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Bioprotocols Working Group

The Bioprotocols Working Group is an open community designing and implementing a specification for scientific protocols, solving common laboratory interchange problems.
Collective - Host: opensource - https://opencollective.com/bioprotocols - Website: http://bioprotocols.org/ - Code: https://github.com/Bioprotocols

Update LICENSE.md

Added requested changes on credit

github.com/Bioprotocols/container-ontology - ba10055d01f0b8cb2daff0bd751206768a856245 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Update LICENSE.md

Instructions say not to include the brackets. Removing.

github.com/Bioprotocols/container-ontology - b18f41a6d6714e1bc5015e181e260aa08cddebc2 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Create LICENSE.md

Add Apache 2.0 LICENSE.md with "2022 Bioprotocols Working Group"

github.com/Bioprotocols/container-ontology - 445f56ad32f082dc42b4963063cb0b732491e794 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Update README.md

Add details on ongoing discussions & Slack threads

github.com/Bioprotocols/instrument-ontology - cc2440181959d04e4f87a970166f257c8b94fe2d authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Update README.md

This is a stub repository

github.com/Bioprotocols/instrument-ontology - cfa909b9e1d704411e16762a92d7d45f50e92119 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Initial commit

github.com/Bioprotocols/instrument-ontology - 8bba70d898333fc535cb7e6adf73941d4f78ba9d authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Add support for opentrons hardware modules

github.com/Bioprotocols/labop - dd82cd088b1881ae052e77d40acf8d9512a842d1 authored over 2 years ago by Bryan Bartley <[email protected]>
Resolve #157

github.com/Bioprotocols/labop - e49fbebe2f2658087b6589f4b419ec463fc0d556 authored over 2 years ago by Bryan Bartley <[email protected]>
Include more protocol metadata in output script, because the machine complains without it

github.com/Bioprotocols/labop - 6813033559bfdf9a9cbb6f2c7b9f41dc4c73c70f authored over 2 years ago by Bryan Bartley <[email protected]>
Fixed source and destination containers mix-up

github.com/Bioprotocols/labop - 20c2dab587ef957875d8bf2ff8f5669d40282b6f authored over 2 years ago by Bryan Bartley <[email protected]>
Working example

github.com/Bioprotocols/labop - d003b0c7086028b52c0e15d8d709939d79a99558 authored over 2 years ago by Bryan Bartley <[email protected]>
checked rubrics

github.com/Bioprotocols/labop - efff423fa8540dbca96354790a4ea2b6d7e25af3 authored over 2 years ago by Daniel Bryce <[email protected]>
fixed tests after rebasing, need to verify rubrics

github.com/Bioprotocols/labop - 0c9df3396b4e6fa5a1296db4d0415554663af268 authored over 2 years ago by Daniel Bryce <[email protected]>
Merge branch 'opentrons' of github.com:Bioprotocols/paml into opentrons

github.com/Bioprotocols/labop - 89a25a9e44fc122dc13fe0c20b77f34699a0d503 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix #152

github.com/Bioprotocols/labop - 0e48be867a591728e8351b345d7165361e52cd19 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix get_aliquot_list breaking when single well coordinate is used instead of range

github.com/Bioprotocols/labop - 252b381433a9e6e39734d23b478454c7303588cc authored over 2 years ago by Bryan Bartley <[email protected]>
Merge pull request #148 from Bioprotocols/interlab_protocol

Interlab protocol

github.com/Bioprotocols/labop - e1f3bbf849f3bf9825563cef63a2d51ec045e0d1 authored over 2 years ago by bbartley <[email protected]>
fix rebasing discrepancies

github.com/Bioprotocols/labop - 9b97fedcaab633cce999070184e483e41deb1c1a authored over 2 years ago by Daniel Bryce <[email protected]>
ignore jekyll stuff

github.com/Bioprotocols/labop - 75bbf339c1851ccba718bd308ab73ec0dc670074 authored over 2 years ago by Daniel Bryce <[email protected]>
Support json output for execution

github.com/Bioprotocols/labop - 8002644cdce93990b4170d171c05e7627a4a3096 authored over 2 years ago by Daniel Bryce <[email protected]>
WIP protocol execution and serialization for json

github.com/Bioprotocols/labop - 2a2db8b74b388ee39bc5750deb6c2f97bd846071 authored over 2 years ago by Daniel Bryce <[email protected]>
permissive execution and tweak specialization api

github.com/Bioprotocols/labop - 0c30d252eb13b43effcb6bee05075d4ff4728ff9 authored over 2 years ago by Daniel Bryce <[email protected]>
unused import

github.com/Bioprotocols/labop - 5351b7ca22ede54338457ade8367b7bc0d976662 authored over 2 years ago by Daniel Bryce <[email protected]>
local version of notebook

