Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

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

fix failing tests

github.com/Bioprotocols/labop - 0aadc01e432a2cc45f65c9bc20118bf6af308769 authored over 3 years ago by Jake Beal <[email protected]>
inference using LocatedData; draft of subprotocol type inference

github.com/Bioprotocols/labop - 7ef183f319db105d9d9b8f4de0e694410ecf25fc authored over 3 years ago by Jake Beal <[email protected]>
library inference fully prototype

github.com/Bioprotocols/labop - f6c92dce11ffa23213e939bb7307d8ad31b2dea4 authored over 3 years ago by Jake Beal <[email protected]>
add numpy to dependencies

github.com/Bioprotocols/labop - d30c16d5dc0470f959e9aba420c40dd0f3241f29 authored over 3 years ago by Jake Beal <[email protected]>
continued work on growth protocol

github.com/Bioprotocols/labop - 6df39f234090f51dd14359ca144e6e38cdd29693 authored over 3 years ago by Jake Beal <[email protected]>
Better approach to coordinate reduction

github.com/Bioprotocols/labop - 2ac1a587442db36aecf2828507e6508c5cfa57e0 authored over 3 years ago by Jake Beal <[email protected]>
working on container inferencing

github.com/Bioprotocols/labop - ca8e5787f7663404bdccc5c0c97047661d547c7d authored over 3 years ago by Jake Beal <[email protected]>
Merge commit '8e5f1a5b9d3d71ad1763e646bbde6734631f962e' into growth-protocol

github.com/Bioprotocols/labop - 7e024644e1cec82b1fc3b38d7112131bcff71830 authored over 3 years ago by Jake Beal <[email protected]>
fix package install

github.com/Bioprotocols/labop - 19f6f7dab604ce172ec5446ee51302fceb3902c3 authored over 3 years ago by Jake Beal <[email protected]>
cleaning up type inference

github.com/Bioprotocols/labop - 20da98a837fe1c5c0f868708c739026f478fbd21 authored over 3 years ago by Jake Beal <[email protected]>
Update script for rendering growth curve protocol

github.com/Bioprotocols/labop - 8e5f1a5b9d3d71ad1763e646bbde6734631f962e authored over 3 years ago by Bryan Bartley <[email protected]>
continued work on type inference

github.com/Bioprotocols/labop - faadeb87676751a0f686fc640ed5c7cd39c70192 authored over 3 years ago by Jake Beal <[email protected]>
working on type inference

github.com/Bioprotocols/labop - 3c18ea36159bb4228f9d073410676171de38523e authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #9 from SD2E/growth-protocol

Growth protocol complete draft

github.com/Bioprotocols/labop - 840c81cddc3fb930aec06f35e42f4516a141202e authored over 3 years ago by Jacob Beal <[email protected]>
complete draft of growth curve protocol

github.com/Bioprotocols/labop - 20348fa7c601db9b0c5f22cddd2b5a5439340181 authored over 3 years ago by Jake Beal <[email protected]>
subprotocol for growth curve is building fully

github.com/Bioprotocols/labop - 332b91337fd1326ffa48dd423e85ff44b942bf56 authored over 3 years ago by Jake Beal <[email protected]>
subprotocol inputs and outputs

github.com/Bioprotocols/labop - 90359dab5cca785033f1ca0a6f46df1d548a0379 authored over 3 years ago by Jake Beal <[email protected]>
macro functions for adding inputs and outputs

github.com/Bioprotocols/labop - f598f929fb15b1b252296e1d7df6d76b6b62efce authored over 3 years ago by Jake Beal <[email protected]>
Remove doc requirement from pin calls, implicit flows through use of activities in input slots

github.com/Bioprotocols/labop - e02bd13804ac9ac85e60a38d855a3d0e96c3e349 authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #8 from SD2E/lazy-libraries

only libraries actually used are imported

github.com/Bioprotocols/labop - f275be70529eb6ad00debe217b33468e2bccbbd4 authored over 3 years ago by Jacob Beal <[email protected]>
only libraries actually used are imported

github.com/Bioprotocols/labop - 1d7b7221df4a03d1befee38a08dae9e88ac93103 authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #7 from SD2E/markdown-package

