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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 hyperlinks for some Components

github.com/Bioprotocols/labop - ed69c4e1e3058be0d851c8db23a4d9c2dd28dffd authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'interlab_protocol' of github.com:Bioprotocols/paml into interlab_protocol

github.com/Bioprotocols/labop - 11a2f933b131ba09e80f1ab4c1c44532a95fcb7a authored over 2 years ago by Bryan Bartley <[email protected]>
Copy over exp1 and exp2 interlab protocols from Alejandro's branch

github.com/Bioprotocols/labop - f7a3586c878af8bc39113c5fca8c783c2f2ca553 authored over 2 years ago by Bryan Bartley <[email protected]>
Update interlab-endpoint.py

github.com/Bioprotocols/labop - 98897e842075aefc48d5f073542c7380608bc867 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Move Outputs section of markdown document

github.com/Bioprotocols/labop - 1d1cb4cac813b30cc0ef446008bb2ecd15dee092 authored over 2 years ago by Bryan Bartley <[email protected]>
Add embedded image to markdown for multicolor particle calibration protocol

github.com/Bioprotocols/labop - 7afc9d266999adc7e1db886b31be53912ed580c0 authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'interlab_protocol' of github.com:Bioprotocols/paml into interlab_protocol

github.com/Bioprotocols/labop - f327385bacfeeb338ce9abadf668da182416d94a authored over 2 years ago by Bryan Bartley <[email protected]>
Insert reagent names into description text

github.com/Bioprotocols/labop - e5dbf83f30a357f4719a3be299035a875f4dee72 authored over 2 years ago by Bryan Bartley <[email protected]>
Move markdown to Execution object instead of ExecutionEngine object

github.com/Bioprotocols/labop - 53921a20c7e601f838c2ca163bd7ba772932391a authored over 2 years ago by Bryan Bartley <[email protected]>
Bump protocol version

github.com/Bioprotocols/labop - 43fb5a87ccf7ce8e9eb247d6b4d13d9e31889299 authored over 2 years ago by Bryan Bartley <[email protected]>
Create serial_dilution.PNG

github.com/Bioprotocols/labop - b12d548a9b42a90a90d7fea15e9d8d9786861001 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Check in markdown rendering for protocols as of now

github.com/Bioprotocols/labop - 00818e822fa662deadf7536a044e9f6fe6e6984e authored over 2 years ago by Bryan Bartley <[email protected]>
Render a table that shows where iGEM parts are located in the distribution kit

github.com/Bioprotocols/labop - f8fb75b76d350de3979c5b36409a68657172c0e1 authored over 2 years ago by Bryan Bartley <[email protected]>
Scripts have been adjusted now that markdown is attached to Execution instances instead of the ExecutionEngine

github.com/Bioprotocols/labop - d3930ed0ad20d21c065a8406a2685410b11d99c3 authored over 2 years ago by Bryan Bartley <[email protected]>
Add parts registry identifiers for test devices

github.com/Bioprotocols/labop - 952dcfa4935fcf1aa0c15b097775cee91eb26e0d authored over 2 years ago by Bryan Bartley <[email protected]>
Don't render section headers for empty sections

github.com/Bioprotocols/labop - 7a29adbc6d390e96b2ee28bcebc44d7c499552f0 authored over 2 years ago by Bryan Bartley <[email protected]>
Hack markdown rendering of Materials section

github.com/Bioprotocols/labop - 476730e0b0bc97980690afe3c6ceab6ae5930c02 authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'interlab_protocol' of github.com:Bioprotocols/paml into interlab_protocol

github.com/Bioprotocols/labop - 608b6fd7bbc478e4a132f326718c05593c58ba17 authored over 2 years ago by Bryan Bartley <[email protected]>
MarkdownSpecialization converts subprotocols into nested markdown rendering

github.com/Bioprotocols/labop - 5654fa2d0d7ddd4df3279dd34835753b05a97f77 authored over 2 years ago by Bryan Bartley <[email protected]>
typo

github.com/Bioprotocols/labop - 674b4cc4cf5568ef0ecf0626a007098b4da9fa68 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Updated well name to match 2022 distro plate 1.

