[OWW-Discuss] Tapping into open source / open access and doingslightly more

[Bryan Bishop]

On Wednesday 14 May 2008, Jason Morrison wrote:
> Bryan, the projects you propose a collection of - are they
> descriptions/data, like a lab protocol description?  If this is the

Yes, they could include lab protocol descriptions [that hopefully one 
day could be followed by machine and human alike, if properly written 
in some machine-parseable format]. But it would also include other 
constructable items, not just constructable life / life-states via 
protocols and chemical concoctions.

> case, I think there's a huge space for the systemization and
> distributed production/annotation of these.  I'd love to have
> well-tagged protocols that other software can say "hey, where's a
> protocol for performing abc on substrate uvw in conditions xyz?"

Yes, this system is completely 'tagged'. You search for data types if 
you want, or you can search the natural language description, and 
really -- how it works now -- you'd want to search for people that 
might be able to point you in the right direction with the least amount 
of pain involved on their end. That's also part of the project, social 
facilitation, in that the project -- SKDB -- can have some files for 
each project that specify data like FOAF (friend of a friend; it's some 
new stuff going around the social-networking scene apparently), or a 
list of contributors to contact. I fully expect these projects to be 
off-site in many cases, although Sourceforge is an example of onsite 
versioning systems. Either way works. Still tagged. 

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

> I'm curious what specific types of files you see going into the
> <centrifuge> or <uncoli> projects.

Centrifuge might have a CAD file or two. This would describe the 
physical structure, or at the very least physical parameters for the 
structure, and then the procedures to make it (it's a manufacturing 
database to some extent). The beauty of it is that you don't have to 
specify it down to every last detail, since you can just blackbox it 
sort of [as long as you provide references to literature that isn't yet 
integrated -- or at least a few names to people to track down in case 
somebody wants to start formalizing it]. But it's important that you 
try to use the same tags, else we get into huge bushes and vineyards 
that criss-cross in weird ways. Maybe an automated program can fix 
these hairy issues, but I suspect if the information is organized 
cleanly enough, and the quality assessment teams that verify packages 
before throwing them into the 'main branch' of SKDB do their job well, 
then it should stay pretty clean. [New ontologies/taggings can be 
ghosted on top if it easily enough, but it takes effort (refactoring)].

> Russell, you bring up a good point about the difference in initial
> capital investment between software and wetware development.  Might a
> http://techshop.ws/ for biology be a game changer here?

I tried signing up for the Austin techshop but nobody has gotten back to 
me on that. So that's peculiar. What I'm thinking of is that if things 
go well enough and the manufacturing systems / SKDB takeoff, I'll do my 
own techshop of sorts so that I can work on bootstrapping the system 
back down to the basics, help make standardized parts, etc. [plus it's 
always neat to have your own shop/lab-space to work in].

>  Specifically: would there be enough interested individuals if the
> capital investment were the same?  Let's say $3/day instead of
> $150/day to do mol bio.  (That's assuming a $100/mo membership to
> TechLab, perhaps a high number.  $150/day from est. $75k to bootstrap
> a mol bio lab plus a year of consumables.  Compare to a $1000
> development box, which brings us back to $3/day for the first year in
> the software realm)

Yikes, $75k to bootstrap a mol bio lab? What if all of these parts were 
manufactured for free, by energy and materials obtained for free? At 
the root of all of this there's the concept of "philanthropic 
bootstrapping", but it needs to be at a very central point; I haven't 
developed this argument fully yet, but I'll probably be trying to hack 
out a few lines on it later this week. I might also call it "a 
philanthropic gateway".
http://heybryan.org/exp.html

- Bryan
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