Markdown package

github.com/Bioprotocols/labop - 51bf99857158a92a199fc44bf5459c2ead89dd77 authored over 3 years ago by Jacob Beal <[email protected]>
use python 3.9, not 3.8

github.com/Bioprotocols/labop - ff599690a5297953eec3fc011176460d5ce2ac67 authored over 3 years ago by Jacob Beal <[email protected]>
add missing dependency

github.com/Bioprotocols/labop - 0f4fba9bc2b8e4c990ba9a9763e3d6b5812f3dec authored over 3 years ago by Jake Beal <[email protected]>
a bit more cleanup

github.com/Bioprotocols/labop - 1a59952dc26a756456344625cafe555bdcbe5aa4 authored over 3 years ago by Jake Beal <[email protected]>
Update python-package.yml

github.com/Bioprotocols/labop - d4e4a7caea168d00a69e9ee32c7731318cadb8b3 authored over 3 years ago by Jacob Beal <[email protected]>
markdown package initial split and test

github.com/Bioprotocols/labop - 41643cc9e9dfae62250bf08b58b40b86e3958848 authored over 3 years ago by Jake Beal <[email protected]>
continuing to work on markdown; also fixing python property names

github.com/Bioprotocols/labop - 10f7f24a9d2c0c7326e1e9545bb02900c26e7b56 authored over 3 years ago by Jake Beal <[email protected]>
starting to split protocol-to-markdown script into package tests

github.com/Bioprotocols/labop - 27365afd460984fb5a100f0244bf9e375c9e0f1d authored over 3 years ago by Jake Beal <[email protected]>
diff-based testing; may have stability issues, may also need to be changed to n-triples

github.com/Bioprotocols/labop - 10571bf4b6b8297c6a9c61fa15bd41f011c327c0 authored over 3 years ago by Jake Beal <[email protected]>
set up library rebuild to operate correctly when run from base directory

github.com/Bioprotocols/labop - 6af906b826731fcde8df648aa364bb2787c3bb4c authored over 3 years ago by Jake Beal <[email protected]>
Merge commit 'e354d3b9d795a9ff6d7721e8208ef25e265d65cb' into main

github.com/Bioprotocols/labop - da19f7e4b894e3ae04a49a7aa605999da9e3f813 authored over 3 years ago by Jake Beal <[email protected]>
working on getting pytest working for PAML

github.com/Bioprotocols/labop - 8ae57677377dd384bd9dbb1b898584945dcaaa6d authored over 3 years ago by Jake Beal <[email protected]>
Update python-package.yml

github.com/Bioprotocols/labop - e354d3b9d795a9ff6d7721e8208ef25e265d65cb authored over 3 years ago by Jacob Beal <[email protected]>
remove linting

sbol_factory classes are guaranteed to fail lint, so remove from the test workflow

github.com/Bioprotocols/labop - 565f8b102cfa6a7c3c31b6d3e5fb0d0703e3e1dc authored over 3 years ago by Jacob Beal <[email protected]>
Create python-package.yml

github.com/Bioprotocols/labop - c9cc742c5b5d1b8820b5e4e9af945efa1fa845bd authored over 3 years ago by Jacob Beal <[email protected]>
working on adding tests

github.com/Bioprotocols/labop - 59c1a8bf48af369ca921be80278596302b021f5e authored over 3 years ago by Jake Beal <[email protected]>
making progress on growth protocol; shifting library from locations to located samples

github.com/Bioprotocols/labop - 0e53ee7b7deb64138157b22b8cb4107d0f728585 authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #6 from SD2E/factor_out_helper_functions

Factor out helper functions

github.com/Bioprotocols/labop - 75e5fc10aea66d3194c53bcd06300aef2d4fc802 authored over 3 years ago by Jacob Beal <[email protected]>
Merge branch 'factor_out_helper_functions' of https://github.com/SD2E/paml into factor_out_helper_functions

