BioBarCamp topic/session suggestions

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Attila Csordas

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Jun 3, 2008, 1:50:34 AM6/3/08
to bioba...@googlegroups.com
Hi All,

This will be a lengthy email (sorry), but with good chance, it covers a lot of topics that will be discussed at BBCAmp. The reason for that length is that I include the
Tentative Table of Contents of the so called BioTech Geek Guide as I would like to organize the closing session of the BBCamp with Deepak and Ricardo with the interactive participation of you all. Let me explain:

The Biotech Geek Guide is also an idea fed by a Twitter stream, just like the BBCamp idea. Deepak complained about the tech world's ignorance about health & genetics (a recurrent theme) and then I suggested to write/edit/compile a biotech, biology book for IT folks specially and publish it as an O'Reilly book. O'Reilly Books have the fame of being the definitive guides, intros, manuals in their technolgical fields. Ricardo came into the conversation too and 10 minutes later I emailed Tim O'Reilly with the suggestion and got almost instantly a very positive answer back followed by a detailed Proposal Guidelines that needs to be filled out to set up a schedule in order to get a final Yes or No answer to the publishing of the book. So we started to work (just a little in the lack of time) on it and I copy here what we've done basically the Book Outline/Tentative Table of Contents. The concept of the book later transformed into the Biotech Geek Guide which is too collect every cool, major topic together that could be of interest for a rookie/advanced biogeek, who is usually tech-savvy and biotech-savvy too.

And so we have an idea, an option to make a product (a book) out of it, and define or delineate the knowledge-base and topic sensitivity of current biotechnology, life sciences well tailored for IT people but we lack an essential component that is behind every good animal covered O'Reilly tech book: we lack the creative and critical community and we need authors and commenters in the spirit of open source and science. (That community also starts to form on FriendFeed as The Life Scientists room, earlier form is a simply Biotecher register at Twitter.)

But I think that the BioBarCamp could collect together exactly the Community that is needed for the succession of that book and the whole biogeek culture!!! The authorship, content and schedule is totally open at that point (publishing an O'Reilly book is not about money, really, at least I think so), I'd (and probably Deepak, if he is interested) serve as a kind of main editor, and the more coauthors and voices we have, the better the book will be.

So by copying the content suggestions here, I'd like to invite you all to this hypothetical closing session and invite you to become future O'Reilly authors to define the biogeek culture. (Disclaimer: I am not an employee of O'Reilly Media, and if they say no I still think that the concept of the book is good enough to publish it elsewhere).

Attila  

Book Outline/Tentative Table of Contents  
  1. All about bio (introduction to the book).  In the introduction we will discuss the the origins of biotechnology and how the field has evolved over the past 25 years?  As biotechnology has evolved, it has had a significant impact on the world around us, from how we approach problems to how we try and cure disease, to the environment and even to DIY hackery.  The world of biotechnology is also increasingly moving towards a systems level approach, as begin to look at our bodies as interconnected, complex machines, changing the way we try and cure diseases.  We will also propose that biology is the ultimate information science and lay the grounds for later discussions on the data challenges and the information that can be gleaned
    1. the biological mindset
    2. biotechnology in general  
  2. biology basics In this chapter we provide a brief introduction of the building blocks of biology.  Here we go a little beyond what you might find in the mainstream media and tell you about how we function and highlight the complexity of human biology
    1. The building blocks (DNA, RNA, protein, organelles, membranes, extracellular matrix, tissues, organs, body).  Do we need anything else here?  Don't want to make it too technical.
  3. methods - 
    1. the lab The par excellence biologist of our time is an experimental scientist working at the bench with different tools and methods: DNA, RNA: isolation, amplification, quantification, protein: western blot, SDS PAGE, antibodies immunocytochemistry organelle: isolation of mitochondria, lysosomes (centrifuge), cell: in vitro cell culture
    2. Biology in silico
      1. Bioinformatics
      2. Modeling and simulation
  4. Postgenomic
    1. proteomics
    2. HapMap
    3. Protein Structure Initiative (Structural Genomics)
  5. Systems Biology Over the past few years, it has become apparent that the traditional reductionist approach to biology was very limited.  The human body is extremely complex, a function of interconnected pathways and networks.  In order to cure many diseases, it becomes necessary to study the human body at a systems level, getting a deep understanding of various pathways and networks.   By combining large quantities of data, complex mathematical modeling and advanced computer models, systems biologists are developling predictive models of organisms and biological systems which will not only help us develop better, more potent drugs, but also develop new fuel sources, clean up the environment and potentially hack the human body.
  6. The future of biotech
    1. Next generation sequencing
    2. Personal Genetics - Genomics
    3. stem cells-regenerative medicine (A) The chapter covers the basic concepts: stem cell, uni-, mult-, pluripotency, embryonic, adult, induced pluripotent, cancer stem cell, stem cell niche, tissue regenerative potential, regenerative medicine.
    4. tissue engineering
    5. The biology of our age: the biology of aging 
    6. synthetic biology Perhaps we can get Jason or someone to do this.  My preference is that we stick to non-famous people but interview Drew and others extensively.
    7. biotech DIY: set up your low budget lab at the backyard 
      The idea of doing biological experiments with current biotechnological methods and conducting research projects at home is very new. There are already many names in use referring to the same concept: bioDIY, home biology, biotech DIY, garage biology.  All you people need is a short course in biotech basics, a few thousands of dollars, some tinkering capability, and enough spare time and space. The beautiful retro idea of tinkering with digital devices in a garage, conveyed by the Make magazine, can be extended to biotech too, and some projects were already published in Make backyard biology issue like the Home Molecular Genetics including DNA isolation.
  7. Applications
    1. industrial biotech
    2. Drug Discovery 
  8. The Web and biotech
    1. Google and biotech Google's interindustrial power reached the biotech sphere through its investment into 23andME and backing George Church's Personal Genome Project amongst others. While personal genomics is in the focus of Google's recent interest, its connection with the biomedical sector is much more complicated. Google Health
    2. Virtual medical education and web 2.0 in medicine
 

