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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

Extend the README

Add a link to the specification repository.

Finish a sentence fragment.

github.com/Bioprotocols/labop - 683d0413b62717b6e4a19eea401614aa03385b87 authored almost 3 years ago by rpgoldman <[email protected]>
Update github workflow to install optional paml-check

github.com/Bioprotocols/labop - f2cc3977d65492aa30a45129ff63231dd0a20251 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge branch 'main' into 78-upgrade_rdflib

github.com/Bioprotocols/labop - aab17a8538a2b44546b1170ad95440a29c6a1a49 authored almost 3 years ago by Bryan Bartley <[email protected]>
Replace opil:compositionalProperty with sbol:directlyComprises

github.com/Bioprotocols/labop - 529d118b5dfb27dfd225c8522e0d140c9ae8b2c4 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #85 from Bioprotocols/81-paml_check

Move paml-check to optional requirements

github.com/Bioprotocols/labop - f8b9a0357527ef18e04372e5ad5cf7ca78bd5e8d authored almost 3 years ago by bbartley <[email protected]>
Move paml-check to optional requirements

github.com/Bioprotocols/labop - 666f68149d40855f3cc0ee91c235d2bb57a62b12 authored almost 3 years ago by Bryan Bartley <[email protected]>
process primitive connections to paml conversion

github.com/Bioprotocols/laboped - 051f362d708b67d903ee3c213f0067f5bca5c6e5 authored almost 3 years ago by Daniel Bryce <[email protected]>
Add support for converting graph primitives to paml primitives

github.com/Bioprotocols/laboped - 5c0a775171e4504f1242b7e1532732ae17574eb9 authored almost 3 years ago by Daniel Bryce <[email protected]>
Edits to run on os x and task to clean all

github.com/Bioprotocols/laboped - f1e56114676c892c7206c620955ea5f7f6de5836 authored almost 3 years ago by Daniel Bryce <[email protected]>
ignore workspace

github.com/Bioprotocols/laboped - 9e726c417b7b05552e11418da34cd3fde38c6503 authored almost 3 years ago by Daniel Bryce <[email protected]>
ignore media files

github.com/Bioprotocols/laboped - ac5e82eaedb4029aaef00f21602c4829b30fcf20 authored almost 3 years ago by Daniel Bryce <[email protected]>
Adapting for version differences on osx

github.com/Bioprotocols/laboped - cb048551a1f0cc1b12197b54a8270c99746669ed authored almost 3 years ago by Daniel Bryce <[email protected]>
fix rebuild command after having switched to viewsets

github.com/Bioprotocols/laboped - 5f5ed49953a623068584e8730d5e53a8aaee0af2 authored almost 3 years ago by Jack Ladwig <[email protected]>
allow download rete graph

github.com/Bioprotocols/laboped - 6bf80e477feef34a87bea93fca330a573158a02e authored almost 3 years ago by Jack Ladwig <[email protected]>
initial capabilities for downloading a file from the backend

github.com/Bioprotocols/laboped - e503ee3d1fa77d9f999b110b45ea6e2d934dd221 authored almost 3 years ago by Jack Ladwig <[email protected]>
update title

github.com/Bioprotocols/laboped - 5e9a12de7597f7b3504de3cf546e81cf09e8f4b9 authored about 3 years ago by Jack Ladwig <[email protected]>
update manifest

github.com/Bioprotocols/laboped - 337f6545eaab263500bc7a1cba9289a84b610a1b authored about 3 years ago by Jack Ladwig <[email protected]>
Merge pull request #7 from Bioprotocols/user-specific-protocols

very basic pass at user account associated protocols

github.com/Bioprotocols/laboped - 4bc2a106a1ae808a482fd5741c235ebfa4f8e0f1 authored about 3 years ago by jgladwig <[email protected]>
very vasic pass at user account assoicated protocols

github.com/Bioprotocols/laboped - 4d47767bb6290b74de0d6349ff6e46bbd9c7ec30 authored about 3 years ago by Jack Ladwig <[email protected]>
append not +=

github.com/Bioprotocols/laboped - b0bbd5fe5e27a3af3ea73b30b5897f93db5f4066 authored about 3 years ago by Jack Ladwig <[email protected]>
ignores

