Bioprotocols Working Group commits | Ecosyste.ms: OpenCollective

Extensive restructuring of container ontology. (#10)

github.com/Bioprotocols/container-ontology - ec387d70d47c72aeb672caaf5a8d31e3268bce03 authored about 3 years ago by rpgoldman <[email protected]>

Add small BBN lab catalog.

github.com/Bioprotocols/container-ontology - d7ad301ce7cf910ee804e4e8fd98af7b43aa1637 authored about 3 years ago by Robert P. Goldman <[email protected]>

Add volume measurement info.

github.com/Bioprotocols/container-ontology - 954a20371e2cf20894624bdbba75dc73d3e90cc3 authored about 3 years ago by Robert P. Goldman <[email protected]>

minor bug fixes to support updates to paml

github.com/Bioprotocols/labop-check - 1ff38079f17ce7bcc75da4a4085a44432468b23a authored about 3 years ago by Daniel Bryce <[email protected]>

minor bug fixes to support updates to paml

github.com/Bioprotocols/labop-check - b429e3c9bf98ff62e0d738bb79b245ce509a8b94 authored about 3 years ago by Daniel Bryce <[email protected]>

plotting for executions and notebook demo

github.com/Bioprotocols/labop - f9cc6a697d299f235b7299f98d6ea7d477d4a3ef authored about 3 years ago by Daniel Bryce <[email protected]>

Use List, Set, etc. typing aliases for type hints

github.com/Bioprotocols/labop - 92b0a1359a14fd36235c5d27431f5ea93172cda6 authored over 3 years ago by Bryan Bartley <[email protected]>

Merge pull request #45 from SD2E/compact-visualization

Create compact visualizations of protocols

github.com/Bioprotocols/labop - 49b87a6178699fd8872a95ae4369293b07184721 authored over 3 years ago by Jacob Beal <[email protected]>

added legend and fixes for ludox protocol

github.com/Bioprotocols/labop - e7b5e6e07822cb105c5bd0f8ea5bc93d8cb46b1d authored over 3 years ago by Daniel Bryce <[email protected]>

Create compact visualizations of protocols

Also fix a bug in GG assembly revealed by visualization

github.com/Bioprotocols/labop - 92d4a061d4eef41bc050fc0a1a5e0df3d3908e59 authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #44 from SD2E/golden-gate

Example: Golden Gate protocol

github.com/Bioprotocols/labop - 011e7b75ff10a8fe25cc36c29116201ae3b45cdc authored over 3 years ago by Jacob Beal <[email protected]>

Merge pull request #41 from SD2E/30-validate_owl-1

OWL validation

github.com/Bioprotocols/labop - 283f5110135bc1c24c8a7254569881af723a4777 authored over 3 years ago by bbartley <[email protected]>

Syntactically correct version of Golden Gate protocol and validated output

Remove redundant (and incorrect) Protocol.initiating_nodes that was overriding Activity.initiatin...

github.com/Bioprotocols/labop - 6a4bfac01c2930061cbd93cba76b243b6b78131a authored over 3 years ago by Jake Beal <[email protected]>

Merge commit 'a790da333cf1aed9018602f983a65b2473d37a8b' into golden-gate

github.com/Bioprotocols/labop - cda65ad1c35a48fdf580b0895603281627c2745a authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #42 from SD2E/execution-records-test

Execution records test

github.com/Bioprotocols/labop - a790da333cf1aed9018602f983a65b2473d37a8b authored over 3 years ago by Daniel Bryce <[email protected]>

First draft of GoldenGate assembly protocol (not yet working)

Also adds a get_last_step() function for protocols, Autoprotocol "spin" primitive, and new "Trans...

github.com/Bioprotocols/labop - 1861d1591339899930ab2fc8ab6737f64e7320ac authored over 3 years ago by Jake Beal <[email protected]>

support for input and output parameters of protocol.