gah...@gmail.com

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Jun 3, 2008, 8:06:42 AM6/3/08
to BioBarCamp
Attila et al.,

I can see better where we're heading (hopefully as a collective) with
this and I like it, although I think the target audience may go beyond
just IT guys. By the way, I am fairly active in the BioIT Coalition
<http://www.bioitcoalition.org/> in the Balt/Washington area. When we
have enough stuff, this may be a good venue for us. Perhaps getting
ahead of myself, but brainstorming. Their reach is currently fairly
local, but the local reach they have is quite deep and there is just a
lot of stuff in our little region due to the preponderance of federal
funding. I have presented for them a couple of times in the past.

I will help where I can, editing, proofing, writing, presenting....

One small thought with regards to Google & Biotech: Google Scholar.
I haven't heard much about this in a while, but I thought one of the
main goals of the Scholar project was to digitize the research
libraries of major research institutions like MIT, Cornell, Harvard,
Duke, etc? Maybe I am wrong about this, though. That was several
years ago I recall reading about it.

Eva Amsen

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Jun 3, 2008, 11:26:58 AM6/3/08
to BioBarCamp
If you're going to add an introduction about DNA etc., you'll
probably also need to explain the "why" of things like tissue
engineering, and discuss some of the basic ethical issues and
misconceptions (mostly a concern for the personal genomics and stem
cell chapters) and touch on the safety of bioDIY. I realize you might
be aiming for a more technical audience who are not opposed to
anything in the first place, but if it's a book any interested
individual can use it as a starting point.