github.com/Bioprotocols/labop-check - 7eb012c1eac960c23d3502e0b666d98afa5382df authored about 3 years ago by Daniel Bryce <[email protected]>
use logger

github.com/Bioprotocols/labop-check - e747efcfe1d0d22b4d3b6427111e33d90b6f1d9d authored about 3 years ago by Daniel Bryce <[email protected]>
simplify trailing slash

github.com/Bioprotocols/laboped - 8d0caf45b0776bc949fabe597a22ded08a4d322d authored about 3 years ago by Jack Ladwig <[email protected]>
make settings.py more configurable

github.com/Bioprotocols/laboped - d6b246642bd7fd40b3cce2efcc235513eb998d88 authored about 3 years ago by Jack Ladwig <[email protected]>
Merge pull request #6 from Bioprotocols/api_cleanup

cleanup api endpoints

github.com/Bioprotocols/laboped - 1e2283319434e43d5dfbbb4033e7ab3de59366a2 authored about 3 years ago by jgladwig <[email protected]>
cleanup api endpoints

github.com/Bioprotocols/laboped - 0a8c4206f653a6fa77a07d6dfab7c63afbab1ee3 authored about 3 years ago by Jack Ladwig <[email protected]>
fix gitignore after rebase

github.com/Bioprotocols/laboped - 4fb4f149c9f528c14e6e2aabfba036842d214108 authored about 3 years ago by Jack Ladwig <[email protected]>
cleanup settings file

github.com/Bioprotocols/laboped - b5a5f4b891599d84c05b9f14c7bd16b3b619b8ab authored about 3 years ago by Jack Ladwig <[email protected]>
enable logging

github.com/Bioprotocols/laboped - c1292d88528192bb9a356626700988e4f4b49bae authored about 3 years ago by Jack Ladwig <[email protected]>
restructure code and use pipenv

github.com/Bioprotocols/laboped - af7b8774b7a94113805221f503a20e84d3f32e45 authored about 3 years ago by Jack Ladwig <[email protected]>
switch to a requirements file for the backend

Then just use pipenv for the dev environment

github.com/Bioprotocols/laboped - cdf936c72376483b6b0cc8a6d2d45cbc28a14446 authored about 3 years ago by Jack Ladwig <[email protected]>
more specific css

github.com/Bioprotocols/laboped - 445726633feb49882c7d02299622cad4c3f9ba72 authored about 3 years ago by Jack Ladwig <[email protected]>
Merge pull request #5 from Bioprotocols/port-types

Port types

github.com/Bioprotocols/laboped - 43d09143b5d835689696c2e9510e94d7daabf3b4 authored about 3 years ago by Daniel Bryce <[email protected]>
remove old workspace

github.com/Bioprotocols/laboped - 9bf6e034638beeead7e602bbb9ee6c1a17f284c9 authored about 3 years ago by Daniel Bryce <[email protected]>
Fixes for saving protocols, port types, and added tabs for nodes in the protocol

github.com/Bioprotocols/laboped - 2d03210bc1ac31b9fd3bbf15c60e448dedbe8fcb authored about 3 years ago by Daniel Bryce <[email protected]>
remove basename

github.com/Bioprotocols/laboped - 428d07a8c32a3fba07fa402876c1dd5b772ea6cc authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint fixing csrf

github.com/Bioprotocols/laboped - e4984431fc180b3987485a78ff3292e3e8a49dee authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint

github.com/Bioprotocols/laboped - 90a676c780724d18bdcc8d2d6e0788f558c24ed9 authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #4 from Bioprotocols/proxy-fix

Use IP instead of host for proxy

github.com/Bioprotocols/laboped - ba3e305d62a05f69a886db012dc2921efa0b3204 authored about 3 years ago by jgladwig <[email protected]>
Use IP instead of host for proxy

github.com/Bioprotocols/laboped - 2c92764ccd5823a2db97cd0713fce49ba9a7421d authored about 3 years ago by Daniel Bryce <[email protected]>
vscode workspace configuration

github.com/Bioprotocols/laboped - 8a8dce4d0dd78013dfdd62d779aaef80e781188a authored about 3 years ago by Jack Ladwig <[email protected]>
minor editor width tweak

github.com/Bioprotocols/laboped - ed6054dfe0c984ab071c9521841a86beb983da6d authored about 3 years ago by Jack Ladwig <[email protected]>
Merge pull request #3 from Bioprotocols/layout-updates

update editor layout

github.com/Bioprotocols/laboped - 81547699eba3dc705dc4188e424b114ab340d8b9 authored about 3 years ago by jgladwig <[email protected]>
update editor layout

github.com/Bioprotocols/laboped - 91fda60945f6de7108cbbefd6a7f72c5cf583217 authored about 3 years ago by Jack Ladwig <[email protected]>
Add "no-clone" pip install instructions.

