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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

Add well properties.

Add `hasWellShape` and `hasOpticalProperty`.
Fixed minor bugs:
* the label of the `length` prop...

github.com/Bioprotocols/container-ontology - 2380655ca2540e09ac2fad10ea6dba9d1161960c authored over 3 years ago by Robert P. Goldman <[email protected]>
rebased on main after ordered values addition

github.com/Bioprotocols/labop - 6960bbffce1f3736ab200051838cdb4ed7ec5d28 authored over 3 years ago by Daniel Bryce <[email protected]>
Script for diffing versions of container ontology

github.com/Bioprotocols/container-ontology - 56d19c602b887a2b5aaab2900c150ce2e794de14 authored over 3 years ago by Robert P. Goldman <[email protected]>
Multiple fixes to container ontology

Removed spurious disjoint properties
Recorded properties that were functional
Added three subcla...

github.com/Bioprotocols/container-ontology - f7f04e5afd07c7897c4ae6f89e9a24cbdc05c96e authored over 3 years ago by Robert P. Goldman <[email protected]>
Ignore PyCharm and Mac metadata.

github.com/Bioprotocols/container-ontology - 444ad1ffde53ae2b0b58228722e6c352b3af9547 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add missing rdfs:label properties.

Automatically scanned over the ontology and added `rdfs:label` properties
to classes that didn't...

github.com/Bioprotocols/container-ontology - 9e33e353676e7a4a7d332e69f51ffe29efbc130c authored over 3 years ago by Robert P. Goldman <[email protected]>
Put container-ontology in rdflib canonical form.

Read container ontology into rdflib and then serialize it.
I hope that this will make further di...

github.com/Bioprotocols/container-ontology - 18f8e7a8e00acb266d0fdc4cd26c4b07e7668583 authored over 3 years ago by Robert P. Goldman <[email protected]>
Extend for SBOL-factory compatibility

Added a `ContainerRoot` class to (optionally) inherit from `sbol:Identified`.
Add `rdfs:label` f...

github.com/Bioprotocols/container-ontology - 85ce1f35af2c8388358935c0659691d323529657 authored over 3 years ago by Robert P. Goldman <[email protected]>
update to remove timepoints from activities. Having bug with prov uri string that leads to unassigned property on time variables.

github.com/Bioprotocols/labop - 9d12bf7a4156b3cedaa87f185dd80c835c5ebcc8 authored over 3 years ago by Daniel Bryce <[email protected]>
updated timepoints for control, primitive, and protocol

github.com/Bioprotocols/labop - 755ecad9eafe702fee3d4144a7df6f9dea8d5112 authored over 3 years ago by Daniel Bryce <[email protected]>
renamed logic constraints

github.com/Bioprotocols/labop - 45e8f50c4280dc0ecf8ec69779f909f83120a641 authored over 3 years ago by Daniel Bryce <[email protected]>
update to remove timepoints from activities. Having bug with prov uri string that leads to unassigned property on time variables.

github.com/Bioprotocols/labop - 97c4c34cf98ff62a3711d6168b26c79977ee334b authored over 3 years ago by Daniel Bryce <[email protected]>
make time optional to fix tests

github.com/Bioprotocols/labop - 9447306d0dfee802ad65b85ae880118e3832bdd4 authored over 3 years ago by Daniel Bryce <[email protected]>
added expressions to ttl

github.com/Bioprotocols/labop - bb40b4a8e5007ce95e08f844bae3eb71906260ea authored over 3 years ago by Daniel Bryce <[email protected]>
update to remove timepoints from activities. Having bug with prov uri string that leads to unassigned property on time variables.

github.com/Bioprotocols/labop - f5a49232063966c950f24adccb4dfed506b72070 authored over 3 years ago by Daniel Bryce <[email protected]>
updated time property to be a datatype property

github.com/Bioprotocols/labop - 41f502d131d5ec38961cb565c0b60e6359da7580 authored over 3 years ago by Daniel Bryce <[email protected]>
simplified api for temporal constraints.