github.com/Bioprotocols/labop - ffde26d14f0865ee744fdfb3f9bd05c5b251768c authored over 2 years ago by Daniel Bryce <[email protected]>
execution demo

github.com/Bioprotocols/labop - 0b75981b1697f595f7230a7bfa0c838578b5fcf4 authored over 2 years ago by Daniel Bryce <[email protected]>
remove old ee funcs

github.com/Bioprotocols/labop - 1fb8efaf06024b555eee4df2c81fd9af79e6abf0 authored over 2 years ago by Daniel Bryce <[email protected]>
examples as package, remove old ee funcs

github.com/Bioprotocols/labop - a90dfeac1710cd368179e58d89b6bd0542e6bf52 authored over 2 years ago by Daniel Bryce <[email protected]>
refactored ee

github.com/Bioprotocols/labop - 35b0e0f8d08467600d5f7a37cdce7f43187f7b2e authored over 2 years ago by Daniel Bryce <[email protected]>
fixes for graphviz w/ subprotocols

github.com/Bioprotocols/labop - 55fea5f1ed42006479e0e567de908b132f95e0e0 authored over 2 years ago by Daniel Bryce <[email protected]>
working ph execution

github.com/Bioprotocols/labop - f2eb399e06fc9a5b800054552e04ca9fb5d078d5 authored over 2 years ago by Daniel Bryce <[email protected]>
execution engine support for ph protocol

github.com/Bioprotocols/labop - bd247fe6815e92b10e200db6c7ed7c7bba2fa099 authored over 2 years ago by Daniel Bryce <[email protected]>
execution engine support for ph protocol

github.com/Bioprotocols/labop - 43c145cd17d3453635ef049014f1e3d03b9906a1 authored over 2 years ago by Daniel Bryce <[email protected]>
formatting

github.com/Bioprotocols/labop - 4f06931e76be5556a54d0d42874d4b4d589d4cf5 authored over 2 years ago by Daniel Bryce <[email protected]>
rough draft

github.com/Bioprotocols/labop - f78798f5e77363313cb857ba03740216b46ecf27 authored over 2 years ago by Daniel Bryce <[email protected]>
checkpoint w/ subprotocol

github.com/Bioprotocols/labop - ef48cc612d58aaadaa4fa7c64be7480738592f69 authored over 2 years ago by Daniel Bryce <[email protected]>
refactor

github.com/Bioprotocols/labop - c1b03e9af4c95764e5c89cd746b309c4c8f9f07d authored over 2 years ago by Daniel Bryce <[email protected]>
checkpoint

github.com/Bioprotocols/labop - b97548d7184289e48ba722ef5c7e824c728a72d2 authored over 2 years ago by Daniel Bryce <[email protected]>
checkpoint

github.com/Bioprotocols/labop - 4da867fda47acc183225961270550759f6fb9fba authored over 2 years ago by Daniel Bryce <[email protected]>
applied black formatting

github.com/Bioprotocols/labop - 0cf6e6a184671f44c27a8edd077e8dff94cb9efa authored over 2 years ago by Daniel Bryce <[email protected]>
clean up and fix finalnode semantics

github.com/Bioprotocols/labop - bcd6a0b23edd754ab8328376056920752e24255e authored over 2 years ago by Daniel Bryce <[email protected]>
helper function for decision nodes

github.com/Bioprotocols/labop - 5b814ca09a1e364e40455cf01bf0bed59658456e authored over 2 years ago by Daniel Bryce <[email protected]>
Initial implementation of DecisionNode w/o else

github.com/Bioprotocols/labop - 45cc62b383e765e4e413f87e52e0cd43f2cf84e8 authored over 2 years ago by Daniel Bryce <[email protected]>
Cherry pick specialization from Friendzymes fork

github.com/Bioprotocols/labop - ebcc32925161b872713b009a46f25c90e468e9dc authored over 2 years ago by Bryan Bartley <[email protected]>
Setup place to add conversion to opentrons. Based on Autoprotocol conversion by removing specifics.

github.com/Bioprotocols/labop - 30671e252269cc07281d127b09f65edc0a30b061 authored over 2 years ago by Daniel Bryce <[email protected]>
Update notebook examples to support markdown attribute on Execution objects

github.com/Bioprotocols/labop - a4be2a5e0906980f39f965543bb6ba80fd211cc6 authored over 2 years ago by Bryan Bartley <[email protected]>
Remove extraneous newline from test files, resolves #150

github.com/Bioprotocols/labop - 9e7e09929c5c08b5670285757e3ae7cc8d9a4832 authored over 2 years ago by Bryan Bartley <[email protected]>
Resolve #151, save CI testfiles as artifact

github.com/Bioprotocols/labop - 6d02b0394757996cbe4dcf8c99d84ba4dadf74ef authored over 2 years ago by Bryan Bartley <[email protected]>
Skip test

