Bioprotocols Working Group issues | Ecosyste.ms: OpenCollective

Add ability to create and attach nodes with context menu

github.com/Bioprotocols/laboped - jamesscottbrown opened this issue over 2 years ago

Fix #138

github.com/Bioprotocols/labop - bbartley opened this pull request over 2 years ago

fix formatting of build instructions

github.com/Bioprotocols/labop-specification - jamesscottbrown opened this pull request over 2 years ago

ValueError: inferring DataArray dimensions from dictionary like ``coords`` is no longer supported. Use an explicit list of ``dims`` instead.

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

Xarrays rebase

github.com/Bioprotocols/labop - danbryce opened this pull request over 2 years ago

Support PAML

github.com/Bioprotocols/labop - bbartley opened this pull request over 2 years ago

Turtle should be compatible with tyto

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

Xarrays bryan

github.com/Bioprotocols/labop - bbartley opened this pull request over 2 years ago

Create Full Golden Gate PAML Protocol

github.com/Bioprotocols/labop - LuHesketh opened this pull request over 2 years ago

Cryptic failures when a required parameter is not specified for an action

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

Add GitHub action tests

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request over 2 years ago

SampleArray, SampleMap, DataSet as Xarrays

github.com/Bioprotocols/labop - danbryce opened this pull request over 2 years ago

Ignore build directory.

github.com/Bioprotocols/labop - rpgoldman opened this pull request over 2 years ago

Is it necessary to import the ENTIRE OM-2 ontology?

github.com/Bioprotocols/labop - rpgoldman opened this issue over 2 years ago

Query formulator for the container server

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 2 years ago

Graphical presentation of the container ontology

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 2 years ago

Add entries for OpenTrons catalog items

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 2 years ago

Add representation of compatibility with some PAML actions

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 2 years ago

Generate documentation from container_api using Sphinx

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 2 years ago

Verify inputs to an action have been added to the Document

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

Support Parameters with unbounded cardinality

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

uml.LiteralReal has no attribute 'value'

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

Generate output objects of execution edges

github.com/Bioprotocols/labop - bbartley opened this issue over 2 years ago

Need a way to specify container volume

github.com/Bioprotocols/container-ontology - bbartley opened this issue over 2 years ago

Remove redundant file.

github.com/Bioprotocols/labop - rpgoldman opened this pull request over 2 years ago

Add new GitHub action to test for bad OWL Restriction's

github.com/Bioprotocols/labop - rpgoldman opened this pull request over 2 years ago

Test on multiple python versions.

github.com/Bioprotocols/labop - rpgoldman opened this pull request over 2 years ago

Check multiple Python versions?

github.com/Bioprotocols/labop - rpgoldman opened this issue over 2 years ago

Should enabled_activity_node raise an exception when required inputs are missing?

github.com/Bioprotocols/labop - bbartley opened this issue almost 3 years ago

Checking for required input Parameters fails

github.com/Bioprotocols/labop - bbartley opened this issue almost 3 years ago

Fix container submodule

github.com/Bioprotocols/labop - bbartley opened this pull request almost 3 years ago

Markdown export of demo notebook has incorrect(?) output

github.com/Bioprotocols/labop - noahsprent opened this issue almost 3 years ago

Readme installation instructions give error as Git clone does not automatically fetch submodules

github.com/Bioprotocols/labop - noahsprent opened this issue almost 3 years ago

Get owlery-client from git repo.

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request almost 3 years ago

[bug] Python API Install Instructions

github.com/Bioprotocols/container-ontology - tsdobbs opened this issue almost 3 years ago

Pull OWLERY_CLIENT out of container ontology

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue almost 3 years ago

[doc] Version dependency - Python 3.9

github.com/Bioprotocols/container-ontology - tsdobbs opened this issue almost 3 years ago

Is it possible to query a local working copy of the ontology?

github.com/Bioprotocols/container-ontology - bbartley opened this issue almost 3 years ago

Should `SampleCollection` be used to represent a single sample?

github.com/Bioprotocols/labop - bbartley opened this issue almost 3 years ago

Indicate required vs optional Parameters for a Primitive

github.com/Bioprotocols/labop - bbartley opened this issue almost 3 years ago

Add license file

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue almost 3 years ago

Is it possible to query for a general container specification given a particular container instance?

github.com/Bioprotocols/container-ontology - bbartley opened this issue almost 3 years ago