`pip` can install with a git URL as argument.

github.com/Bioprotocols/labop - 99ea91857547fb129391b52d07d752a9dbe2693c authored about 3 years ago by rpgoldman <[email protected]>
Update README.md

github.com/Bioprotocols/labop - 8155a2a6eebedf26fc6f97c0bcdab8fa7080f805 authored about 3 years ago by Jacob Beal <[email protected]>
Merge pull request #2 from Bioprotocols/user-accounts

Initial user accounts

github.com/Bioprotocols/laboped - 128a5ca6fed4dfaae454b71e7aafa9110ffb0901 authored about 3 years ago by jgladwig <[email protected]>
cleanup login code

also hides the edtior behind the login screen and adds an account
dropdown for logging out.

github.com/Bioprotocols/laboped - 11168cdd49bb0ddfd1dd2b3fdd645269d90d6d71 authored about 3 years ago by Jack Ladwig <[email protected]>
adjust CORS setup

disable axios proxy since we are instead using allowed CORS
origins. Also send along the credent...

github.com/Bioprotocols/laboped - 2b5be0c2a53fbea567bbb26bfa286a2011d94278 authored about 3 years ago by Jack Ladwig <[email protected]>
initial configuring of sessions

Add a login and signup page that connect to the django backend.

Some CORS issues still need res...

github.com/Bioprotocols/laboped - 9d4256c2efc83484d0c22c714b8b34f6e88cf88d authored about 3 years ago by Jack Ladwig <[email protected]>
Merge pull request #1 from Bioprotocols/react-integration

React integration

github.com/Bioprotocols/laboped - edb426380ceb815c0dbcd583a35a5f576962ac79 authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint on RDF serialization

github.com/Bioprotocols/laboped - b628e65424fa9de7b12db5483bda7897ed7eb933 authored about 3 years ago by Daniel Bryce <[email protected]>
Temporarily downgrade RDF-related dependencies (#82)

Fix the GitHub CI by avoiding RDFLIB 6-related issues

github.com/Bioprotocols/labop - d030b266338aaeebfe6a9bda140bd8258bfa0aea authored about 3 years ago by rpgoldman <[email protected]>
Fixed menu and primitive port bugs

github.com/Bioprotocols/laboped - c252ec8e74d1074eb61cd75e8781f0470bd21e90 authored about 3 years ago by Daniel Bryce <[email protected]>
Round tripping from front to back end.

github.com/Bioprotocols/laboped - 6372a2a5c7187466767f246df32f6c3d2635334b authored about 3 years ago by Daniel Bryce <[email protected]>
sending protocols to backend for storage.

github.com/Bioprotocols/laboped - 13a1d2476352113c8557ae4e4b0f55cd11ce23bc authored about 3 years ago by Daniel Bryce <[email protected]>
Setup menu and initial actions

github.com/Bioprotocols/laboped - ab81d339cd9eb3d33b09c992eab84766be04c671 authored about 3 years ago by Daniel Bryce <[email protected]>
setup api to give primitive inputs and outputs

github.com/Bioprotocols/laboped - 36a88b893cd54b7ab039cc5f37e143c876161112 authored about 3 years ago by Daniel Bryce <[email protected]>
main layout adjustments

github.com/Bioprotocols/laboped - 02693e7f8adc0cc88e8ed87bc7b87d3fcba8a92e authored about 3 years ago by Daniel Bryce <[email protected]>
Added axios config to API.js

github.com/Bioprotocols/laboped - fd9cad61a3b3124d320711e70ba45aabf5a34339 authored about 3 years ago by Daniel Bryce <[email protected]>
fixed /rebuild endpoint

