bd9c274 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.]
 
=== Legal Discussions from the BioBrick Foundation ===
* [http://biobricks.org/pipermail/legal_biobricks.org/2008-September/000019.html Drew Endy: update on legal matters, including hiring a legal firm]
* [http://biobricks.org/pipermail/legal_biobricks.org/2008-September/000021.html Bootstrapping an open parts collection]
* [http://www.youtube.com/profile?user=BioBricksFoundation&view=videos&query=legal Videos of the BioBrick Foundation talking about legal concerns]
 
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== What's all this about "open", anyway? ==
 
This is the desire to continue to apply [http://sciencecommons.org/about/ open source concepts] to biology and related fields for great benefits.
 
"Open" means sharing the biological protocols, the instructions for building the equipment and sources of the materials, the directions for using the equipment, the source code of the software used for the equipment, the raw data from the experiment, the results and any other aspects of the experimental process, in a digital format, on the internet.  All of this sharing occurs under typical information technology process (such as on a wiki, or source control, or open database) so that revisions of documents and data can be compared or copied to a new method (called "branching" in software terms).  The sharing can be performed under a variety of [http://creativecommons.org/about/licenses/ permissions such as open source licenses] which allow others to re-use, modify and distribute their own designs of the technology.  Benefits:
* Patents. By using "Open" methods, [http://www6.miami.edu/ethics/jpsl/archives/papers/biotechPatent.html patent lockup (a big complaint in biotechnology)] is reduced. The hope is that "Open" will energize innovation in biology similarly to how "Open" has performed in computer/software engineering. 
* Collaboration.  Even nearing 2010, much of the raw data, working methods, or equipment improvements in biology are kept in hand-written lab notebooks in biology labs, so there are large gains to be made by moving towards "Open".  Access to scientific data can regain openness through open access publishing, as stated in the ''Public Library of Science FAQ'': [http://www.plos.org/about/principles.html Access to the vast majority of scientific and medical literature is currently restricted to those individuals and institutions that can afford to pay for subscriptions. Even though the vast majority of the research is publicly financed, access to research literature—the product of that research—is not freely and publicly available. Even institutions find it increasingly difficult to provide access to all the journals that their communities need. The Internet makes it possible to provide access to the literature to anyone in the world who has an Internet connection.]
* Re-use and cost.  As biology is inherently self-reproducing, it has the ability to make low-cost copies of itself for users.  The copies may also allow modification and re-design.
 
 
Background and References:
 
* [http://www.synbioproject.org/events/archive/opensource/ Synthetic Biology: Feasibility of the Open Source Movement].
* [http://onthecommons.org/content.php?id=436 A New Movement for Open Source Biology Is Launched.  16 Dec 2004].
* [http://rsss.anu.edu.au/~janeth/OpenSourceBiotechnology27July2005.pdf J Hope, Open Source Biotechnology (PhD Thesis), The Australian National University, Canberra, 2004].
::''Dramatic recent expansion of intellectual property protection in the field of biotechnology has led to concerns that ongoing innovation will be blocked unless actionis taken to preserve access to and freedom to operate with those tools that are important for further research and development.''
* [http://synthesis.cc/2007/03/thoughts-on-open-biology.html Thoughts on Open Biology, Rob Carlson, March 2, 2007]. [http://www.synthesis.cc/Biol_Tech_2050.pdf "Biological Technology in 2050", Robert Carlson, 2001].
:: ''A great deal of the innovation we need to see will not come from academia or existing corporations, but from people noodling around in their garages or in start-ups yet to be founded.''




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= What Projects has DIYBio completed?  What projects are DIYBio contributors working on now?  How do I offer to collaborate on a project? =
= What Projects has DIYBio completed?  What projects are DIYBio contributors working on now?  Who is working on what?  How do I offer to collaborate on a project? =


This section to be written soon.
This section to be compiled from many sources soon.




