Re: [DIYbio] Protocols sharing and standards

Today was talking about this topic with some lab mate....

I think a centralised and curated protocols database not only should be based in a common coding language, but also on how to reference to one specific protocol and like/dont like (in the fb way) approval by community. 

Whom has never tried a protocol found in a paper and it didn't work for several reasons?

El lunes, 20 de febrero de 2017, 12:29:02 (UTC+1), Cathal Garvey escribió:

I'd like to see a community-powered, open solution to this, also.

I personally think that antha-lang.org presents a strong end-goal, that
of transposable protocols from human-instructions to scaleable
machine-instructions. But, the language isn't well documented yet and,
even when it is, it's a programming model that many scientists won't be
comfortable with.

But, knowing Antha's a great end-goal might inspire a way to design
"Human Friendly" protocol markup that's more easily converted to a
formalised "Program" like Antha, down the line?

Btw., protocols.io is a patented system, so not exactly the right place
to start for an open standard or community-powered solution.

--
@onetruecathal / @cat...@quitter.is


On Mon, Feb 20, 2017 at 11:24 AM, Ra Ramana
<emailrav...@gmail.com> wrote:
> Hi,
>
> I'm presently exploring the standards of sharing of protocols used
> across different bio labs. I haven't found a repository of protocols
> that is
> data 'mining' ready. http://protocols.io comes the closest. Not much
> found on github either (though some have shared their lab protocols &
> opentrons
> also has posted some)
>
> I'd like to hear your opinion and comments about the present status
> of this area.
>
> Has 'Autoprotocol' from Transcriptic established itself to be the way
> to communicate human protocols to machines? Are there alternatives ?
> Is there a nice corpus to mine the protocols and come up with
> schemas/ontologies (a la
> http://www.aber.ac.uk/en/cs/research/cb/dss/exact/ - which is from
> 2008!)
>
> Any info in MITs Biostream that later became Biocoder but nothing is
> there to be seen or heard about that on the internets? Besides from
> 2009 with this promising title "BioStream: a high-level programming
> language for biology protocols" -
> https://groups.google.com/forum/#!topic/diybio/g-o4sq75jY0
> Wonder why so many promising things like this fizzle out without any
> further note. Such ontologies will clearly help accelerate
> machinizing biology and automation of routine procedures (also my
> interest)
>
> Looking forward to your comments/approaches/suggestions!
>
> TIA,
> Ra
>
>
>
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