On Jun 3, 1:50 am, "Attila Csordas" <attilacsor...@gmail.com> wrote:
> Hi All,
>
> This will be a lengthy email (sorry), but with good chance, it covers a lot
> of topics that will be discussed at BBCAmp. The reason for that length is
> that I include the Tentative Table of Contents of the so called *BioTech
> Geek Guide* as I would like to organize the closing session of the BBCamp
> with Deepak and Ricardo with the interactive participation of you all. Let
> me explain:
>
> The *Biotech Geek Guide* is also an
> idea<http://pimm.wordpress.com/2008/02/28/lets-compile-a-biotech-for-it-fo...>fed
> by a Twitter stream, just like the BBCamp idea. Deepak complained
> about
> the tech world's ignorance about health & genetics (a recurrent theme) and
> then I suggested to write/edit/compile a biotech, biology book for IT folks
> specially and publish it as an O'Reilly book. O'Reilly Books have the fame
> of being the definitive guides, intros, manuals in their technolgical
> fields. Ricardo came into the conversation too and 10 minutes later I
> emailed Tim O'Reilly with the suggestion and got almost instantly a very
> positive answer back followed by a detailed Proposal Guidelines that needs
> to be filled out to set up a schedule in order to get a final Yes or No
> answer to the publishing of the book. So we started to work (just a little
> in the lack of time) on it and I copy here what we've done basically the *Book
> Outline/Tentative Table of Contents*. The concept of the book later
> transformed into the *Biotech Geek Guide* which is too collect every cool,
> major topic together that could be of interest for a rookie/advanced
> biogeek, who is usually tech-savvy and biotech-savvy too.
>
> And so we have an idea, an option to make a product (a book) out of it, and
> define or delineate the knowledge-base and topic sensitivity of current
> biotechnology, life sciences well tailored for IT people but we lack an
> essential component that is behind every good animal covered O'Reilly tech
> book: we lack the creative and critical community and we need authors and
> commenters in the spirit of open source and science. (That community also
> starts to form on FriendFeed as *The Life
> Scientists*<http://friendfeed.com/rooms/the-life-scientists>room,
> earlier form is a simply
> Biotecher <http://twitter.com/biotecher>
> register<http://pimm.wordpress.com/2008/04/14/follow-biotecher-a-solution-to-f...>at
> Twitter.)
>
> But I think that the BioBarCamp could collect together exactly the Community
> that is needed for the succession of that book and the whole biogeek
> culture!!! The authorship, content and schedule is totally open at that
> point (publishing an O'Reilly book is not about money, really, at least I
> think so), I'd (and probably Deepak, if he is interested) serve as a kind of
> main editor, and the more coauthors and voices we have, the better the book
> will be.
>
> So by copying the content suggestions here, I'd like to invite you all to
> this hypothetical closing session and invite you to become future O'Reilly
> authors to define the biogeek culture. (Disclaimer: I am not an employee of
> O'Reilly Media, and if they say no I still think that the concept of the
> book is good enough to publish it elsewhere).
>
> Attila
>
> *Book Outline/Tentative Table of Contents* *
> *
>
> 1. *All about bio* (introduction to the book). In the introduction we
> will discuss the the origins of biotechnology and how the field has evolved
> over the past 25 years? As biotechnology has evolved, it has had a
> significant impact on the world around us, from how we approach problems to
> how we try and cure disease, to the environment and even to DIY hackery.
> The world of biotechnology is also increasingly moving towards a systems
> level approach, as begin to look at our bodies as interconnected, complex
> machines, changing the way we try and cure diseases. We will also propose
> that biology is the ultimate information science and lay the grounds for
> later discussions on the data challenges and the information that can be
> gleaned
> 1. the biological mindset
> 2. biotechnology in general
> 2. biology basics In this chapter we provide a brief introduction of the
> building blocks of biology. Here we go a little beyond what you might find
> in the mainstream media and tell you about how we function and highlight the
> complexity of human biology
> 1. The building blocks (DNA, RNA, protein, organelles, membranes,
> extracellular matrix, tissues, organs, body). *Do we need anything
> else here? Don't want to make it too technical.*
> 3. methods -
> 1. the lab The par excellence biologist of our time is an experimental
> scientist working at the bench with different tools and methods:
> DNA, RNA:
> isolation, amplification, quantification, protein: western blot,
> SDS PAGE,
> antibodies immunocytochemistry organelle: isolation of mitochondria,
> lysosomes (centrifuge), cell: in vitro cell culture
> 2. Biology in silico
> 1. Bioinformatics
> 2. Modeling and simulation
> 4. Postgenomic
> 1. proteomics
> 2. HapMap
> 3. Protein Structure Initiative (Structural Genomics)
> 5. Systems Biology Over the past few years, it has become apparent
> that the traditional reductionist approach to biology was very limited. The
> human body is extremely complex, a function of interconnected pathways and
> networks. In order to cure many diseases, it becomes necessary to study the
> human body at a systems level, getting a deep understanding of various
> pathways and networks. By combining large quantities of data, complex
> mathematical modeling and advanced computer models, systems biologists are
> developling predictive models of organisms and biological systems which will
> not only help us develop better, more potent drugs, but also develop new
> fuel sources, clean up the environment and potentially hack the human body.
> 6. The future of biotech
> 1. Next generation sequencing
> 2. Personal Genetics - Genomics
> 3. stem cells-regenerative medicine (A) The chapter covers the basic
> concepts: stem cell, uni-, mult-, pluripotency, embryonic, adult, induced
> pluripotent, cancer stem cell, stem cell niche, tissue regenerative
> potential, regenerative medicine.
> 4. tissue engineering
> 5. The biology of our age: the biology of aging
> 6. synthetic biology* *Perhaps we can get Jason or someone to do
> this. My preference is that we stick to non-famous people but interview
> Drew and others extensively.
> 7. biotech DIY: set up your low budget lab at the backyard
> The idea of doing biological experiments with current biotechnological
> methods and conducting research projects at home is very new. There are
> already many names in use referring to the same concept: bioDIY, home
> biology, biotech DIY, garage biology. All you people need is a
> short course
> in biotech basics, a few thousands of dollars, some tinkering capability,
> and enough spare time and space. The beautiful retro idea of
> tinkering with
> digital devices in a garage, conveyed by the
> Make<http://www.makezine.com/>magazine, can be extended to biotech
> too, and some projects were already
> published in Make backyard biology issue like the Home Molecular Genetics
> including DNA isolation.
> 7. Applications
> 1. industrial biotech
> 2. Drug Discovery
> 8. The Web and biotech
> 1. Google and biotech Google's interindustrial power reached the
> biotech sphere through its investment into 23andME and backing George
> Church's Personal Genome Project amongst others. While personal
> genomics is
> in the focus of Google's recent interest, its connection with
> the biomedical
> sector is much more complicated. Google Health
> 2. Virtual medical education and web 2.0 in medicine