github.com/Bioprotocols/labop - 0381103364e67a335164c40037bc560c2955c2dc authored over 3 years ago by Daniel Bryce <[email protected]>
refactored time extensions to build upon uml

github.com/Bioprotocols/labop - a27656297b46f75c4a9f6d636a3e1f1b0ac27735 authored over 3 years ago by Daniel Bryce <[email protected]>
testing constraint checking

github.com/Bioprotocols/labop - 778cc1af141559ad5b8ea6c42683047d455816f1 authored over 3 years ago by Daniel Bryce <[email protected]>
setting timepoints and durations for ludox protocol

github.com/Bioprotocols/labop - 64d7bf805a2981abcff20fcb3264b14a1bb5b9e4 authored over 3 years ago by Daniel Bryce <[email protected]>
Don't use rdfs:subPropertyOf

github.com/Bioprotocols/labop - 3a4e875c8c0a7de1a256e1055dbe93e0adcdbe49 authored over 3 years ago by Bryan Bartley <[email protected]>
support for additional, general constraints

github.com/Bioprotocols/labop - c6bb3a766105bee62e02e48e84ba4206d0cdcae4 authored over 3 years ago by Daniel Bryce <[email protected]>
Added Time to paml ontology

github.com/Bioprotocols/labop - 8c135f067d60a51e2e85028175e684e7cadbeda9 authored over 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #38 from SD2E/ordered-values

Ordered values

github.com/Bioprotocols/labop - 2eab6b4d2a49538ffb838349d28dfe9e2660c810 authored over 3 years ago by Jacob Beal <[email protected]>
Merge branch 'main' into ordered-values

github.com/Bioprotocols/labop - a4f482ced552055e9468d1640ed31721d3e3d3e4 authored over 3 years ago by Daniel Bryce <[email protected]>
addressed Jake's comments

github.com/Bioprotocols/labop - 2c1578153e560f70d73fee1ee0b139a2436c3728 authored over 3 years ago by Daniel Bryce <[email protected]>
addressed Jake's comments

addressed Jake's comments

github.com/Bioprotocols/labop - 070ba4b64bf86d5456514376b976863ed9b106b2 authored over 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #39 from SD2E/37-update_package_config

Update for compatibility with SBOLFactory v1.0a6

github.com/Bioprotocols/labop - e90b9d65d27b9bf40b852d8235dbbe79f3eb520a authored over 3 years ago by bbartley <[email protected]>
Update for compatibility with SBOLFactory v1.0a6

github.com/Bioprotocols/labop - 4fd14c084999bd2ee08251f5bbee7aad40f78c90 authored over 3 years ago by Bryan Bartley <[email protected]>
missed a rubric

github.com/Bioprotocols/labop - 629bb2275fac183f4494557d57bf1a9e4844a4d6 authored over 3 years ago by Daniel Bryce <[email protected]>
updated test rubric and downgraded rdflib

github.com/Bioprotocols/labop - 0859fcb513fe78eae0e619f91e966e69079686fa authored over 3 years ago by Daniel Bryce <[email protected]>
use ordered values in behavior parameters

github.com/Bioprotocols/labop - b8ccda2551d5a1bb55a52b27fea5be58bbe6aa52 authored over 3 years ago by Daniel Bryce <[email protected]>
use ordered values in behavior parameters

github.com/Bioprotocols/labop - e7ecf9d580f7fb613f8b98f4650dd4d16e3cf207 authored over 3 years ago by Daniel Bryce <[email protected]>
tests for parameter ordering

github.com/Bioprotocols/labop - 43c1726cc6579cda17545dddb8ae3c0ef6319e35 authored over 3 years ago by Daniel Bryce <[email protected]>
added ordered parameter

github.com/Bioprotocols/labop - 971cc07939caeb2a2a022eea285c021eb2f02ce3 authored over 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #36 from SD2E/fix/issue-35

Fix issue 35.

github.com/Bioprotocols/labop - d0796dedb58ecedd0151ef82af27007dee807f47 authored over 3 years ago by Jacob Beal <[email protected]>
Fix issue 35. Depending on the order of nodes added to a UML Activity was fragile (and broken); track steps explicitly in a scratch property instead.

github.com/Bioprotocols/labop - dc22bd7343d006ce6b71e28d55314dbbe5c0e5a0 authored over 3 years ago by Jake Beal <[email protected]>
Fix pervasive syntax errors in OWL Restrictions (#33)

These were in an abbreviated form that for some reason, none of our tools flagged clearly as err...

github.com/Bioprotocols/labop - ba730d4cfa97954f75c83f583668b6529fd35d02 authored over 3 years ago by rpgoldman <[email protected]>
Merge pull request #31 from SD2E/update-primitive-types

Primitives hadn't been updated from old Location class to new SampleArray class.

github.com/Bioprotocols/labop - 1a2743465e295e4482a0b7a85fedda385ecbc320 authored over 3 years ago by Jacob Beal <[email protected]>
Primitives hadn't been updated from old Location class to new SampleArray array class.