# Conflicts:
# paml/__init__.py
# paml/paml.ttl

github.com/Bioprotocols/labop - 75e75349092c48a7c5f2b8303307b7c2056c0728 authored over 3 years ago by Jake Beal <[email protected]>
end-to-end run using library operators

github.com/Bioprotocols/labop - 728642f1a8622c007f3e3a39c8d980a97cba7644 authored over 3 years ago by Jake Beal <[email protected]>
Merge branch 'factor_out_helper_functions' of https://github.com/sd2e/paml into factor_out_helper_functions

github.com/Bioprotocols/labop - 14213eacf2f09d4a03fc3817bf52474cb249b499 authored over 3 years ago by Bryan Bartley <[email protected]>
Update README

github.com/Bioprotocols/labop - 72c4abd064dd5f85bcf29f748ce99e23d8be2f6a authored over 3 years ago by Bryan Bartley <[email protected]>
Use graphviz clusters to organize object compositions

github.com/Bioprotocols/labop - 2a8549b5364e4861726b193b10a0a9ab89aaa9b8 authored over 3 years ago by Bryan Bartley <[email protected]>
Merge branch '4-fix_datatype_properties' into factor_out_helper_functions

github.com/Bioprotocols/labop - 0395b1cb625e9be1ca1e8ef549a7c7265bbf615c authored over 3 years ago by Bryan Bartley <[email protected]>
Fix #4

github.com/Bioprotocols/labop - d2ecb43ce374204fc3afd8ba79df7b99d4e90581 authored over 3 years ago by Bryan Bartley <[email protected]>
Add script for visualizing Document tree

github.com/Bioprotocols/labop - 101f3be15854e0e70a4d9ede0f819415bd65c080 authored over 3 years ago by Bryan Bartley <[email protected]>
working on libraries

github.com/Bioprotocols/labop - 6d809c78c79c97634b715e96ea0b2f07009aa674 authored over 3 years ago by Jake Beal <[email protected]>
working on library-based protocol building

github.com/Bioprotocols/labop - b102daa623ef0474c90e08f41f582cd871903b46 authored over 3 years ago by Jake Beal <[email protected]>
add libraries for growth protocol

github.com/Bioprotocols/labop - 3ffb59f4be76438cc74f0efca55ba985ea13fb7c authored over 3 years ago by Jake Beal <[email protected]>
Merge branch 'main' into factor_out_helper_functions

github.com/Bioprotocols/labop - 48ef3af81c1c3e30a85ffbe316666ea663f686fe authored over 3 years ago by Jake Beal <[email protected]>
working on library-building

github.com/Bioprotocols/labop - d85d8ea3dc4afcac5a0f84cbb65d79ead2452984 authored over 3 years ago by Jake Beal <[email protected]>
Add helper functions for instantiating PrimitiveExecutables

github.com/Bioprotocols/labop - 37ea70098301aabc02f3e239259ac18d0eb8930f authored over 3 years ago by Bryan Bartley <[email protected]>
library-building in progress

github.com/Bioprotocols/labop - 1a26d6c8362f50e778b125e49af3e1980328fe32 authored over 3 years ago by Jake Beal <[email protected]>
fix to work with current sbol-factory release

github.com/Bioprotocols/labop - dcec60c62928f300ee5118f6a648b30dcb1632b1 authored over 3 years ago by Jake Beal <[email protected]>
moving smoke-test examples into a test directory, refactoring to match sbol factory

github.com/Bioprotocols/labop - 51ff94d237a9e86c17e5f1db97e5e694d6cc938b authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #2 from rpgoldman/de-figurize

Improve formatting of UML diagrams.

github.com/Bioprotocols/labop-specification - 7ba2e50442675bcd309fb8087b4d32606468ab68 authored over 3 years ago by Jacob Beal <[email protected]>
Improve formatting of UML diagrams.

Removed the "figure" environments, because it creates floats, causing
the diagrams to move away ...

github.com/Bioprotocols/labop-specification - 9d1b353f54bee91515e62139df72fcb36adae6be authored over 3 years ago by Robert P. Goldman <[email protected]>
Add LaTeX build instructions

github.com/Bioprotocols/labop-specification - 80ca98cf1d04bedb7b711e3d8723b6764634a83a authored almost 4 years ago by Jacob Beal <[email protected]>
add missing diagrams

github.com/Bioprotocols/labop-specification - ad879250651c36ceb8d4b052970d4781bcc1e274 authored almost 4 years ago by Jake Beal <[email protected]>
Merge pull request #3 from SD2E/remove_git_sumbodule