John Cumbers

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Jun 3, 2008, 11:27:09 AM6/3/08
to bioba...@googlegroups.com
Sounds good Atilla,
I'd suggest synthetic biology get a chapter of its own, it's here now, rather than a future technology.  If Jason (Kelly?) isn't up for it then I'd be happy to coordinate the writing of this section.  I could also write a section on gene and genome synthesis, in particular the companies, technologies and individuals involved and what the future holds in terms of falling costs.

cheers,
John
--
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371
Moffett Field, CA 94035

John Cumbers

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Jun 3, 2008, 11:31:12 AM6/3/08
to bioba...@googlegroups.com
I'd also encourage to hire a cool graphics person, particularly with cell bio, a great picture can tell 1000 words...  Would also be good to have a website linked to the book full of all the cool videos explaining the central dogma etc.

re: how to introduce the topic... I've found it can help to work from the ground up, start off with what you'd need if you were a new life form (some machinery to replicate and a way to store how to replicate) and build up from there....

cheers,
John

Attila Csordas

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Jun 3, 2008, 11:35:26 AM6/3/08
to bioba...@googlegroups.com
Eva,

totally agreed, ethical reflexions are needed, but the focus is on the technological introduction. Maybe in the form of a separate chapter, or little tails to every sensitive issues, I don't know. What I don't like to have in the book is a specific, lengthy, uniform "philosophy/ideology" that tries to "establish" all this with one line of biased arguments. The whole thing is more diverse than that.

Attila



--
Attila Csordas
research scientist
Tulane University, Center for Gene Therapy
1430 Tulane Ave., SL-99
New Orleans, LA 70112
Phone: (504) 988-7709
Mobile: (504) 388-6710
blog: http://pimm.wordpress.com

Tito Jankowski

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Jun 3, 2008, 11:38:22 AM6/3/08
to bioba...@googlegroups.com
I'd love to take part in the synthetic bio section. 'Here and now' is the right way to put it!
Tito

Sent from my iPhone

Attila Csordas

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Jun 3, 2008, 11:44:12 AM6/3/08
to bioba...@googlegroups.com
Yes, it is rather present than future and it deserves an own chapter, that's my opinion too.
A particular state of the art genome synthesis chapter with industrial background on the existing top machines sounds good, but too much industry is not preferred.

I suggest here to discuss topic suggestions on BioBarCamp and hopefully we can frame all the discussions in the closing session.

Attila

PS: John, please, learn my name finally, it's Attila with double tt and 1 l. Thanks,

John Cumbers Gmail

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Jun 3, 2008, 12:12:51 PM6/3/08
to bioba...@googlegroups.com
I apologize Attila  ;-)
John

Alexis Madrigal

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Jun 3, 2008, 12:14:26 PM6/3/08
to bioba...@googlegroups.com
Not sure that O'Reilly books need writers per se, but I'd offer my services to smooth out the tone between sections and try to meld all the individual contributions into one readable tome.

The illustrator for this site: exploringorigins.org contacted me recently too, if anyone is interested in that style.

Best,

Alexis

Attila Csordas

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Jun 3, 2008, 12:15:15 PM6/3/08
to bioba...@googlegroups.com
Thanks, John. :) My day is perfect now.