This commit makes that changes and all of its related changes down the tree.

github.com/Bioprotocols/labop - 0fe0e737246cdddcbc25053b41bd8b3578d7a55f authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #29 from SD2E/fix-owl-errors

Fix broken OWL

github.com/Bioprotocols/labop - f153a126d417a60696cf693c44a3b197d952dd83 authored over 3 years ago by rpgoldman <[email protected]>
Fix broken OWL: all values of owl:onClass should actually be owl:allValuesFrom

github.com/Bioprotocols/labop - 847f298823436d1a0c93f39b5a9077412a2ef4fa authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #25 from SD2E/sbol-uml

SBOL UML first implementation

github.com/Bioprotocols/labop - dbe533da0145d1586c74c3303c2f9a66147f7130 authored over 3 years ago by Jacob Beal <[email protected]>
Add UML model as standard turtle.

`uml-flattened.ttl` is the Turtle version of `uml.ttl`, which seems to
be Turtle*.

github.com/Bioprotocols/labop - 6d9300f883279d17205b775deca09ea6dcd51899 authored over 3 years ago by Robert P. Goldman <[email protected]>
Improve documentation

Adds a sentence about what PAML is to the README.
Adds references to the defining UML section fo...

github.com/Bioprotocols/labop - 7de0c9668951c557983fc79260812f765bb7f6b9 authored over 3 years ago by Jake Beal <[email protected]>
Extend description of PAML purpose (#6)

* Add more details to the purpose statement.

Add an itemized list of subtasks from which to e...

github.com/Bioprotocols/labop-specification - c469d166b1f29ce346bf107b830ced4ff46d4ef7 authored over 3 years ago by rpgoldman <[email protected]>
Address #13 through implicit injection of ForkNodes

When an ObjectFlow is added using the Activity.use_value helper function, the code now automatic...

github.com/Bioprotocols/labop - 6a72159ac9d423792864ae67ad8754f7aeeb901a authored over 3 years ago by Jake Beal <[email protected]>
Implement validation check for nondeterministic multi-outputs per discussion on #13

This commit adds a validator for uml.Activity objects that checks to see whether any of the Acti...

github.com/Bioprotocols/labop - b1b16d39878587d780376fb7c625fe949c24a516 authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #5 from rpgoldman/ignore-latex-compiler-outputs

Ignore latex output files.

github.com/Bioprotocols/labop-specification - 5cf9696a7b08065f1f0bb1eabbed7bf73974891f authored over 3 years ago by Jacob Beal <[email protected]>
include library tweak

github.com/Bioprotocols/labop - 283c676d6f87e31ee453d976bf519df25ea65fab authored over 3 years ago by Jake Beal <[email protected]>
fix more case bugs, stabilize ordering of action builds; clean out some obsolete material

github.com/Bioprotocols/labop - dd81685909323bc408fe8957c9a9e1c3e7aeff74 authored over 3 years ago by Jake Beal <[email protected]>
nearly there on protocol smoke-test

github.com/Bioprotocols/labop - 639005c5f6741817ab31c4c9567563162598180b authored over 3 years ago by Jake Beal <[email protected]>
get utils test running by temporarily disabling some non-yet-converted materials

github.com/Bioprotocols/labop - b98a49d5f18aa7f07e06ae22be76b3461aac0189 authored over 3 years ago by Jake Beal <[email protected]>
another build typo

github.com/Bioprotocols/labop - ca982212fd19e9dcb0b91bb816baf0716b51a1e4 authored over 3 years ago by Jake Beal <[email protected]>
Add uml package to setup.py

github.com/Bioprotocols/labop - 4ada3b90bc2f042c9eda42c71c6343267f76028a authored over 3 years ago by Jake Beal <[email protected]>
successful test of library building with UML classes

github.com/Bioprotocols/labop - 24c4d35efb9d077c19bec6c9e50f9901eedf182c authored over 3 years ago by Jake Beal <[email protected]>
working up to UML-based smoke test

github.com/Bioprotocols/labop - 3b3605428d9e9cf8881c74756e2784d2d7524d17 authored over 3 years ago by Jake Beal <[email protected]>
Add ANSI/SLAS standards.