github.com/Bioprotocols/labop - f942cb1095fa5cfbb514cab2c4436c8403be1675 authored over 3 years ago by Daniel Bryce <[email protected]>

Remove test_invalid for now until we find a better test case

github.com/Bioprotocols/labop - a2130da6a180e0a673353a72be5171cc5b98797f authored over 3 years ago by Bryan Bartley <[email protected]>

Clean up some junk

github.com/Bioprotocols/labop - 7ea3b52caca97d8c76cfe9c446c76ad61e86c014 authored over 3 years ago by Bryan Bartley <[email protected]>

Add a test case with malformed OWL

github.com/Bioprotocols/labop - 06db2113fb6bdc0d9c830a709787216566563410 authored over 3 years ago by Bryan Bartley <[email protected]>

Merge branch 'main' into 30-validate_owl-1

github.com/Bioprotocols/labop - 2f257be2ae91082e006665212b6f3d2efea0a47b authored over 3 years ago by Bryan Bartley <[email protected]>

Modify github action yaml to run OWL validation tests

github.com/Bioprotocols/labop - e1b0615e8b960e11991b1a89964c3c7ed4dc2266 authored over 3 years ago by Bryan Bartley <[email protected]>

completed support for optional pins

github.com/Bioprotocols/labop - f9d9db907822090f2104057004004e1f2e199884 authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #40 from SD2E/execution-records-test

Execution records test

github.com/Bioprotocols/labop - 936e13b32d27edb08df35833463a57f479492be5 authored over 3 years ago by Jacob Beal <[email protected]>

turning off file stability check for now on execution

github.com/Bioprotocols/labop - 8959b8a5341468be0594f2588205cc624b003202 authored over 3 years ago by Jake Beal <[email protected]>

don't try to show a PDF in a headless environment

github.com/Bioprotocols/labop - 7233d6f43bf576768978443b10f3dcf168fc439c authored over 3 years ago by Jake Beal <[email protected]>

add graphviz to workflow

github.com/Bioprotocols/labop - 4dd1f8d58fff342089d7d8069d94e5deb82e0151 authored over 3 years ago by Jake Beal <[email protected]>

use safe execution path

github.com/Bioprotocols/labop - d629e0300121b9c1bf2774483ef94b600d8b4581 authored over 3 years ago by Jake Beal <[email protected]>

version pin is ==, not =

github.com/Bioprotocols/labop - b5983e3d6eec1f92e191a7b03c341789ece0f809 authored over 3 years ago by Jake Beal <[email protected]>

pin sbol factory version

github.com/Bioprotocols/labop - 39ed7690fc02341d8bac18bb982f9d0199bd0b9a authored over 3 years ago by Jake Beal <[email protected]>

validation tests passing

github.com/Bioprotocols/labop - e458994026961b20fc2ec61e8e0d7a5366252b90 authored over 3 years ago by Jake Beal <[email protected]>

Merge branch 'execution-records-test' of https://github.com/SD2E/paml into execution-records-test

github.com/Bioprotocols/labop - 3e2000f9da730b763a033bda06f323a0751324bc authored over 3 years ago by Jake Beal <[email protected]>

added protocol input for ludox test

github.com/Bioprotocols/labop - 5ecb153b49a2872817c2fdaadccf8a4e8ce4e968 authored over 3 years ago by Jake Beal <[email protected]>

missing test rubric file

github.com/Bioprotocols/labop - 73d3bf440ed8e264d5c554995a0eaaf5dda3997f authored over 3 years ago by Daniel Bryce <[email protected]>

broken state adding protocol outputs.

github.com/Bioprotocols/labop - 9b5a152422712e94f23e7b3844bb25c156fba8ed authored over 3 years ago by Daniel Bryce <[email protected]>

passing comparison after stashing expected output.

github.com/Bioprotocols/labop - 33be2afd019820c399bd4a358f3a15041c280981 authored over 3 years ago by Daniel Bryce <[email protected]>

Allow edge flows to have no edge. Used to capture link between input pins and activity that has an implicit edge.

github.com/Bioprotocols/labop - fb9ae52150975fe4d6730c51ccec808fd382e5d6 authored over 3 years ago by Daniel Bryce <[email protected]>

stable execution checkpoint. Still getting validation errors due to tokens without values.

github.com/Bioprotocols/labop - 753e7f69fd47bd5519e49a991a048156672a35cb authored over 3 years ago by Daniel Bryce <[email protected]>

Update server configuration.