Bryan Bishop

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Jun 7, 2008, 11:04:17 AM6/7/08
to bioba...@googlegroups.com
On Tuesday 03 June 2008, Attila Csordas wrote:
> Hi All,
>
> This will be a lengthy email (sorry), but with good chance, it covers
> a lot of topics that will be discussed at BBCAmp. The reason for that
> length is that I include the Tentative Table of Contents of the so
> called *BioTech Geek Guide* as I would like to organize the closing

> session of the BBCamp with Deepak and Ricardo with the interactive
> participation of you all. Let me explain:
>
> The *Biotech Geek Guide* is also an
> idea<http://pimm.wordpress.com/2008/02/28/lets-compile-a-biotech-for-
>it-folks-book-and-publish-it/>fed by a Twitter stream, just like the

> BBCamp idea. Deepak complained about
> the tech world's ignorance about health & genetics (a recurrent
> theme) and then I suggested to write/edit/compile a biotech, biology
> book for IT folks specially and publish it as an O'Reilly book.
> O'Reilly Books have the fame of being the definitive guides, intros,
> manuals in their technolgical fields. Ricardo came into the
> conversation too and 10 minutes later I emailed Tim O'Reilly with the
> suggestion and got almost instantly a very positive answer back
> followed by a detailed Proposal Guidelines that needs to be filled
> out to set up a schedule in order to get a final Yes or No answer to
> the publishing of the book. So we started to work (just a little in
> the lack of time) on it and I copy here what we've done basically the
> *Book Outline/Tentative Table of Contents*. The concept of the book
> later transformed into the *Biotech Geek Guide* which is too collect

> every cool, major topic together that could be of interest for a
> rookie/advanced biogeek, who is usually tech-savvy and biotech-savvy
> too.

I was talking with Deepak and others a few weeks ago about offering the
Synthetic Biology Toolkit as a basis for the book. There's tons of
content in the download and I think that it would be a good place to
start.

http://biohack.sf.net/
http://heybryan.org/mediawiki/

So the table contents, I would think, should focus mostly on (1)
protocols, (2) equipment -- mostly improvised, (3) introduction to the
online communities, including the broader world of bioinformatics,
programming, open source communities, friendly people to talk to on the
internet (seriously, an email address to me, Deepak, pimm, etc.),
diybio.org groups, etc. The entire field is very quickly moving along,
so it has to be a book that will not be dead in a few months (books
aren't good for content like that).

> And so we have an idea, an option to make a product (a book) out of
> it, and define or delineate the knowledge-base and topic sensitivity
> of current biotechnology, life sciences well tailored for IT people
> but we lack an essential component that is behind every good animal
> covered O'Reilly tech book: we lack the creative and critical
> community and we need authors and commenters in the spirit of open
> source and science. (That community also starts to form on FriendFeed

Woah, I think we /do/ have that community. Check out the biohack.sf.net
community. There's a good number of people on the mailing list. We just
need to get them rallied up on a project. :-)

> as *The Life
> Scientists*<http://friendfeed.com/rooms/the-life-scientists>room,


> earlier form is a simply

> Biotecher <http://twitter.com/biotecher>
> register<http://pimm.wordpress.com/2008/04/14/follow-biotecher-a-solu
>tion-to-find-all-biotwitters-in-1-place/>at Twitter.)


>
> But I think that the BioBarCamp could collect together exactly the
> Community that is needed for the succession of that book and the
> whole biogeek culture!!! The authorship, content and schedule is
> totally open at that point (publishing an O'Reilly book is not about
> money, really, at least I think so), I'd (and probably Deepak, if he
> is interested) serve as a kind of main editor, and the more coauthors
> and voices we have, the better the book will be.

Let's make it on a wiki, instead of requiring it a BioBarCamp-only book.
I don't know if BioBarCamp would be a good venue at which to write the
book, but for rapid outlining (sit there on a wiki and have a live
brainstorming session) it might prove an awesome mechanism.

> So by copying the content suggestions here, I'd like to invite you
> all to this hypothetical closing session and invite you to become
> future O'Reilly authors to define the biogeek culture. (Disclaimer: I
> am not an employee of O'Reilly Media, and if they say no I still
> think that the concept of the book is good enough to publish it
> elsewhere).

To _define_ the biotecher culture? I don't know about that. That one is
already in progress. For example, biopunk.org, the F/OSS communities,
the typical lab culture.