Add classes for ANSI/SLAS x-2004 standards for multi-well plates.

github.com/Bioprotocols/container-ontology - 58e01a572a7cd18e43270630ad57db0f346b66bc authored over 3 years ago by Robert P. Goldman <[email protected]>
working on implementation of first UML test

github.com/Bioprotocols/labop - 4d217200e30b4eab7a9345dc13b0c38e4ff70748 authored over 3 years ago by Jake Beal <[email protected]>
Fixes to Miles Rogers' microplate example.

github.com/Bioprotocols/container-ontology - eed589d3290a476cc3e0c44dd8969e5ea6eef599 authored over 3 years ago by Robert P. Goldman <[email protected]>
start including UML classes

github.com/Bioprotocols/labop-specification - 0137ab992e662a0c9a196520cf07e100fb429c4c authored over 3 years ago by Jake Beal <[email protected]>
working on shift to UML

github.com/Bioprotocols/labop-specification - 246a460c20a60e0b2426a0403414abf01e2eb3e9 authored over 3 years ago by Jake Beal <[email protected]>
Merge branch 'samplearray' into sbol-uml

# Conflicts:
# paml/paml.ttl

github.com/Bioprotocols/labop - 9c6306835668899eb137c3b51236e9248e7be5f0 authored over 3 years ago by Jake Beal <[email protected]>
rebuild other two libraries as well

github.com/Bioprotocols/labop - 1accc74a5ae69660ae7138f05e288c6168c79a36 authored over 3 years ago by Jake Beal <[email protected]>
working on UML implementation

github.com/Bioprotocols/labop - 87b121067f255eb4b5a41c2ae776a0595a687a82 authored over 3 years ago by Jake Beal <[email protected]>
move uml ttl to its own package, ensure that it can load

github.com/Bioprotocols/labop - 6ddb92c80c8b456624209f46c7ae556953c1b04f authored over 3 years ago by Jake Beal <[email protected]>
Add value specifications and constraints

github.com/Bioprotocols/labop - d0efcfe0279349af73225ceeaa1f082e8ced7b02 authored over 3 years ago by Jake Beal <[email protected]>
First translation of a spec from Miles Rogers.

github.com/Bioprotocols/container-ontology - ca69d4ba46a165a81eae2f6bcf50929bb8536b4c authored over 3 years ago by Robert P. Goldman <[email protected]>
added properties; need to add two more classes

github.com/Bioprotocols/labop - ddb7f4c9ac7b9d3c97dac172839b330432d6207f authored over 3 years ago by Jake Beal <[email protected]>
Add pins and behavior invocations, define PAML Protocol as a uml:Activity, Primitive as a uml:Behavior.

github.com/Bioprotocols/labop - 9d0d739b5381228314957af2e7eceaf2d8b6da47 authored over 3 years ago by Jake Beal <[email protected]>
First draft of UML classes, though still missing all properties

github.com/Bioprotocols/labop - 30ec6efef39fab0152d2a60a36ad0e3d20d65e7b authored over 3 years ago by Jake Beal <[email protected]>
First, partial draft.

github.com/Bioprotocols/container-ontology - 9767093cde6397860bc9472950b8d99027d3af55 authored over 3 years ago by Robert P. Goldman <[email protected]>
Update README.md

Some initial description and links.

github.com/Bioprotocols/container-ontology - b4e826d0b48ad21ba5210f703f696e36bd78334f authored over 3 years ago by rpgoldman <[email protected]>
Initial commit

github.com/Bioprotocols/container-ontology - 5e623488bae51c75dc184ae441fc8bf55e431d6b authored over 3 years ago by rpgoldman <[email protected]>
require z3-solver, version 0.1.2

github.com/Bioprotocols/labop-check - b556e733705273c0a87b15787ff62a9d7ddcca91 authored over 3 years ago by Jack Ladwig <[email protected]>
set version to 0.1.1

github.com/Bioprotocols/labop-check - efbed8ecc8287d53bcbf0928583bc000e008bcb1 authored over 3 years ago by Jack Ladwig <[email protected]>
Squashed commit of the following:

commit 21e5716d8b1a7255a32d7ee0103110128e12c639
Author: Jack Ladwig <[email protected]>
Date: W...

github.com/Bioprotocols/labop-check - dcf8134187146195b8149ebcfbe91de287350db3 authored over 3 years ago by Jack Ladwig <[email protected]>
Filling in properties on containers and data

github.com/Bioprotocols/labop - 8434467e882ae532e866aed858175fb92a1e98b0 authored over 3 years ago by Jake Beal <[email protected]>
Process paml (#2)

* initial pass at extracting data from paml.