Use my own copy of the Owlery docker image to ensure compatibility.

github.com/Bioprotocols/container-ontology - 70671d37e4615042eed19ee08b724023af325fb5 authored over 3 years ago by Robert P. Goldman <[email protected]>

Create gradle.yml

github.com/Bioprotocols/labop - 20ad77445653344b88c2cc78429797765d04fce5 authored over 3 years ago by bbartley <[email protected]>

Add catalog file.

Jim Balhoff suggests loading the main ontology (here strateos-catalog-individuals.ttl) and letti...

github.com/Bioprotocols/container-ontology - b0667f7fa8bcda5758b366e6da40843ae22fbbff authored over 3 years ago by Robert P. Goldman <[email protected]>

checkpoint on execution. Need to update paml for ordered parameters in the lib functions.

github.com/Bioprotocols/labop - bd7f5e38b4be740bda302b95eb7f1f3df363dc03 authored over 3 years ago by Daniel Bryce <[email protected]>

Reset ontology IRI to main branch.

Was on `owlery-server` branch, which has been deleted.

github.com/Bioprotocols/container-ontology - 806706e60974024f73f7dea74edde0aadb32067c authored over 3 years ago by Robert P. Goldman <[email protected]>

Add logging.

Add JAVA_ARGS to Makefile invocation of docker image for logging.
Also tee the logging output to...

github.com/Bioprotocols/container-ontology - 8be8913ee96736741325f2d47d69214a6a7e350e authored over 3 years ago by Robert P. Goldman <[email protected]>

Add more instructions for the server.

github.com/Bioprotocols/container-ontology - 36a31d35b11a593e0f0162ae7d5ea8301b575cce authored over 3 years ago by rpgoldman <[email protected]>

Add an Owlery server (#9)

Owlery provides a server that can incorporate a knowledge base of OWL ontologies and respond to ...

github.com/Bioprotocols/container-ontology - 8f8006dc67594d781c09dbbba00b4be603a0988b authored over 3 years ago by rpgoldman <[email protected]>

partially drafted commit for execution engine class

github.com/Bioprotocols/labop - 034ec3897a71cfd9954b987d43dfa1a94436e2cd authored over 3 years ago by Jake Beal <[email protected]>

Allow literals to be constructed as references

Add helper functions for checking required inputs and outputs for behaviors, finding the root of ...

github.com/Bioprotocols/labop - 8118f96c10d1f23fad4b56c3f764406afe1acf44 authored over 3 years ago by Jake Beal <[email protected]>

Adjust validation to allow make incoming edges optional for ActivityParameterNode

github.com/Bioprotocols/labop - b8c2599244c1e50d3d160223f301a18fa5f7a22a authored over 3 years ago by Jake Beal <[email protected]>

Add parameter value records and "completedNormally" field

Kludge in prov:Activity properties while cannot inherit directly due to sbol_factory issues 22 an...

github.com/Bioprotocols/labop - 51d24b7018455027936a04cbc3f0d43a10405ea6 authored over 3 years ago by Jake Beal <[email protected]>

added test case for executions

github.com/Bioprotocols/labop - 26d00c59ee84ccc83954c0465a5c5ac2e3d7332c authored over 3 years ago by Daniel Bryce <[email protected]>

Allow literals to be constructed as references

Add helper functions for checking required inputs and outputs for behaviors, finding the root of ...

