Ecosyste.ms: OpenCollective

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

github.com/Bioprotocols/labop

Laboratory Open Protocol (LabOP) Language
https://github.com/Bioprotocols/labop

Fix row and column mix up causing masks to fail

85d4e7bed8fd4c53d47ef5d2c0cd372783ad3121 authored over 2 years ago by Bryan Bartley <[email protected]>
Extend liquid handling primitives

645131adf9328b6ee5522784d3b1dedbb83dd540 authored over 2 years ago by Bryan Bartley <[email protected]>
Function to show primitive libraries

ee30726eecb6cfda2eb57f7c135343382ce632f4 authored over 2 years ago by Bryan Bartley <[email protected]>
Clean up debugging output

9b45ace95221d39f6d3c436035eafcf62dcbaae0 authored over 2 years ago by Bryan Bartley <[email protected]>
checkpoint

da94d7d582f3b6dfdbcb584f8f520c06ccbc14d5 authored over 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #136 from Bioprotocols/HARMONY22

Support PAML

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

fd4781db5ef50f0eeafa9cabd552b2ce7daf305b authored over 2 years ago by Bryan Bartley <[email protected]>
Incorporate Alejandro's and Jacky's revisions

b5d4e716c8c418b47cc9de38cb70c47ad6bca171 authored over 2 years ago by Bryan Bartley <[email protected]>
Challenging (timepoint) version of growth curve protocol

cc9eb23098ecbb538c1006fb285e757f69fa15b8 authored over 2 years ago by Bryan Bartley <[email protected]>
Track versions of the markdown protocols

eabd49e05e5b60922207255e554aecc663a4dadb authored over 2 years ago by Bryan Bartley <[email protected]>
Support custom names of measurement steps

8069c0501a7fc57835503e6e3065d00e4ca4756f authored over 2 years ago by Bryan Bartley <[email protected]>
Add multicolor particle calibration protocol

6af9d099f5ab6de74d41a239f1493927892690bc authored over 2 years ago by Bryan Bartley <[email protected]>
Replicates parameter for Transfer primitves

355af5c1fbf07f41ef1fdbff67ac3b132038f7af authored over 2 years ago by Bryan Bartley <[email protected]>
Stamp version on markdown protocol

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

dc731150e137ec9304058a99f10907d823c425ad authored over 2 years ago by Bryan Bartley <[email protected]>
Created using Colaboratory

abfec5915e86d9a317b952aa64c71035518512d9 authored over 2 years ago by Daniel Bryce <[email protected]>
Draft 2022 cell calibration protocol

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...

328891df745a9842061ebe890b040f456be3caea authored over 2 years ago by Robert P. Goldman <[email protected]>
Ignore build directory.

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...

9e794611f9be34c385e8e031f10c2b6f203ca235 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Test on multiple python versions.

29864764984f768cbfd474d0d367527073b67db6 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Fix output to transcript.

744daa4a01d21e3d605f29bffd4b4e9155587888 authored almost 3 years ago by Robert P. Goldman <[email protected]>
End-to-end demonstration of SampleArray operations, including serialization for contents field. See #113

630151cfa22697400df9a9929bc9d5f1cc9015bf authored almost 3 years ago by Bryan Bartley <[email protected]>
Working demonstration of protocol execution using batch samples represented by SampleArrays.