Still needs cleanup.

* cleanup and take a par...

github.com/Bioprotocols/labop-check - dc23b881dd0855345f4d7c7b553497109230b640 authored over 3 years ago by Daniel Bryce <[email protected]>
also remove properties

github.com/Bioprotocols/labop - b7f5920d06f5d992b654bdb6b5d85e10595aff6d authored over 3 years ago by Jake Beal <[email protected]>
working on a new approach to samples

github.com/Bioprotocols/labop - 0c4dffc0b81c7d11c2261bd0c859b2311f7a0974 authored over 3 years ago by Jake Beal <[email protected]>
Ignore latex output files.

github.com/Bioprotocols/labop-specification - 9433fdc73ac092ddd331d0b92aa983cbcc492fa1 authored over 3 years ago by Robert P. Goldman <[email protected]>
Merge pull request #1 from SD2E/master

Master

github.com/Bioprotocols/labop-check - a29cb9d59195f215b5491744084aa2cbdbfeb36f authored over 3 years ago by Daniel Bryce <[email protected]>
initial commit

github.com/Bioprotocols/labop-check - 55877b4c29b295395a0c2c76b429c6369ab04534 authored over 3 years ago by Daniel Bryce <[email protected]>
initial commit

github.com/Bioprotocols/labop-check - ad7f12b94d08bab0ad363b085cf98984fd650493 authored over 3 years ago by Daniel Bryce <[email protected]>
Cleanup and removed smtlib stuff

github.com/Bioprotocols/labop-check - b1aea36b794935eb3fa2299fa3d78657ec820124 authored over 3 years ago by Daniel Bryce <[email protected]>
initial commit

github.com/Bioprotocols/labop-check - 64526bb988f0e8b924c2a8c1d5ff160a35f7229d authored over 3 years ago by Daniel Bryce <[email protected]>
Initial commit

github.com/Bioprotocols/labop-check - 10aba980e89edfa1eb0f71bfa3c72a13d51cf9fa authored over 3 years ago by Daniel Bryce <[email protected]>
upgrade sbol3, sbol-factory, correct incorrect link in growth protocol

github.com/Bioprotocols/labop - 66a90a36c7056ca7fec59da2a82751dd841bbb7a authored over 3 years ago by Jake Beal <[email protected]>
update library mappings file to match current state of libraries

github.com/Bioprotocols/labop - c98c94ec1ea8ec020570f24451a658bf0c4e843a authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #10 from SD2E/growth-protocol

Growth protocol

github.com/Bioprotocols/labop - f8e2f207520ab9348512f21234203ade4e5cc9b8 authored over 3 years ago by Jacob Beal <[email protected]>
Complete growth curve protocol

github.com/Bioprotocols/labop - 6a432515b57525dfd962f296893ce2039dbc9000 authored over 3 years ago by Jake Beal <[email protected]>
First successful end-to-end generation of markdown for growth protocol

github.com/Bioprotocols/labop - f684f8cccf993de1c4682421367e28ecfdb55c7a authored over 3 years ago by Jake Beal <[email protected]>
making progress toward resolving growth curve

github.com/Bioprotocols/labop - 0392a053290a89e67fee0b41a72de433a9fef385 authored over 3 years ago by Jake Beal <[email protected]>
debugging markdown conversion of growth protocol

github.com/Bioprotocols/labop - f98d2a5129c3b2006624bc38a7d80385fcecaff3 authored over 3 years ago by Jake Beal <[email protected]>
generalize conversion to handle multi-protocol documents

github.com/Bioprotocols/labop - e11a69c9fbcf56485f99d0d2a4c517257e3bf4ae authored over 3 years ago by Jake Beal <[email protected]>
add markdown expansion for most primitives, fix broken test

github.com/Bioprotocols/labop - e15ab1400a4d626fa09b8168522eb57330abcb21 authored over 3 years ago by Jake Beal <[email protected]>
automatic merging of ranges

github.com/Bioprotocols/labop - 0ba4d153d803a7780b728513b9a8509892067b3e authored over 3 years ago by Jake Beal <[email protected]>
continued cleanup of markdown conversion

github.com/Bioprotocols/labop - b96833622580bcef6a6b43b9a0c149fbd31bb181 authored over 3 years ago by Jake Beal <[email protected]>
generalizing markdown conversion

github.com/Bioprotocols/labop - fba5a5998477d51f3bd25bae71617cddb424eb8a authored over 3 years ago by Jake Beal <[email protected]>