Protocols sharing and standards

[Ra Ramana]

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

[Cathal Garvey]

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.

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[Kermit Henson]

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?

[Ra Ramana]

Absolutely. Community ranking/validation is the best way to go. I thought some resource like that existed but looks it doesn't. 

Thanks @Cathal Garvey for pointing to Antha. Came across it just didn't explore more. On my to do.  As am exploring it in the context 

of a repository (validated) to mine further and preferably towards automating it.  (output could be Autoprotocol or other relevant ones but 

what's the input ? )

More people on the know could comment and suggest as well - will be helpful.

Thanks

[Ra Ramana]

Just as an update to this thread : 

The old BioCoder code is still available for download at: https://www.microsoft.com/en-us/download/details.aspx?id=52556

But looks it doesn't really have any automation as it hard codes the protocols and does generation of text well. It doesn't read/interpret any 

new ones to generate new protocol outputs. 

Automated protocol parsing & generation is a hard challenge. Also wonder how much adoption & application it will carry, but it's a challenge

to solve nevertheless.

Those on the know about the developments in the field - automation in biology 

(driven by companies like Transcriptic, Emerald, Synthace etc.), could comment more! 

Thanks