github.com/Bioprotocols/labop - 39eae402be05b83f9a9f3ce9cabe6c438b19ef32 authored over 3 years ago by Jake Beal <[email protected]>

Draft implementation of representation for recording protocol executions

github.com/Bioprotocols/labop - aa5e593be191162c124f55dde17b6d4c82f6a909 authored over 3 years ago by Jake Beal <[email protected]>

use main of paml now that time branch is merged

github.com/Bioprotocols/labop-check - 75fc5337c4c8cae4ea7245da51cafa34bc006864 authored over 3 years ago by Daniel Bryce <[email protected]>

sort activities based upon start time

github.com/Bioprotocols/labop-check - b28617f92aa7b5960a7b2c1a432fcb0ef62787c4 authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #24 from SD2E/time

Time

github.com/Bioprotocols/labop - cd026c524d67f6a1ed6aa0edf760594f2ea7d42c authored over 3 years ago by Daniel Bryce <[email protected]>

Expand testing (#9)

* checkpoint on improving testing

* cleanup

- remove unneeded fork constraint
- add time ...

github.com/Bioprotocols/labop-check - b652f20d073dfe2b36d98ebdfb3f2ad74235a958 authored over 3 years ago by jgladwig <[email protected]>

removed abstract properties and changed string to uri.

github.com/Bioprotocols/labop - 60b2210eeb1387c8c8b716d8e83c2e3326e68918 authored over 3 years ago by Daniel Bryce <[email protected]>

edited purpose section

github.com/Bioprotocols/labop-specification - 0b039d1e0a8aa73f77176bb19a4116010498444a authored over 3 years ago by Jake Beal <[email protected]>

Subprotocol test (#8)

* added subprotocol test and support for subprotocols

* added second test case for nested pro...

github.com/Bioprotocols/labop-check - ff60edf546a1d2788d3e9ef97bfaa22f42682762 authored over 3 years ago by Daniel Bryce <[email protected]>

Todot (#7)

* creating constraint graph in dot

* stable plotting for constraints and schedule.

* remov...

github.com/Bioprotocols/labop-check - b0c8c029dcb462fb76bb2bf7f70cfdfbfffda2e2 authored over 3 years ago by Daniel Bryce <[email protected]>

fixed order of parameter handling and setup gantt chart

github.com/Bioprotocols/labop - 9330b8fade6cb790934b099c1ace1d7937941355 authored over 3 years ago by Daniel Bryce <[email protected]>

fixed one test failure

github.com/Bioprotocols/labop-check - efb6c1bdc5e6ac2c4045543dcc6449e31cf6f818 authored over 3 years ago by Daniel Bryce <[email protected]>

fixed order of parameter handling and setup gantt chart

github.com/Bioprotocols/labop-check - 7afb77dc1ff16d688b65f60c94318fb95e510448 authored over 3 years ago by Daniel Bryce <[email protected]>

Cicd (#6)

* Create python-app.yml

* fix linting errors

* Update python-app.yml

* Create requireme...

github.com/Bioprotocols/labop-check - 4a5e1f3ec4a1102bae952bfc09e222bc3cafa8e8 authored over 3 years ago by Daniel Bryce <[email protected]>

Update setup.py

github.com/Bioprotocols/labop - 3dd3bd16640e678ebc198bc077c9e432e4cc3daf authored over 3 years ago by Daniel Bryce <[email protected]>

Create python-app.yml (#5)

* Create python-app.yml

* fix linting errors

* Update python-app.yml

* Create requireme...

github.com/Bioprotocols/labop-check - d9fd124b0724c66ea8c4e1fcfbe4e1f1d76169d7 authored over 3 years ago by Daniel Bryce <[email protected]>

removing failing debugging from test.

github.com/Bioprotocols/labop-check - 37e119727aec9b47c802cf33b00ae7b22489418b authored over 3 years ago by Daniel Bryce <[email protected]>