github.com/Bioprotocols/labop - 464a02793bfb89a9fc0452cc9855bf23964ab46d authored over 2 years ago by Bryan Bartley <[email protected]>
Update test file

github.com/Bioprotocols/labop - a0b4e2defe0b3789189e799f370bb53e294fbe91 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix _materials breaks when a container spec can't be resolved

github.com/Bioprotocols/labop - 202c1567b03b3d01617cab00c4f3f6493f5749ca authored over 2 years ago by Bryan Bartley <[email protected]>
cleanup pages

github.com/Bioprotocols/labop - 61d1ec0aa12a1674d6e6df9e9f727e778910a383 authored over 2 years ago by Daniel Bryce <[email protected]>
Handle container exceptions better

github.com/Bioprotocols/labop - 4ce9211aa03b9634f264a8bc3ba348db9810a1ac authored over 2 years ago by Bryan Bartley <[email protected]>
Turn on failsafe

github.com/Bioprotocols/labop - 8c27f015cda0dccf22d010268a83cef6ddbf9d35 authored over 2 years ago by Bryan Bartley <[email protected]>
Update pages.yml

github.com/Bioprotocols/labop - 6a9b8f0862c3d1ee78d6ba9b3bb685a88d23d7c3 authored over 2 years ago by Daniel Bryce <[email protected]>
www dir

github.com/Bioprotocols/labop - 661998bf48a9b48c5c5f61327a2f26045bea375d authored over 2 years ago by Daniel Bryce <[email protected]>
Update pages.yml

github.com/Bioprotocols/labop - 66cefe731d59551b5e6018a44bc04dc2c41e3a6c authored over 2 years ago by Daniel Bryce <[email protected]>
Create pages.yml

github.com/Bioprotocols/labop - c8948191091106a9db551287155a4b6458e88c16 authored over 2 years ago by Daniel Bryce <[email protected]>
Update test file

github.com/Bioprotocols/labop - eaca89063369e307f052183a466f642874ac8efb authored over 2 years ago by Bryan Bartley <[email protected]>
Cherry pick specialization from Friendzymes fork

github.com/Bioprotocols/labop - 8809072514b39b4407a6fb7543ce88e1c1b7d63d authored over 2 years ago by Bryan Bartley <[email protected]>
Fix bad uri

github.com/Bioprotocols/labop - e5ad51118631019ede314a5b957084a20445bdb7 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix some broken lookups

github.com/Bioprotocols/labop - e880051e9fe1822f4d365ae35ce9c35514395b8f authored over 2 years ago by Bryan Bartley <[email protected]>
PlateCoordinates now supports single well coordinate in addition to ranges

github.com/Bioprotocols/labop - c38e6a6102f74616a7a6ffda5e3e32eef5aaae46 authored over 2 years ago by Bryan Bartley <[email protected]>
Merge changes in compute_output method

github.com/Bioprotocols/labop - c8af38209c7564f5a62e465f7f9d1d38c14d58c7 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix paml:contents specification

github.com/Bioprotocols/labop - ac6dec9b3f79fc38c2b5f1a2a445e75e4e453068 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix test_subexecutions namespace error

github.com/Bioprotocols/labop - 345668667a2a0f32a4be61faf15045772183b76c authored over 2 years ago by Bryan Bartley <[email protected]>
Fix missing execution argument

github.com/Bioprotocols/labop - 2e8dd5a62045df141843a9e7d0a511aa7e6ce748 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix test_subexecutions namespace error

github.com/Bioprotocols/labop - 0f4258fc4f23910ed6a3f0f206504c4a08d141bd authored over 2 years ago by Bryan Bartley <[email protected]>
Improve documentation of test cases

github.com/Bioprotocols/labop - 97aa8af33ceaa318d16d2dc291b6bcfd806ee1ef authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'main' into interlab_protocol

github.com/Bioprotocols/labop - a1d4849f6a825c8de2518020fbdbc134ed1d1ec5 authored over 2 years ago by Bryan Bartley <[email protected]>
Correcte Exp3, made docx and PDF

github.com/Bioprotocols/labop - 54626a59df64a7ac4431ca80febdee86c83aa25d authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Check in markdown documents

github.com/Bioprotocols/labop - 6be0c6b00edd92bac3af844c02342f5de2933173 authored over 2 years ago by Bryan Bartley <[email protected]>
Specify missing protocol outputs

github.com/Bioprotocols/labop - 261a638d236a3eb2f89aa49f769b977e51ae2ddd authored over 2 years ago by Bryan Bartley <[email protected]>
Add debugging output

github.com/Bioprotocols/labop - 96cbf56bb0eb1454a167145cb8e1c70998634942 authored over 2 years ago by Bryan Bartley <[email protected]>
trying to make challenge work