github.com/Bioprotocols/laboped - 14f99cd2b7b7a354ed456563838985f66eedc0f8 authored about 3 years ago by Daniel Bryce <[email protected]>
set primitiveview for rebuild

github.com/Bioprotocols/laboped - 9d1c884fe0a8839d74276aac0dbaa93d04c11fc7 authored about 3 years ago by Daniel Bryce <[email protected]>
removed vue and opened /rebuild

github.com/Bioprotocols/laboped - 8556c11b0c57aa6fc7dad2fb163f1de663d758ef authored about 3 years ago by Daniel Bryce <[email protected]>
broken django blocking requests

github.com/Bioprotocols/laboped - 6df1ac8d8bc3966238281cd11a1f60adb53cd3ae authored about 3 years ago by Daniel Bryce <[email protected]>
Debug

github.com/Bioprotocols/labop - 31066f6b1718c304477ee58b98a4049f6c37e062 authored about 3 years ago by Bryan Bartley <[email protected]>
Upgrade pysbol and sbol_factory dependency

github.com/Bioprotocols/labop - 55bf90296a54cb6001b47ba0d649cca939a4441d authored about 3 years ago by Bryan Bartley <[email protected]>
Upgrade rdflib dependency

github.com/Bioprotocols/labop - 398085839cb6176fb403c722461a9adea9199b9c authored about 3 years ago by Bryan Bartley <[email protected]>
simple integration

github.com/Bioprotocols/laboped - f72906d457264574d05a546738779f18b18d89fa authored about 3 years ago by Daniel Bryce <[email protected]>
saving progress on vue to try out react

github.com/Bioprotocols/laboped - 4547d5e5cf0ac8a7453681abe865758300e55a83 authored about 3 years ago by Daniel Bryce <[email protected]>
use requirements in readme

github.com/Bioprotocols/laboped - 43638e1a99ae947f47bc3f2dd8f98573aed7d98b authored about 3 years ago by Daniel Bryce <[email protected]>
requirements.txt addition

github.com/Bioprotocols/laboped - 5c6a5ef14257253f30d17ae7343a96ae811f2249 authored about 3 years ago by Daniel Bryce <[email protected]>
tweaked readme markdown

github.com/Bioprotocols/laboped - 480506b38a424e6bc1b0b0b5200fba1a3df8bf87 authored about 3 years ago by Daniel Bryce <[email protected]>
added secret key instructions

github.com/Bioprotocols/laboped - 5b30967851c86f2b208c9f02aa130303ab68647f authored about 3 years ago by Daniel Bryce <[email protected]>
initial commit

functioning front and back ends

ignores

added client to repo after move from top level

Initia...

github.com/Bioprotocols/laboped - cb5c5dafd6df09a1324cec04031e520f566075b0 authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #73 from Bioprotocols/interactive-notebook-readme

Update README.md

github.com/Bioprotocols/labop - 60064fc82d4c911d2c39e7f4b33862ee4f4c0c83 authored about 3 years ago by Daniel Bryce <[email protected]>
Update README.md

github.com/Bioprotocols/labop - ef4be6779c2166713b7d624980edd167a3cdc4b6 authored about 3 years ago by Daniel Bryce <[email protected]>
Update README.md

github.com/Bioprotocols/labop - c4b97659909b50e4689928b2ae820bc4f92f1a74 authored about 3 years ago by Daniel Bryce <[email protected]>
Require minimum plotly version

github.com/Bioprotocols/labop-check - 120cc01227de622e250a3162d03f9e45120057f3 authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #65 from Bioprotocols/to-autoprotocol

This branch adds functionality to output different "specializations" of a protocol to either mar...