780ddb4296c48d631374c33deaf51b14cf1f17e9 authored almost 3 years ago by Bryan Bartley <[email protected]>
Make SampleArray contents an unbounded list of URI references

7c016097c1ec69db9b114ece4ccf92ea78fe99c0 authored almost 3 years ago by Bryan Bartley <[email protected]>
Support unbounded parameters, resolves #127

cb3c28c16894d6c9833dcdfce58538ba84b55720 authored almost 3 years ago by Bryan Bartley <[email protected]>
Markdown specialization handles designated protocol outputs more gracefully. Related to #125

06a57d2dfc2d37abc931fc8c775c31270597e884 authored almost 3 years ago by Bryan Bartley <[email protected]>
Improve Markdown display for Transfer execution

29a259a5951e35f9828113bd45da245061cf97be authored almost 3 years ago by Bryan Bartley <[email protected]>
Add primitive for Hold

0f4d34d50ed150dbcd1fab919a10df612b485e9a authored almost 3 years ago by Bryan Bartley <[email protected]>
CallBehaviorExecutions generate output tokens. Resolves #125

59965a0cc51369d7c87890cc0a0605af7fbda57d authored almost 3 years ago by Bryan Bartley <[email protected]>
Save interlab-growth-curve notebook

951deb101d8ba1e0c67fbd5ce21b839647019a5f authored almost 3 years ago by Bryan Bartley <[email protected]>
Fix #130 and add test

8748593aa4c16afb9152d5e7a61d29b2b8306d64 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add test for optional and required Parameters

9fdea5e6508cecbcaa9d5926b48e74aeb9fb84ec authored almost 3 years ago by Bryan Bartley <[email protected]>
Add test cases for Pins mismatched with Parameters

fdbaeff3c365e2b92acdf15640d2c58e125678ec authored almost 3 years ago by Bryan Bartley <[email protected]>
Format error message for greater clarity

26dc9b01c26a6db959422b9f83b594129b5db212 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #76 from Bioprotocols/data-link

Prototype representation of SampleArray and SampleData

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

Add Markdown converter documentation

d4cacc5de27fd088a8043ba94d3a9c2b5026bcd3 authored almost 3 years ago by Daniel Bryce <[email protected]>
Add Vortex to liquid handling library

0bf43247b72cc48a58b10524b0016a67da888daf authored almost 3 years ago by Bryan Bartley <[email protected]>
small cleanup

c2b9926211f3d2295c89da8601aeefc112655d7d authored almost 3 years ago by Daniel Bryce <[email protected]>
add pandas to install

6c5e9239fb2c834fc723277dd7ef4256b9621fdd authored almost 3 years ago by Daniel Bryce <[email protected]>
add pandas to install

efde8448c577c64e437463dd3c481d6557833796 authored almost 3 years ago by Daniel Bryce <[email protected]>
Save sampledata as string CSV

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

f0f3e930762f381d7552ae88f846147ef60e6ca3 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add Vortex primitive

ba02640cd6a64a8e80bf92032c8a0ad5726f64ee authored almost 3 years ago by Bryan Bartley <[email protected]>
updated rubric due to whitespace change

05ea858ebf58423d951c38160b965bd9239dd678 authored almost 3 years ago by Daniel Bryce <[email protected]>
pre-commit file fixes

9aaeb89b336eda6b308b625c3f7c147732696f8a authored almost 3 years ago by Daniel Bryce <[email protected]>
fixed issues with rebase and tests

070c090b8e17b15b5a47a03c1a252f16401a209b authored almost 3 years ago by Daniel Bryce <[email protected]>
Spec for PrimitiveArray

39b8b9483da690e82bb484fa0487efd1fbc7a7c2 authored almost 3 years ago by Daniel Bryce <[email protected]>
Fix some grammatical snafus

ad55db90ac860c1aa8078a587f585608aa784adc authored almost 3 years ago by bbartley <[email protected]>
Add Markdown converter example

6bd12562385db14dd25ea6cbbe09d022fb853f10 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #103 from Bioprotocols/nb-tests

Nb tests

daafdeb328d45f36d7fd2abbfc2aca8b4b6fc9a9 authored almost 3 years ago by Daniel Bryce <[email protected]>
skip test with nondeterminsm in nt file output

2871f94b733ff786fbc17e54e11de11654673424 authored almost 3 years ago by Daniel Bryce <[email protected]>
updated rubric

f4e9b0d959a60539bf670ac8a295372ac0e5b6b6 authored almost 3 years ago by Daniel Bryce <[email protected]>
address Jake's review