Rebase jack (#4)

* added algorithm to minimize duration of protocol

* reconfigure protocol example to use prot...

github.com/Bioprotocols/labop-check - 969065139509893288f557fe9a918a72a4f7f3ba authored over 3 years ago by Daniel Bryce <[email protected]>

Update ontology URIs for main branch.

github.com/Bioprotocols/container-ontology - ca4a80f8311d07d90f22685107754cc345a858e6 authored over 3 years ago by Robert P. Goldman <[email protected]>

Add Makefile for relocating the ontology.

github.com/Bioprotocols/container-ontology - 0e4292cb4471a49b9d6cb6932a19a4a073ea1883 authored over 3 years ago by Robert P. Goldman <[email protected]>

Merge pull request #8 from rpgoldman/iss7

github.com/Bioprotocols/container-ontology - 291ef0376a9bf6747fdbd109de14946ee7704713 authored over 3 years ago by rpgoldman <[email protected]>

Branch-specific OWL catalog.

github.com/Bioprotocols/container-ontology - c165c96a416c0eb1989ab06db9186f9b20872048 authored over 3 years ago by Robert P. Goldman <[email protected]>

Commit branch-specific TTL files.

This is an ugliness made necessary by the fact that the files must
have their own URL in them. ...

github.com/Bioprotocols/container-ontology - cd296ecaad1f84e630b7e67861d6c1edcd1651bb authored over 3 years ago by Robert P. Goldman <[email protected]>

Use M4 to store ontology files.

Need to be able to put the ontology files at temporary locations that
vary based on the git branch.

github.com/Bioprotocols/container-ontology - dba0afcc8267df9267906392092641760d0513a6 authored over 3 years ago by Robert P. Goldman <[email protected]>

Store old copy before changes.

github.com/Bioprotocols/container-ontology - 2df28524989393a3dbdc58f354daa91abb10f6b5 authored over 3 years ago by Robert P. Goldman <[email protected]>

Ordered parameters for time constraints.

github.com/Bioprotocols/labop - 19dfc6298cd15be30a879decc870e94d6f28980e authored over 3 years ago by Daniel Bryce <[email protected]>

Add ability to record availability.

Add the `availableAt` property and the `Lab` class to fill that property. This will allow us to...

github.com/Bioprotocols/container-ontology - 80a1a88d056bcdeac0eda77698348ff9f41acb82 authored over 3 years ago by Robert P. Goldman <[email protected]>

Improve ignores.

github.com/Bioprotocols/container-ontology - 468fb40efaf0e2b6cd44010458709ef98ee58f4d authored over 3 years ago by Robert P. Goldman <[email protected]>

Add source format of Strateos Catalog.

github.com/Bioprotocols/container-ontology - cc6c5701bab8ac1c28107497180af6a8122e4fa0 authored over 3 years ago by Robert P. Goldman <[email protected]>

Refine the model and translator.

Fixed the definition of Standard96WellPlate to be more useful.
Also fix some translator errors.

github.com/Bioprotocols/container-ontology - b41667297cae36600e5d9c1e9a1b608c794427b1 authored over 3 years ago by Robert P. Goldman <[email protected]>

checkpoint

github.com/Bioprotocols/labop - 732b56a8f747fcc515a1bd1110d0d00e6bc1a15a authored over 3 years ago by Daniel Bryce <[email protected]>

Make two different catalog versions

One has the catalog entries as classes, and one as individuals. The latter supports more efficie...

github.com/Bioprotocols/container-ontology - d048860476a5e843c34d803c1e2f67edf09f3e86 authored over 3 years ago by Robert P. Goldman <[email protected]>

Add standard 384- and 1536-well plate.

github.com/Bioprotocols/container-ontology - 0f82a13b048d4a50871822d81e81c87cbb754b97 authored over 3 years ago by Robert P. Goldman <[email protected]>

Add catalog_translator python module

This is not yet properly packaged, but works to the extent that it's
worth sharing.

github.com/Bioprotocols/container-ontology - 800346e9fa739dd02eedf17f3e9182e5b7f21f36 authored over 3 years ago by Robert P. Goldman <[email protected]>

Replace Individuals with Classes.