github.com/Bioprotocols/labop - c33e872f86f0ac4d08cba6f2e6325056e1d9849c authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Exp 1 and 2 MI, and some corrections

github.com/Bioprotocols/labop - 124f251e3412c5b4e9d2e8e92fd7ab9c5ac6b7be authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Merge branch 'interlab_protocol' of https://github.com/Bioprotocols/paml into interlab_protocol

github.com/Bioprotocols/labop - ebc2ccc6bfface18ea5625b3eef5aa2f2bfa98b8 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Create Layout_Exp2.png

github.com/Bioprotocols/labop - af816e4df7386bac67a6218d2e125f94a065091e authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Wrong fig corrected in Exp1

github.com/Bioprotocols/labop - 910f73d0a152149429e253f1fde9d6bccd7a3f01 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Corrected Exp1, and added Exp1MINI

github.com/Bioprotocols/labop - 7dfc1cda8e7b2c3b42b4dc09ab82acd5c8b1d92b authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Corrected J428106 in Exp1

github.com/Bioprotocols/labop - cab20d3c79bae061ba6693d91778a2f446eaedd2 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Edited serial dilution image

github.com/Bioprotocols/labop - bf0dd9d1b66c08a3523eeaf5b8207b180e22a549 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
final versions for publish in web.

github.com/Bioprotocols/labop - 0ee39b240c9b76d8204fad11e6dcdc1685f8efda authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Updated Culture specialization to MD (overnight if hours > 14)

github.com/Bioprotocols/labop - 42b4e1905bcf85217a3a94f35e7fdf1ce0246d91 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
final modifications

github.com/Bioprotocols/labop - 9cb052aede769f7edf38ec17c4d6ab745e6153e3 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
final touches to Standard exp3

github.com/Bioprotocols/labop - e56497968fa8572320574a41dd12f12026e062b7 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Bump protocol version

github.com/Bioprotocols/labop - a26041fb944c58de8cd15ac84e5b85429233f39f authored over 2 years ago by Bryan Bartley <[email protected]>
Add description

github.com/Bioprotocols/labop - 429cee27eac95e9f4e4a28c0ecc3430bba750b9c authored over 2 years ago by Bryan Bartley <[email protected]>
Add microplate seal to container ontologyand list it in the Materials section

github.com/Bioprotocols/labop - 01980313a1109605073fd7ca23b418925a684f05 authored over 2 years ago by Bryan Bartley <[email protected]>
Minor fix to protocol description

github.com/Bioprotocols/labop - af66baf3b87066d6c2d30b65d9202fcae78f2840 authored over 2 years ago by Bryan Bartley <[email protected]>
Insert updated figures into Markdown document

github.com/Bioprotocols/labop - 0c59e411a2de09e5046dfc570ee7fc25d17468cf authored over 2 years ago by Bryan Bartley <[email protected]>
Some corrections to Exp1 Standard.

github.com/Bioprotocols/labop - 15ae41100d178e62982acd613a8f20689162701c authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Incorporate Traci's and Vinoo's suggested edits

github.com/Bioprotocols/labop - e497203cdaf472df3dbcd05d0313d9fa7c6fc1ea authored over 2 years ago by Bryan Bartley <[email protected]>
Tweak Table title

github.com/Bioprotocols/labop - d5c0cdaff0185a59d892b3d553bbc2528ddac896 authored over 2 years ago by Bryan Bartley <[email protected]>
List containers under Materials section of markdown document

github.com/Bioprotocols/labop - df5f38cab9a55f51996032cd9ec17f2c3fbf7d6f authored over 2 years ago by Bryan Bartley <[email protected]>
Round rpm measures

github.com/Bioprotocols/labop - f76e82f8f7d7d953ecffb938063477361a52c691 authored over 2 years ago by Bryan Bartley <[email protected]>
Change wording of provision primitives to be more readable

github.com/Bioprotocols/labop - 6bc1655783931d5a84ba2f099bc23e5d88db42a0 authored over 2 years ago by Bryan Bartley <[email protected]>
Support captions for embedded images

github.com/Bioprotocols/labop - 2a928c1c3892d9a0a1371392daa64db58785d631 authored over 2 years ago by Bryan Bartley <[email protected]>
Add HoldOnIce primitive

github.com/Bioprotocols/labop - 9a55cede9f61f44a95dc18556995096a93c5850a authored over 2 years ago by Bryan Bartley <[email protected]>
Version 1.1 of protocols, includes PickColony primitive

github.com/Bioprotocols/labop - 58db2c2c95a0dbd5fd8dab79187a46d59709d54a authored over 2 years ago by Bryan Bartley <[email protected]>
Add PickColony and CulturePlates primitives

github.com/Bioprotocols/labop - 1ffac44f2050d0aaa6fdb46913e858244908ea2c authored over 2 years ago by Bryan Bartley <[email protected]>