71bca2c47499a140673fe3d18e43667c52d8a5ff authored almost 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #108 from Bioprotocols/fix-execution-tokens

Fixed bug in token generation for outputs that chose additional proto…

76b58606c81441a69dedc75e556a85cc0a8d124b authored almost 3 years ago by Daniel Bryce <[email protected]>
Fixed bug in token generation for outputs that chose additional protocol edges.

fabaf44aa9c160d75bbb0ec29474006744ab0e72 authored almost 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #105 from Bioprotocols/activity-primitive-disjoint-fresh

Add disjoint relationship

d88c3b4d06a7c8f8cdb295a08b81f94bc503eda0 authored almost 3 years ago by bbartley <[email protected]>
Merge pull request #63 from Bioprotocols/docs-refactor

WIP: Docs refactor

168eb725d9b635eacf1369a3a376c9b40ede1627 authored almost 3 years ago by bbartley <[email protected]>
Merge branch 'main' into docs-refactor

e4f899a764db664ecf4ee110c12c71c397632700 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add disjoint relationship

70b68e6ba9fc4417d35f2dece0e65b93f04e6007 authored almost 3 years ago by Bryan Bartley <[email protected]>
remove paml_check dep from demo

0dbe6c3b821041d08eb81704cbce17a39bf6bdb5 authored almost 3 years ago by Daniel Bryce <[email protected]>
conditionally run container_api if import succeeds

79c99b16f47948eb7c2d341f8dcefa1ea40f5e78 authored almost 3 years ago by Daniel Bryce <[email protected]>
enable nbtest and pre-commit

7f35107df105400a9291aa759c756a3f17408ba6 authored almost 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #70 from Bioprotocols/installation-readme

Correct the installation information in README.txt

590ef15bfe25b29bac509765e6c41c20cf320db6 authored almost 3 years ago by bbartley <[email protected]>
Merge branch 'main' into installation-readme

f6983bea353557c0a722a024d37d6a803c63f849 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #68 from rpgoldman/fix-restrictions

Fix the malformed OWL restrictions.

81c3ade34837cd39339dc290ed6bdaad1438e228 authored almost 3 years ago by bbartley <[email protected]>
Merge pull request #100 from Bioprotocols/backward_compatibility

Backward compatibility

2d6daaa50850e4d309f69a65a73f534b08d0037a authored almost 3 years ago by bbartley <[email protected]>
Set minimum Python version to 3.7

fb980e2ec13b349d8b40c5107ffed591cda1c2c3 authored almost 3 years ago by Bryan Bartley <[email protected]>
Update workflow

f2aee721b57462a2b530406d780dc2163d08a3b4 authored almost 3 years ago by Bryan Bartley <[email protected]>
Unpin sbol3 version

f220b148092f37fed12ad3d2201054f77456e5e7 authored almost 3 years ago by Bryan Bartley <[email protected]>
Fix directlyComprises predicate

4060791228c2217795551252a19a6de753cd6719 authored almost 3 years ago by Bryan Bartley <[email protected]>
Remove obsolete notebooks

These notebooks (and the ancillary data) were there to help develop the code that is now in owl_...

4c24a410f91dec73af56fdbff1a6aeeff87d8d17 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Test fix.

521794d4649f30eec4b921146e87647293ac5b56 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Add crude RDF diff script.

e2dbdba85a38ee6359ddefbeda23a28aefee0efd authored almost 3 years ago by Robert P. Goldman <[email protected]>
Fix restrictions tests.

a7ed38e2b9b402a3e052c65e1b620fe79455939b authored almost 3 years ago by Robert P. Goldman <[email protected]>
Add owl_rdf_utils to the list of packages to install.

Also:

1. Reformat with black
2. Remove unused imports

3. owl_rdf_utils is not a dependency.

f1e278fb699c1ecba048fcb6aa39f6c16c6760d2 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Multiple script fixes.