Configure pip module

github.com/Bioprotocols/labop - 3cbe803adc1d48d055e03d53a0fb0a3797a203b0 authored almost 4 years ago by Jacob Beal <[email protected]>
Configure module

github.com/Bioprotocols/labop - 8e25d866a73a7b98ed52040a596fdc38520bd28e authored almost 4 years ago by Bryan Bartley <[email protected]>
Add Robert's middle initial

github.com/Bioprotocols/labop-specification - 82abac6408a20719f1cae91cdee98850a2de167e authored almost 4 years ago by Jacob Beal <[email protected]>
add paml.tex file, which was accidentally omitted

github.com/Bioprotocols/labop-specification - c19b0c49b47a8b02adfee17f236453911e104dc3 authored almost 4 years ago by Jake Beal <[email protected]>
comment out some classes that look like they will not be useful

github.com/Bioprotocols/labop - 6b9a4ab1d7ea4413c8d073996734d967057a9b39 authored almost 4 years ago by Jake Beal <[email protected]>
update readme, fix author

github.com/Bioprotocols/labop-specification - 664e494566f35c1171f2e3abeff1fc34e0aeb8cd authored almost 4 years ago by Jake Beal <[email protected]>
improved README

github.com/Bioprotocols/labop-specification - e0aa71398d779681cd2f25780d37b2d453b928fa authored almost 4 years ago by Jake Beal <[email protected]>
initial partial spec

github.com/Bioprotocols/labop-specification - d4adeabc8aee64fe14c990e637e4838c69c13316 authored almost 4 years ago by Jake Beal <[email protected]>
end to end complete test

github.com/Bioprotocols/labop - 91cf4a14ee57b64b438379ea30e4d27dd964dc4f authored almost 4 years ago by Jake Beal <[email protected]>
Fix fencepost error on step number in Excel

github.com/Bioprotocols/labop - db162d2a8bbede08794c94f71e62d2e753bc67f7 authored almost 4 years ago by Jake Beal <[email protected]>
first full output including datasheet

github.com/Bioprotocols/labop - 11d494cd1096dcae4c173b00d402c40df9d397ec authored almost 4 years ago by Jake Beal <[email protected]>
first end-to-end pass on a protocol

github.com/Bioprotocols/labop - 20187ddc22697725dcea597bcf1cea1d5f2f365b authored almost 4 years ago by Jake Beal <[email protected]>
cleaning up bugs in paml.ttl

github.com/Bioprotocols/labop - f82045c5d02708f3cea1a209a170d0dd1044be6a authored almost 4 years ago by Jake Beal <[email protected]>
added locations, fixed some bugs

github.com/Bioprotocols/labop - 27bc6ee9d57a022d5fcd2eb721a8abedbb78b328 authored almost 4 years ago by Jake Beal <[email protected]>
first output version

github.com/Bioprotocols/labop - b16150a56f7ad9b89c01905e56495d2a147e6164 authored almost 4 years ago by Jake Beal <[email protected]>
first end-to-end protocol draft

github.com/Bioprotocols/labop - 2aea883906e9a23323ae920a8dead3206537a41e authored almost 4 years ago by Jake Beal <[email protected]>
paml WIP

github.com/Bioprotocols/labop - 411a565e928193b7d6a3ba05e821fa14463ed4aa authored almost 4 years ago by Jake Beal <[email protected]>
Update README.md

github.com/Bioprotocols/labop - dbdaf5a6d070da8f00f61a6263c2b876f466fbd4 authored almost 4 years ago by bbartley <[email protected]>
Create README.md

github.com/Bioprotocols/labop - f76f66600b6dfd2f16a55bbab734623bd7f2eaa4 authored almost 4 years ago by bbartley <[email protected]>
Configure with opil submodule

github.com/Bioprotocols/labop - f8b811a1394cf822f46229f3041f661437fe3d70 authored almost 4 years ago by Bryan Bartley <[email protected]>
Fix syntax errors using turtle validator at https://www.w3.org/2015/03/ShExValidata/

github.com/Bioprotocols/labop - ed2c5d3763671604bd3753ee0dbb30e3c8c49817 authored almost 4 years ago by Bryan Bartley <[email protected]>
notes and adjustments from CPR meeting

github.com/Bioprotocols/labop - 055ab80171a40bba197515fc5a8dca591000c030 authored almost 4 years ago by Jake Beal <[email protected]>
first draft of paml

github.com/Bioprotocols/labop - 4802b9b79581e079bad2d076e8e5a8494f4c2fdc authored almost 4 years ago by Jake Beal <[email protected]>