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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
36 stars 13 forks source link

DSL for generating models #75

Closed cmungall closed 9 years ago

cmungall commented 10 years ago

I am addicted to https://www.websequencediagrams.com/

some kind of DSL for LEGO would be cool. E.g.

Shh activates Sox9 in cytosol via binding Sox9 regulates Wnt3 via transcription factor activity Shh and Sox9 part of limb development

kltm commented 10 years ago

Nice, but not a go-mme item? Maybe bbop or bbopx. Or, more likely, a separate application/widget framework (that could possibly talk to Noctua). A parser would be the first step.

kltm commented 10 years ago

Thinking about our architecture, essentially a mapper from the AST to bbopx.minerva.requests/request_set (https://kltm.github.io/bbopx-js/docs/files/minerva/requests-js.html). It would have to be an all-or-nothing operation.

Okay, maybe a go-mme item them, with reliance on bbopx.

kltm commented 9 years ago

Beyond wishlist and considering all of the machinations that have to happen to with barista, I think it would be best to group this with geneontology/noctua-repl (https://github.com/geneontology/noctua-repl) for now. It should also have a file runner for scripting at some point in addition to the REPL, which could be extended into a DSL if the current environment was not enough (it's pretty easy to build complicated requests as it stands).

It's initially being built up to test the new models and wire protocol so specific cases can be tried as the graph editor as being changed to handle all of the recent changes on the backend and in the libraries. But it will be very handy/fun afterwards--it's neat to see your models change in the browser from simple commands given interactively to a node module. It will also answer the question: can't there be an expert/power user mode?