> 1. *All about bio* (introduction to the book). In the


> introduction we will discuss the the origins of biotechnology and how
> the field has evolved over the past 25 years? As biotechnology has

That's a pretty challenging part. Maybe we could start by looking over
at wikibooks and see if there's anything already written that we might
import. There's a lot of important people to mention from the field of
bio and biotech and so on, so we need somebody pretty knowledgable and
able to integrate all of the information together, showing the broader
vision that people started out with (or acquired), and then integrating
it all back together to make sense. I think this could be done if we
ruthlessly recursively read Wikipedia for the broad overview aspects,
but then we need to reinterpret in light of (1) actual research
articles (references to open access papers, etc.), and (2) an
interpretation in terms of the do-it-yourself culture.

> evolved, it has had a significant impact on the world around us, from
> how we approach problems to how we try and cure disease, to the

I think it's important to emphasize just how awesome disease curing can
be. I wasn't aware of the World Health Organization's attempt to cure
polio via a world-wide campaign until a few years ago. That was a
terribly massive medical front that I doubt can be emphasized enough.
And what would happen if people were able to do that on their own? Hrm.

> environment and even to DIY hackery. The world of biotechnology is
> also increasingly moving towards a systems level approach, as begin
> to look at our bodies as interconnected, complex machines, changing
> the way we try and cure diseases. We will also propose that biology
> is the ultimate information science and lay the grounds for later
> discussions on the data challenges and the information that can be
> gleaned

> 1. the biological mindset
> 2. biotechnology in general

> 2. biology basics In this chapter we provide a brief introduction


> of the building blocks of biology. Here we go a little beyond what
> you might find in the mainstream media and tell you about how we
> function and highlight the complexity of human biology

> 1. The building blocks (DNA, RNA, protein, organelles, membranes,
> extracellular matrix, tissues, organs, body). *Do we need
> anything else here? Don't want to make it too technical.*

So, a list of general componentry that people can investigate in trying
to make their projects a reality. Not just "building blocks of life",
but 'parts and tools that you can use to do cool stuff'.

> 3. methods -

I suspect that including a CD of protocols wouldn't be a bad idea. We
could start with protocols-online and OpenWetWare. In fact, if there's
going to be a CD, let's include the biohacking toolkit and the entire
wiki output of major wikis like OWW, biodatabase.org, biohack, etc. And
then we can probably also include the portions of Wikipedia that are
relevant. This is critical. There's no way that we can talk about
everything in a book that we all want to be published in a reasonable
amount of time ... so a CD, plus the book as more of a creative 'index'
(in discussion format) to the contents, might be a good idea.

> 1. the lab The par excellence biologist of our time is an


> experimental scientist working at the bench with different tools and
> methods: DNA, RNA:
> isolation, amplification, quantification, protein: western
> blot, SDS PAGE,
> antibodies immunocytochemistry organelle: isolation of
> mitochondria, lysosomes (centrifuge), cell: in vitro cell culture

> 2. Biology in silico

http://heybryan.org/mediawiki/index.php/Computational_biology

> 1. Bioinformatics

http://bioinformatics.org/

> 2. Modeling and simulation

http://heybryan.org/mediawiki/index.php/Computational_biology

> 4. Postgenomic
> 1. proteomics

http://heybryan.org/mediawiki/index.php/List_of_bioinformatics_databases

> 2. HapMap
> 3. Protein Structure Initiative (Structural Genomics)

CASP?

> 5. Systems Biology Over the past few years, it has become

http://sbml.org/

> apparent that the traditional reductionist approach to biology was
> very limited. The human body is extremely complex, a function of
> interconnected pathways and networks. In order to cure many
> diseases, it becomes necessary to study the human body at a systems
> level, getting a deep understanding of various pathways and networks.

http://reactome.org/

> By combining large quantities of data, complex mathematical
> modeling and advanced computer models, systems biologists are
> developling predictive models of organisms and biological systems
> which will not only help us develop better, more potent drugs, but
> also develop new fuel sources, clean up the environment and

> potentially hack the human body. 6. The future of biotech

Re: future of biotech. George Church is supposedly making some
incredibly cheap biotech equipment (polonator.org and so on);
sequencing for everybody on the planet; do-it-yourself pharmacy; brain
augmentation; etc.

http://www.innerspacefoundation.org/
http://heybryan.org/recursion.html

> 1. Next generation sequencing

http://heybryan.org/mediawiki/index.php/DNA_sequencing

Is pyrosequencing still next generation? There's also scanning tunneling
microscopy for DNA (like ZS Genetics plans to be doing later this
year). The STM setups technically don't cost much, but getting the
reoslution needed to do nucleotide-by-nucleotide scanning, ehh. That
gets tricky. See:

http://heybryan.org/instrumentation/instru.html
http://heybryan.org/graphene.html (sort of)

> 2. Personal Genetics - Genomics

http://polonator.org/

Also, the $0 genomics project. Community sequencing projects, brief
notes on how to deploy something like that (run around with cotton
swabs and baggies and refridgerators in a van), etc. Also, the
prospects of viral gene therapy in relation to personal genomics; the
prospects of downloading genes from the internet from "gene pools"
(i.e., "hey, look at this!" blogs).