github.com/Bioprotocols/labop - a26b2c4d3247660aca5bd75b0841e71404ea3ae2 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Update revised-interlab-growth-curve.py

Updated, and modified the well location in the distribution

github.com/Bioprotocols/labop - 668c8780e2901b72c7b4849c70c3852671b046da authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Update revised-interlab-growth-curve.py

github.com/Bioprotocols/labop - b77f907c18615540400b2e9f257f8e6402e64cb7 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
DefaultBehaviorSpecialization supports subprotocols

github.com/Bioprotocols/labop - 4f727f685ab569eb9483e0758c5759beca44079a authored over 2 years ago by Bryan Bartley <[email protected]>
update wordage

github.com/Bioprotocols/.github - b1c14cb3c56aec6fb57baa27bb51105f1334125b authored over 2 years ago by Timothy R. Fallon <[email protected]>
github image paths, how do they work?

github.com/Bioprotocols/.github - b81a6c78605abffb9017de0bbe94c0163a9c8006 authored over 2 years ago by Timothy R. Fallon <[email protected]>
fix readme

github.com/Bioprotocols/.github - b025623034ad3f9dab1d1358e9f3b505d179f71a authored over 2 years ago by Timothy R. Fallon <[email protected]>
update

github.com/Bioprotocols/.github - def18985ff8a105dd95090e08343604aeaf4ae68 authored over 2 years ago by Timothy R. Fallon <[email protected]>
Initial commit

github.com/Bioprotocols/.github - 6f0c3398224d754c73e7f6c9cb294285e1b3433d authored over 2 years ago by Timothy R. Fallon <[email protected]>
Add specialized behaviors for subprotocols

github.com/Bioprotocols/labop - f1e3e50936fbb44b37500df2832b416ebd0a69fe authored over 2 years ago by Bryan Bartley <[email protected]>
iGEM interlab examples

github.com/Bioprotocols/labop - 2bcde6500ab516f326df777249bc5fb471754f46 authored over 2 years ago by Bryan Bartley <[email protected]>
Add timepoints parameter to measurement primitives

github.com/Bioprotocols/labop - 84ea6906ba8f17af928c7d6301304c2f9b80b7aa authored over 2 years ago by Bryan Bartley <[email protected]>
Timepoint version of protocol

github.com/Bioprotocols/labop - 87ba6007644cc57d9fd29423b585616833640aa4 authored over 2 years ago by Bryan Bartley <[email protected]>
Incorporate feedback for the cell calibration protocol

github.com/Bioprotocols/labop - f007d41404d9268438b964b0f5fd32314115e92e authored over 2 years ago by Bryan Bartley <[email protected]>
fix link to Owlery API docs

github.com/Bioprotocols/container-ontology - 72b8b2f6af391e41032e915fa011e49df42c944c authored over 2 years ago by James Scott-Brown <[email protected]>
Merge pull request #140 from jamesscottbrown/patch-1

README: enable syntax highlighting

github.com/Bioprotocols/labop - a1597f9e889be63a7cfb76f869224f200ca0e58f authored over 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #11 from jamesscottbrown/patch-1

fix formatting of build instructions

github.com/Bioprotocols/labop-specification - d86de95f805889adc4d0808b53fefefba79406e6 authored over 2 years ago by Daniel Bryce <[email protected]>
README: enable syntax highlighting

github.com/Bioprotocols/labop - d08134410e5662f50fffe18b6a9bd82a5f31b81b authored over 2 years ago by James Scott-Brown <[email protected]>
fix formatting of build instructions

github.com/Bioprotocols/labop-specification - 21b0114e9630968a4be3944f191396eacd30c3ca authored over 2 years ago by James Scott-Brown <[email protected]>
Merge pull request #137 from Bioprotocols/xarrays-rebase