Minor bugs here and there and some clarifying docs

4d44ab3edc48b11f947e24c4370628e5c131e07f authored almost 3 years ago by Robert P. Goldman <[email protected]>
Update dependencies

02a26956bcd80b0c3d6b35d3b6fa20476f67562f authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge branch 'main' into fix-restrictions

02fc89b1649da4d8123e535801952d455f817f6f authored almost 3 years ago by Bryan Bartley <[email protected]>
Add test to validate Restriction syntax for paml and uml

23a04c04baa9a206e2863addaadeed48b80f5516 authored almost 3 years ago by Bryan Bartley <[email protected]>
Clean up Restrictions in ontology files

69c36897682e01404fde26dba49ce329df366614 authored almost 3 years ago by Bryan Bartley <[email protected]>
Update README.md

4a2bebd24d57baf227a58898bf24e52751ee1e1f authored almost 3 years ago by bbartley <[email protected]>
Merge pull request #94 from Bioprotocols/66-package

66 package

53347ff09de8745514bfadaa6714cb8e4cbd2a28 authored almost 3 years ago by bbartley <[email protected]>
Disable jupyter notebook tests

a3277764de8bbe496333e589748fc537e01c5992 authored almost 3 years ago by Bryan Bartley <[email protected]>
Disable tests

2db2d1509e0bb0bbbbf4f387ef18e20859073f74 authored almost 3 years ago by Bryan Bartley <[email protected]>
Disable container_api

bc234f27136b849c013df49d5a611ce5a95d3068 authored almost 3 years ago by Bryan Bartley <[email protected]>
That's not working--remove container-ontology

1cbb1e7334f181ae5ade37f7393237f1a17f5f48 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add wrapper for setup script that installs git submodules

d00ec2f611cb2d100500264ab735b63a898f0cb2 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add container ontology as git submodule

59569801701cf804b4abad51f3af00459e3c8db5 authored almost 3 years ago by Bryan Bartley <[email protected]>
Remove paml-check from extras

68c7f62873d853d8e460c26ec39cfca12072e9ab authored almost 3 years ago by Bryan Bartley <[email protected]>
Move paml-check to git submodule

4b93f650050deffa8b8c3ad71554c60b9c39026a authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #90 from Bioprotocols/71-license

Add license

dea4b554b0b9ae1c1aaf15f676fce28e3d078370 authored almost 3 years ago by bbartley <[email protected]>
Change package name to pypaml

faa166dc63480cd94ce850a45a006f2afeed98eb authored almost 3 years ago by Bryan Bartley <[email protected]>
Add license

2649772cd409e6b31c8b54f852a5d24d5af4378b authored almost 3 years ago by Bryan Bartley <[email protected]>
Setup place to add conversion to opentrons. Based on Autoprotocol conversion by removing specifics.

09b5b9037571cd38838b1d224b14a57f3940663d authored almost 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #88 from Bioprotocols/58-clean_out_opil

Remove references to opil

8a49978ec03f0ec78bcaf9592ebe88e64a5d1271 authored almost 3 years ago by bbartley <[email protected]>
Remove references to opil

cea48a31edd7e8066c8e3a5ba7cf8a69aaf149f0 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add instructions for installing paml-check

4e76529f2a2c3e44d9c01955f2a8d6c1ef880d20 authored almost 3 years ago by bbartley <[email protected]>
Merge pull request #79 from Bioprotocols/78-upgrade_rdflib

Upgrade rdflib dependency

1c0548e7cae8f36a066eecb5baad336b4751fd5a authored almost 3 years ago by bbartley <[email protected]>
Extend the README

Add a link to the specification repository.

Finish a sentence fragment.

683d0413b62717b6e4a19eea401614aa03385b87 authored almost 3 years ago by rpgoldman <[email protected]>