> 3. stem cells-regenerative medicine (A) The chapter covers the


> basic concepts: stem cell, uni-, mult-, pluripotency, embryonic,
> adult, induced pluripotent, cancer stem cell, stem cell niche, tissue
> regenerative potential, regenerative medicine.

The biohacking toolkit includes some papers by Yamanaka re: iPS cells.
I'm still looking into protocols for adult fibroblast extraction and
colonies, but it's looking interesting.

> 4. tissue engineering

http://heybryan.org/mediawiki/index.php/Neuropod
organotypical neural slices, also see the heart-in-a-jar and prospects
of the brain-in-a-jar projects. Stem cell engineering too. Hrm. Ah, and
most importantly, the in vitro meat stuff.

http://heybryan.org/mediawiki/index.php/Meat_on_a_stick

> 5. The biology of our age: the biology of aging

Emphasis on how to do "anti-aging research" in your own home.

http://sens.org/
http://grg.org/ has some people that we might want to contact (Coles?
Aubrey?)

> 6. synthetic biology* *Perhaps we can get Jason or someone to


> do this. My preference is that we stick to non-famous people but
> interview Drew and others extensively.

http://syntheticbiology.org/
http://partsregistry.org/
http://biobricks.org/
http://biohack.sf.net/
http://diybio.org/

> 7. biotech DIY: set up your low budget lab at the backyard


> The idea of doing biological experiments with current
> biotechnological methods and conducting research projects at home is
> very new. There are already many names in use referring to the same
> concept: bioDIY, home biology, biotech DIY, garage biology. All you
> people need is a short course
> in biotech basics, a few thousands of dollars, some tinkering
> capability, and enough spare time and space. The beautiful retro idea
> of tinkering with
> digital devices in a garage, conveyed by the

> Make<http://www.makezine.com/>magazine, can be extended to biotech


> too, and some projects were already
> published in Make backyard biology issue like the Home
> Molecular Genetics including DNA isolation.

By the way. There's a few projects out there (bioreactor project from
the biohacking group) that are trying to make a completely biological
setup for do-it-yourself biology experimentation. For example, in vitro
DNA synthesis.

http://heybryan.org/mediawiki/index.php/In_vitro_DNA_synthesizer

And also having cells generate the proteins (T7, etc.) necessary to do
transcription, or other various reactions that will be needed. This
way, the entire kit is self-replicable except for the metal or plastic
chasis.

> 7. Applications
> 1. industrial biotech

Might want to mention something about 'industrial ecology' and the
biosphere as another ecology and how this could all fit together
productively for various interests.

> 2. Drug Discovery
> 8. The Web and biotech

> 1. Google and biotech Google's interindustrial power reached


> the biotech sphere through its investment into 23andME and backing
> George Church's Personal Genome Project amongst others. While
> personal genomics is
> in the focus of Google's recent interest, its connection with
> the biomedical
> sector is much more complicated. Google Health

> 2. Virtual medical education and web 2.0 in medicine

Maybe the diybio.org guys would like to run some of those virtual
educational seminars eventually. I've been holding weekly lectures on
IRC on freenode in #hplusroadmap for a while now, but it's really just
whenever people feel like showing up and pestering me about some
awesome topics. Anybody is welcomed to join and contribute. :)

- Bryan
________________________________________
http://heybryan.org/

Bryan Bishop

unread,
Jun 7, 2008, 11:06:13 AM6/7/08
to bioba...@googlegroups.com
On Tuesday 03 June 2008, gah...@gmail.com wrote:
> One small thought with regards to Google & Biotech:  Google Scholar.
> I haven't heard much about this in a while, but I thought one of the
> main goals of the Scholar project was to digitize the research
> libraries of major research institutions like MIT, Cornell, Harvard,
> Duke, etc?  Maybe I am wrong about this, though.  That was several
> years ago I recall reading about it.