Xarrays rebase

github.com/Bioprotocols/labop - 802b65dc1628c53b149af47a525af8828ce516f5 authored over 2 years ago by bbartley <[email protected]>
represent arrays with serialized xarray

github.com/Bioprotocols/labop - 3b491ec331cf8ac3307787aff5cd58e92bf24f0d authored over 2 years ago by Daniel Bryce <[email protected]>
SampleArray and TransferByMap as Xarray

github.com/Bioprotocols/labop - 310196109af8b965a0d996cdaa7eb91897c23cfb authored over 2 years ago by Daniel Bryce <[email protected]>
added support for sample maps

github.com/Bioprotocols/labop - 54d3295f2080edf15dc515ba5600c0324c0ecb76 authored over 2 years ago by Daniel Bryce <[email protected]>
Convenience methods for getting active coordinates from a SampleArray/Mask

github.com/Bioprotocols/labop - 561452d4fce909277b83b248147877c5be6d9645 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix row and column mix up causing masks to fail

github.com/Bioprotocols/labop - 85d4e7bed8fd4c53d47ef5d2c0cd372783ad3121 authored over 2 years ago by Bryan Bartley <[email protected]>
Extend liquid handling primitives

github.com/Bioprotocols/labop - 645131adf9328b6ee5522784d3b1dedbb83dd540 authored over 2 years ago by Bryan Bartley <[email protected]>
Function to show primitive libraries

github.com/Bioprotocols/labop - ee30726eecb6cfda2eb57f7c135343382ce632f4 authored over 2 years ago by Bryan Bartley <[email protected]>
Clean up debugging output

github.com/Bioprotocols/labop - 9b45ace95221d39f6d3c436035eafcf62dcbaae0 authored over 2 years ago by Bryan Bartley <[email protected]>
checkpoint

github.com/Bioprotocols/labop - da94d7d582f3b6dfdbcb584f8f520c06ccbc14d5 authored over 2 years ago by Daniel Bryce <[email protected]>
fix error resolving literals

github.com/Bioprotocols/labop - a8ca6a5680708534a8b8123a74424a3ac12b2940 authored over 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #136 from Bioprotocols/HARMONY22

Support PAML

github.com/Bioprotocols/labop - 167d225b4a02d60ea6d821ef3203c9079f863ce6 authored over 2 years ago by Daniel Bryce <[email protected]>
Label some classes in the turtle to enable lookup via tyto. See #135

github.com/Bioprotocols/labop - fd4781db5ef50f0eeafa9cabd552b2ce7daf305b authored over 2 years ago by Bryan Bartley <[email protected]>
Incorporate Alejandro's and Jacky's revisions

github.com/Bioprotocols/labop - b5d4e716c8c418b47cc9de38cb70c47ad6bca171 authored over 2 years ago by Bryan Bartley <[email protected]>
Challenging (timepoint) version of growth curve protocol

github.com/Bioprotocols/labop - cc9eb23098ecbb538c1006fb285e757f69fa15b8 authored over 2 years ago by Bryan Bartley <[email protected]>
Track versions of the markdown protocols

github.com/Bioprotocols/labop - eabd49e05e5b60922207255e554aecc663a4dadb authored over 2 years ago by Bryan Bartley <[email protected]>
Support custom names of measurement steps

github.com/Bioprotocols/labop - 8069c0501a7fc57835503e6e3065d00e4ca4756f authored over 2 years ago by Bryan Bartley <[email protected]>
Add multicolor particle calibration protocol

github.com/Bioprotocols/labop - 6af9d099f5ab6de74d41a239f1493927892690bc authored over 2 years ago by Bryan Bartley <[email protected]>
Replicates parameter for Transfer primitves

github.com/Bioprotocols/labop - 355af5c1fbf07f41ef1fdbff67ac3b132038f7af authored over 2 years ago by Bryan Bartley <[email protected]>
Stamp version on markdown protocol

github.com/Bioprotocols/labop - 9882d3525035debb3b7910f156cb2e279d002fe0 authored over 2 years ago by Bryan Bartley <[email protected]>
End-to-end demonstration of cell calibration protocol

github.com/Bioprotocols/labop - dc731150e137ec9304058a99f10907d823c425ad authored over 2 years ago by Bryan Bartley <[email protected]>
Created using Colaboratory

github.com/Bioprotocols/labop - abfec5915e86d9a317b952aa64c71035518512d9 authored over 2 years ago by Daniel Bryce <[email protected]>
Draft 2022 cell calibration protocol

github.com/Bioprotocols/labop - c2271e4d6c510d25170eb6331037e89d673e58d0 authored over 2 years ago by Bryan Bartley <[email protected]>
Squashed commit of test-for-bad-restrictions (#123).