Previously, translated catalog entries in the Strateos catalog into
Individuals, with property a...

github.com/Bioprotocols/container-ontology - 6f1cfc542bcd0c8071f7eee228cefd46019f82e6 authored over 3 years ago by Robert P. Goldman <[email protected]>

added pointer from time constraints to protocols

github.com/Bioprotocols/labop - fe419f3bbd37dd5f96db0b51e19cf4436d001dcf authored over 3 years ago by Daniel Bryce <[email protected]>

checkpoint on ordered values

github.com/Bioprotocols/labop - 3e1900b2f169c789768701c13245596957723659 authored over 3 years ago by Daniel Bryce <[email protected]>

Add standard classes.

github.com/Bioprotocols/container-ontology - ae2164b33581e9e5ae2b894fdc1cf5d3cf19d011 authored over 3 years ago by Robert P. Goldman <[email protected]>

Improve translator Strateos catalog to OWL.

github.com/Bioprotocols/container-ontology - a596b2163c2c117ee7f467458b0b0a3278e81005 authored over 3 years ago by Robert P. Goldman <[email protected]>

Change IRI and add fixes.

For now I gave the ontology a routable name -- even if a stupid one -- because I have been havin...

github.com/Bioprotocols/container-ontology - db3687fc37b63d1c8860460d7454b8121ebd9ed1 authored over 3 years ago by Robert P. Goldman <[email protected]>

Replace misnamed file.

Turtle file had `.owl` extension, instead of `.ttl`.

github.com/Bioprotocols/container-ontology - 600f9a372fa80fd1be4308ccfd1e711e40661642 authored over 3 years ago by Robert P. Goldman <[email protected]>

Hand-repaired auto-generated file.

github.com/Bioprotocols/container-ontology - 857f5483f94264b8b2d0d88562959de45c5553a0 authored over 3 years ago by Robert P. Goldman <[email protected]>

fixed time constraints to be at top level and have identities.

github.com/Bioprotocols/labop - 58581614b1b7ebce46556a7181bfd3b81c8fab47 authored over 3 years ago by Daniel Bryce <[email protected]>

Add colors for optical properties.

These were one of the properties that the group called out as most important.
Replaced the `Opti...

github.com/Bioprotocols/container-ontology - 4276adc3be17f6672fe95cf6e81c86efd5ac3691 authored over 3 years ago by Robert P. Goldman <[email protected]>

Replace volume with wellVolume.

Make it more clear what is intended by the `volume` property.

github.com/Bioprotocols/container-ontology - 047863bcaaff965ec75112a9124d6a24b5ae3085 authored over 3 years ago by Robert P. Goldman <[email protected]>

Notebook for translating plate data to OWL classes.

github.com/Bioprotocols/container-ontology - 3b9e422499e99a5f070559b5b07f37204c9f006a authored over 3 years ago by Robert P. Goldman <[email protected]>

Plate classes from the Strateos catalog spreadsheet.

github.com/Bioprotocols/container-ontology - 27dde5737dfaf1aa96bbe3faa9027ab9ced5a294 authored over 3 years ago by Robert P. Goldman <[email protected]>

Notebook for translating plate data spreadsheet.

github.com/Bioprotocols/container-ontology - 21c76a01b52e20c727f77c18a118ff62f1a1e480 authored over 3 years ago by Robert P. Goldman <[email protected]>

Add ThermoFisher plates by hand.

github.com/Bioprotocols/container-ontology - e4ca94fed54dcc27cce10782658ad26b2b5bb632 authored over 3 years ago by Robert P. Goldman <[email protected]>