Google Scholar is more like an interface to the academic journals via
their publisher's website. It then allows you to search through it. You
can search, but only if you are at an academic institution will you be
able to get the majority of the articles. There are a few free PDFs
that pop up from time to time, but it's a pain.

http://scholar.google.com/
http://heybryan.org/projects/autoscholar/

I've automated my interface to Google Scholar. I hate clicking.

I might implement an email mechanism to request articles from authors
(via searching for their email address via institutional websites) when
they are in a nonfree academic journal. This doesn't work when the
thing is decades old and the author might be, you know, dead.

Bryan Bishop

unread,
Jun 7, 2008, 11:07:23 AM6/7/08
to bioba...@googlegroups.com
On Tuesday 03 June 2008, John Cumbers wrote:
> I'd suggest synthetic biology get a chapter of its own, it's here
> now, rather than a future technology.  If Jason (Kelly?) isn't up for
> it then I'd be happy to coordinate the writing of this section.  I
> could also write a section on gene and genome synthesis, in
> particular the companies, technologies and individuals involved and
> what the future holds in terms of falling costs.

John, go throw this up on a wiki. Here's a good place to start:
http://heybryan.org/mediawiki/index.php/Synthetic_biology

Or even:
http://openwetware.org/wiki/Synthetic_biology

Or even:
http://en.wikiversity.org/wiki/Topic:Synthetic_biology

Bryan Bishop

unread,
Jun 7, 2008, 11:08:19 AM6/7/08
to bioba...@googlegroups.com
On Tuesday 03 June 2008, Attila Csordas wrote:
> A particular state of the art genome synthesis chapter with
> industrial background on the existing top machines sounds good, but
> too much industry is not preferred.

For genome synthesis we could mention something like the DNA synthesizer
projects that are already out there.

http://heybryan.org/mediawiki/index.php/DNA_synthesizer

Including schematics and technical documentation would be good.

Bryan Bishop

unread,
Jun 7, 2008, 11:11:50 AM6/7/08
to bioba...@googlegroups.com
On Tuesday 03 June 2008, Eva Amsen wrote:
> engineering, and discuss some of the basic ethical issues and
> misconceptions (mostly a concern for the personal genomics and stem
> cell chapters) and touch on the safety of bioDIY. I realize you might
> be aiming for a more technical audience who are not opposed to
> anything in the first place, but if it's a book any interested
> individual can use it as a starting point.

A few sentences on ethics might be okay, but anything more is
significantly distracting from the purpose of the book. The ethics have
already been established by many different groups, like WTA,
extropians, etc. I suppose we could put in some passing references,
but:

http://synbiosafe.eu/forum/viewtopic.php?f=15&t=44
http://synbiosafe.eu/forum/viewtopic.php?f=16&t=45
http://extropy.org/
http://heybryan.org/transhumanism_def.html

Bryan Bishop

unread,
Jun 7, 2008, 11:12:46 AM6/7/08
to bioba...@googlegroups.com
On Tuesday 03 June 2008, John Cumbers wrote:
> I'd also encourage to hire a cool graphics person, particularly with
> cell bio, a great picture can tell 1000 words...  Would also be good
> to have a website linked to the book full of all the cool videos
> explaining the central dogma etc.

Who was the artist behind Drew's comic book? Perhaps Randall Munroe
(xkcd) would be willing to throw some stuff in.

Deepak Singh

unread,
Jun 7, 2008, 11:53:50 AM6/7/08
to bioba...@googlegroups.com
We should keep in mind the audience that Attila and I originally had.  Techies, most of whom do not really understand some of the core principles of the life sciences, what the methods aim to do, what are the challenges, etc.  The discussions on Wired, Reddit, etc tend to suggest almost negligible knowledge.  From my side, I'd also like to run people through the drug development process, which even a lot of academics are mostly unaware of, except at a very high level.  In other words, keep it simple, emphasize the present and hint at the future.

Attila Csordas

unread,
Jun 25, 2008, 11:37:36 AM6/25/08
to bioba...@googlegroups.com
I asked Alexis Madrigal to organize a session on the California personal genetics cease-and-desist scandal and he was positive about that. http://blog.wired.com/wiredscience/2008/06/navigenics-to-c.html
We have a very interesting paradigmatic story unfolding just before our eyes and screens.
Also this session could be interesting for those who are  interested in regulation, bioethics, society et cetera...and not just the technological side.

Also alarmed David Bolinsky to stop by http://www.ted.com/index.php/talks/view/id/147 he is the maker of the coolest The Inner life of the cell animation.

Attila
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