* Fix test script (`check-turtle-files`): Check for empty string in list
of files to check.

* A...

github.com/Bioprotocols/labop - 328891df745a9842061ebe890b040f456be3caea authored over 2 years ago by Robert P. Goldman <[email protected]>
Ignore build directory.

github.com/Bioprotocols/labop - 96690281f6cf97acbd41e80db87036d0e89a625f authored over 2 years ago by Robert P. Goldman <[email protected]>
Remove redundant file.

uml-flattened.ttl was a version of uml.ttl with the reification applied (blank nodes added expli...

github.com/Bioprotocols/labop - 9e794611f9be34c385e8e031f10c2b6f203ca235 authored over 2 years ago by Robert P. Goldman <[email protected]>
Fix output to transcript.

github.com/Bioprotocols/labop - 744daa4a01d21e3d605f29bffd4b4e9155587888 authored over 2 years ago by Robert P. Goldman <[email protected]>
Test on multiple python versions.

github.com/Bioprotocols/labop - 29864764984f768cbfd474d0d367527073b67db6 authored over 2 years ago by Robert P. Goldman <[email protected]>
End-to-end demonstration of SampleArray operations, including serialization for contents field. See #113

github.com/Bioprotocols/labop - 630151cfa22697400df9a9929bc9d5f1cc9015bf authored over 2 years ago by Bryan Bartley <[email protected]>
Working demonstration of protocol execution using batch samples represented by SampleArrays.

github.com/Bioprotocols/labop - 780ddb4296c48d631374c33deaf51b14cf1f17e9 authored over 2 years ago by Bryan Bartley <[email protected]>
Make SampleArray contents an unbounded list of URI references

github.com/Bioprotocols/labop - 7c016097c1ec69db9b114ece4ccf92ea78fe99c0 authored over 2 years ago by Bryan Bartley <[email protected]>
Support unbounded parameters, resolves #127

github.com/Bioprotocols/labop - cb3c28c16894d6c9833dcdfce58538ba84b55720 authored over 2 years ago by Bryan Bartley <[email protected]>
Markdown specialization handles designated protocol outputs more gracefully. Related to #125

github.com/Bioprotocols/labop - 06a57d2dfc2d37abc931fc8c775c31270597e884 authored over 2 years ago by Bryan Bartley <[email protected]>
Improve Markdown display for Transfer execution

github.com/Bioprotocols/labop - 29a259a5951e35f9828113bd45da245061cf97be authored over 2 years ago by Bryan Bartley <[email protected]>
Add primitive for Hold

github.com/Bioprotocols/labop - 0f4d34d50ed150dbcd1fab919a10df612b485e9a authored over 2 years ago by Bryan Bartley <[email protected]>
CallBehaviorExecutions generate output tokens. Resolves #125

github.com/Bioprotocols/labop - 59965a0cc51369d7c87890cc0a0605af7fbda57d authored over 2 years ago by Bryan Bartley <[email protected]>
Save interlab-growth-curve notebook

github.com/Bioprotocols/labop - 951deb101d8ba1e0c67fbd5ce21b839647019a5f authored over 2 years ago by Bryan Bartley <[email protected]>
Fix #130 and add test

github.com/Bioprotocols/labop - 8748593aa4c16afb9152d5e7a61d29b2b8306d64 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add test for optional and required Parameters

github.com/Bioprotocols/labop - 9fdea5e6508cecbcaa9d5926b48e74aeb9fb84ec authored almost 3 years ago by Bryan Bartley <[email protected]>
Add test cases for Pins mismatched with Parameters

github.com/Bioprotocols/labop - fdbaeff3c365e2b92acdf15640d2c58e125678ec authored almost 3 years ago by Bryan Bartley <[email protected]>
Format error message for greater clarity

github.com/Bioprotocols/labop - 26dc9b01c26a6db959422b9f83b594129b5db212 authored almost 3 years ago by Bryan Bartley <[email protected]>
Get owlery-client from git repo. (#23)

Remove the owlery-client, automatically generated from the spec, to a separate repo, from which ...