Revision as of 21:35, 16 September 2009

DIYbio FAQ v1.2: "The biohacker's FAQ"

Please update this FAQ mercilessly with Q&A !


This Frequently Asked Questions document is for the DIYBio mailing list. This FAQ is now split into multiple topics for easier reading.


FAQ Revision History

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 or professional biologists, industry professional or amateur engineers, biomedical engineers, life scientists, computer scientists, etc. Our activities range across a broad spectrum, from molecular naturalism (sequencing part of your own genome or bacterial populations) to biological engineering to building low-cost, open-source alternative lab equipment (Gel Box 2.0) to writing open source software for biology, to creating open source hardware systems and manufacturing.

<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&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=00ADEF&amp;fullscreen=1" /><embed src="http://vimeo.com/moogaloop.swf?clip_id=3454392&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=00ADEF&amp;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?

Who is a "biohacker"?

How can I find out more and contribute?

Many ways! Here's a brief overview:

So far, we mainly communicate through the mailing list. There is also a lower volume DIYbio announce mailing list, which occassionally has announcements that the community might be interested in. Also, there are groups for:

You're welcome to subscribe to the mailing lists- in fact, we encourage it.

There are other forums:

What are the Guidelines for Posting to the DIYBio mailing lists and/or Forums?

As the DIYBio mailing list membership grows, it is more important to follow good guidelines for easier readability within discussions.

Please:

  • Follow conventional netiquette rules.
    • When quoting another author, keep the attribution line ("On such-and-such-date, Jonathan Cline wrote:").
    • Delete portions of the paragraph which do not pertain to the new reply. This is known as "Trimming the post".
      • Replace deleted text with "[...]" if it changes the placement of words or sentences in a paragraph.
  • Trim all quoted text to be the minimum necessary to follow the discussion.
  • Add your message below any quoted text. This means "write your reply at the bottom".
    • Do not "top post". "Top posting" is when the reply is added above the quoted text. This is not as easy to read when there are many replies in a thread. For this reason, do not "top post", only add the reply at the bottom.
  • Change the 'Subject' of the email when the topic changes.


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

Right over here.

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


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.

<html> <iframe width="575" height="350" frameborder="0" scrolling="no" marginheight="0" marginwidth="0" src="http://maps.google.com/maps/ms?ie=UTF8&amp;hl=en&amp;msa=0&amp;ll=42.358163,0.0&amp;z=1&amp;spn=0,0&amp;msid=117373025318808082442.00045fd549f07830e0465&amp;output=embed&amp;s=AARTsJqk9drOPzgJzPIckjwHnoC0bQwDAA"></iframe><br />

<a href="http://maps.google.com/maps/ms?ie=UTF8&amp;hl=en&amp;msa=0&amp;ll=42.358163,0.0&amp;z=2&amp;spn=0,0&amp;msid=117373025318808082442.00045fd549f07830e0465&amp;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. Here's a <a href="http://skitch.com/jasonmorrison/bycdy/add-a-point.png-png-image-864x494-pixels-scaled-70">screenshot of how to add a new point on the map</a>. </html>

You may also be interested in other local science groups around the world:

Are there any videos from regional groups?

DIYbio-NYC: Shot glass DNA extraction

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DIYbio-SF: Tito's food coloring electrophoresis

<html><div style="clear:both;"></div></html>

DIYbio-boston: diybio visits the fablab

<html><div style="clear:both;"></div></html>


Has DIYbio been in the news?

Yes.


What are some educational resources for DIYBio and Biology? What are all these terms and technologies DIYBio keeps discussing?

See DIYBio FAQ: Education & Resources


What equipment do I need to perform DIYBio-related projects?

See DIYBio FAQ: Equipment


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.

'Slashdot discussions


What Projects has DIYBio completed? What projects are DIYBio contributors working on now? Who is working on what? How do I offer to collaborate on a project?

This section to be compiled from many sources soon.


Appendix 1 - list of Synthetic Biology Companies

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