github.com/Bioprotocols/labop - ac03faf1cfdf29fa4a9a72753454f718598a8a83 authored about 3 years ago by Daniel Bryce <[email protected]>
undo github action to run specific notebooks

github.com/Bioprotocols/labop - 939b108b437f624302b090ea1601a8d9a5bfaa09 authored about 3 years ago by Daniel Bryce <[email protected]>
use github action to run specific notebooks

github.com/Bioprotocols/labop - ac29b6a7c66203cfb6f0d01a9380e97d946e4f24 authored about 3 years ago by Daniel Bryce <[email protected]>
use github action to run specific notebooks

github.com/Bioprotocols/labop - 779ef7e62ec577346c961199971955a41ee5ce3f authored about 3 years ago by Daniel Bryce <[email protected]>
install paml-check dep

github.com/Bioprotocols/labop - e40e0da2cc93632161bb162470d21fc5496ee5b3 authored about 3 years ago by Daniel Bryce <[email protected]>
install paml-check dep

github.com/Bioprotocols/labop - 20f213e63e3504f49318d38f8fa4a35ddf1113f2 authored about 3 years ago by Daniel Bryce <[email protected]>
use default env for notebooks

github.com/Bioprotocols/labop - 8c072a7daefd2716122c2ba113b17018c2ce7778 authored about 3 years ago by Daniel Bryce <[email protected]>
install test dependencies for pytest

github.com/Bioprotocols/labop - 2c70725bb9617323d12f8ca1f920b41c14f71172 authored about 3 years ago by Daniel Bryce <[email protected]>
install test dependencies for pytest

github.com/Bioprotocols/labop - 51610f5b00263548b6df9303dda4a031e0bee95b authored about 3 years ago by Daniel Bryce <[email protected]>
merge request cleanups and notebook testing enabled in github

github.com/Bioprotocols/labop - 39048beddb990afad69e929d88622bd0d40dce6f authored about 3 years ago by Daniel Bryce <[email protected]>
Added Notebook tests and pre-commit hooks for removing notebook output and some other source checks.

github.com/Bioprotocols/labop - 01f4d76ce9073c41ae4daa16a975408cb77b128a authored about 3 years ago by Daniel Bryce <[email protected]>
using ordered parameters for execution, but still getting non-deterministic output.

github.com/Bioprotocols/labop - 5482a9d24e462d955dcd3829b3360e10cd48a3ac authored about 3 years ago by Daniel Bryce <[email protected]>
prepared notebooks for test.

github.com/Bioprotocols/labop - 3052e4558f59ff5b9f0ad71c6d03d2fbcf1ae042 authored about 3 years ago by Daniel Bryce <[email protected]>
Propagated change to using LiteralReference for EE values into the conversion output formats.

github.com/Bioprotocols/labop - 27b052c4aa053ddd277d599a63bc8830c5b57f2e authored about 3 years ago by Daniel Bryce <[email protected]>
Added Strateos instructions to README. Modified references to Transcriptic to be Strateos.

github.com/Bioprotocols/labop - d2e76b3ed97e273595fca7286e967095675565b9 authored about 3 years ago by Daniel Bryce <[email protected]>
Add executable scripts.

Added `restrictions` and `to_sorted_ntriples` scripts to be installed with pip install. These ma...

github.com/Bioprotocols/labop - a2ddb7b1332ef0af5fa74bd9d6da189cc326b617 authored about 3 years ago by Robert P. Goldman <[email protected]>
use more supported version of dict merge

github.com/Bioprotocols/labop - eb891fcde5471ed8cdfde679a5f400df00eae648 authored about 3 years ago by Daniel Bryce <[email protected]>
fixed references to call parameter values

github.com/Bioprotocols/labop - 1eaf23eb16b1b008251748e8a65b4cb0a5d9382f authored about 3 years ago by Daniel Bryce <[email protected]>
Restore old TTL files.

github.com/Bioprotocols/labop - 4ecbf9a52467557db749a4589a7c0233b23f80f6 authored about 3 years ago by Robert P. Goldman <[email protected]>
Fixes to OWL RDF utils.

Another fix.

github.com/Bioprotocols/labop - c9e7e2a9ae01f0964a1dac1c213025b1ea1b7c70 authored about 3 years ago by Robert P. Goldman <[email protected]>
Add owl_rdf_utils module.

This contains code for handling bad restrictions and code for translating a graph into sorted nt...

github.com/Bioprotocols/labop - 51b2dec57d3de74fc54e12e052846ebe87db23c4 authored about 3 years ago by Robert P. Goldman <[email protected]>
Correct the installation information in README.txt

Corrected the installation information in README, also adapted basic API docs

github.com/Bioprotocols/labop - d6b457dd47d835a5bc34c22f78c2764dffde29a0 authored about 3 years ago by Jacob Beal <[email protected]>