github.com/Bioprotocols/container-ontology - ff1d61e93bb75995c2144b3996f5a6d9a788d6b6 authored almost 3 years ago by rpgoldman <[email protected]>
Merge pull request #76 from Bioprotocols/data-link

Prototype representation of SampleArray and SampleData

github.com/Bioprotocols/labop - 2d99c40e7e29391bfad6c805c6630a68a33bb6a5 authored almost 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #112 from Bioprotocols/110-execution_example

Add Markdown converter documentation

github.com/Bioprotocols/labop - d4cacc5de27fd088a8043ba94d3a9c2b5026bcd3 authored almost 3 years ago by Daniel Bryce <[email protected]>
Add note about the GitHub Discussions.

Try to point readers to the Discussions tab for Q&A.

github.com/Bioprotocols/container-ontology - d39b6326d4b5ece6fa754a9c391add1bf89ca47d authored almost 3 years ago by rpgoldman <[email protected]>
Add Vortex to liquid handling library

github.com/Bioprotocols/labop - 0bf43247b72cc48a58b10524b0016a67da888daf authored almost 3 years ago by Bryan Bartley <[email protected]>
small cleanup

github.com/Bioprotocols/labop - c2b9926211f3d2295c89da8601aeefc112655d7d authored almost 3 years ago by Daniel Bryce <[email protected]>
add pandas to install

github.com/Bioprotocols/labop - 6c5e9239fb2c834fc723277dd7ef4256b9621fdd authored almost 3 years ago by Daniel Bryce <[email protected]>
add pandas to install

github.com/Bioprotocols/labop - efde8448c577c64e437463dd3c481d6557833796 authored almost 3 years ago by Daniel Bryce <[email protected]>
Save sampledata as string CSV

github.com/Bioprotocols/labop - d18d81c83bedff20c7339fa0614e113ba6c958c9 authored almost 3 years ago by Daniel Bryce <[email protected]>
Workaround for #114, fix mark_optional choking on Parameters without a lower_bound specified

github.com/Bioprotocols/labop - f0f3e930762f381d7552ae88f846147ef60e6ca3 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add Vortex primitive

github.com/Bioprotocols/labop - ba02640cd6a64a8e80bf92032c8a0ad5726f64ee authored almost 3 years ago by Bryan Bartley <[email protected]>
updated rubric due to whitespace change

github.com/Bioprotocols/labop - 05ea858ebf58423d951c38160b965bd9239dd678 authored almost 3 years ago by Daniel Bryce <[email protected]>
pre-commit file fixes

github.com/Bioprotocols/labop - 9aaeb89b336eda6b308b625c3f7c147732696f8a authored almost 3 years ago by Daniel Bryce <[email protected]>
fixed issues with rebase and tests

github.com/Bioprotocols/labop - 070c090b8e17b15b5a47a03c1a252f16401a209b authored almost 3 years ago by Daniel Bryce <[email protected]>
Fix imports for owlery_client.

Previously, sub-modules were not imported.

github.com/Bioprotocols/container-ontology - 1af1623e06494670c9a5cb1e0a653b39e6ca386f authored almost 3 years ago by Robert P. Goldman <[email protected]>
Update the Makefile with fixes needed for new Docker image.

github.com/Bioprotocols/container-ontology - f5b052d5a3abfb2e3443920c73016bd21f367a1e authored almost 3 years ago by Robert P. Goldman <[email protected]>
Spec for PrimitiveArray

github.com/Bioprotocols/labop - 39b8b9483da690e82bb484fa0487efd1fbc7a7c2 authored almost 3 years ago by Daniel Bryce <[email protected]>
Update README.md

github.com/Bioprotocols/laboped - 2368eb51659a5422059b62ea1803510faa150da0 authored almost 3 years ago by Daniel Bryce <[email protected]>
Create README.md

github.com/Bioprotocols/laboped - 62332b8c072ed96cade21477764a47612d565a26 authored almost 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #18 from Bioprotocols/examples

Examples

github.com/Bioprotocols/laboped - ebea50168930fe8f92092d1d156b11fe47a2dd80 authored almost 3 years ago by Daniel Bryce <[email protected]>