Representation of array data

github.com/Bioprotocols/labop - jakebeal opened this issue almost 3 years ago

Hosted instance: enable persistent demo user(s)

github.com/Bioprotocols/laboped - jcahill opened this issue almost 3 years ago

More flexible editor

github.com/Bioprotocols/laboped - jcahill opened this issue almost 3 years ago

More significant use of color

github.com/Bioprotocols/laboped - jcahill opened this issue almost 3 years ago

Hosted instance: http2 error over firewall, VPN

github.com/Bioprotocols/laboped - jcahill opened this issue almost 3 years ago

Examples

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

Demo workflows

github.com/Bioprotocols/laboped - mfero opened this issue almost 3 years ago

Add Markdown converter documentation

github.com/Bioprotocols/labop - bbartley opened this pull request almost 3 years ago

added disclaimer modal

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

minor ui adjustments

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

Title image with icon from Noun Project

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request almost 3 years ago

Output serialize

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

Alpha Release Candidate

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

Gui adjust

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

Configure Admin Access Controls

github.com/Bioprotocols/laboped - jgladwig opened this issue almost 3 years ago

Add execution test

github.com/Bioprotocols/labop - bbartley opened this pull request almost 3 years ago

Readme update

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

[request] Documentation for markdown execution engine

github.com/Bioprotocols/labop - tsdobbs opened this issue almost 3 years ago

Add support for NCBI,NCIT,SBO, and SO Ontologies

github.com/Bioprotocols/labop - palibhasataolamang opened this issue almost 3 years ago

Support for inputs, outputs, and parameters.

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

PAML name collisions

github.com/Bioprotocols/labop - photocyte opened this issue almost 3 years ago

paml_demo.ipynb not working

github.com/Bioprotocols/labop - photocyte opened this issue almost 3 years ago

uml.ttl vs. uml-flattened.ttl

github.com/Bioprotocols/labop - jakebeal opened this issue almost 3 years ago

Prune old branches and merge requests

github.com/Bioprotocols/labop - jakebeal opened this issue almost 3 years ago

Double-check restrictions on UML properties

github.com/Bioprotocols/labop - bbartley opened this issue almost 3 years ago

Create a pip package

github.com/Bioprotocols/container-ontology - bbartley opened this issue almost 3 years ago

Rdf roundtrip

github.com/Bioprotocols/laboped - danbryce opened this pull request almost 3 years ago

Setup place to add conversion to opentrons.

github.com/Bioprotocols/labop - danbryce opened this pull request almost 3 years ago

[feature request] Adapter for Opentrons Execution

github.com/Bioprotocols/labop - tsdobbs opened this issue almost 3 years ago

Enhancement: Add a "native" JSON serialization

github.com/Bioprotocols/labop-specification - rpgoldman opened this issue almost 3 years ago

AttributeError on paml import

github.com/Bioprotocols/labop - tsdobbs opened this issue almost 3 years ago

very basic pass at user account associated protocols

github.com/Bioprotocols/laboped - jgladwig opened this pull request about 3 years ago

cleanup api endpoints

github.com/Bioprotocols/laboped - jgladwig opened this pull request about 3 years ago

Port types

github.com/Bioprotocols/laboped - danbryce opened this pull request about 3 years ago

Use IP instead of host for proxy

github.com/Bioprotocols/laboped - danbryce opened this pull request about 3 years ago

update editor layout

github.com/Bioprotocols/laboped - jgladwig opened this pull request about 3 years ago

Initial user accounts

github.com/Bioprotocols/laboped - jgladwig opened this pull request about 3 years ago

React integration

github.com/Bioprotocols/laboped - danbryce opened this pull request about 3 years ago

Data link

github.com/Bioprotocols/labop - danbryce opened this pull request about 3 years ago

avoid re-writing the test rubric every time.

github.com/Bioprotocols/labop - danbryce opened this pull request about 3 years ago

Client API for container ontology server.

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request about 3 years ago

Automated PDF build as artifacts

github.com/Bioprotocols/labop-specification - jakebeal opened this issue about 3 years ago

Should this repo have a PDF or link to the PDF?

github.com/Bioprotocols/labop-specification - Zulko opened this issue about 3 years ago

Reformat master LaTeX file to facilitate automatic documentation generation

github.com/Bioprotocols/labop-specification - bbartley opened this pull request about 3 years ago

Use a less cumbersome temporary IRI prefix.

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request about 3 years ago

Extensive restructuring of container ontology.

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request about 3 years ago

Export check_doc function.

github.com/Bioprotocols/labop-check - rpgoldman opened this pull request about 3 years ago

Add an Owlery server

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request over 3 years ago

Visualizing protocols with PAML-check

github.com/Bioprotocols/labop-check - danbryce opened this issue over 3 years ago

Expand testing

github.com/Bioprotocols/labop-check - jgladwig opened this pull request over 3 years ago

Subprotocol test

github.com/Bioprotocols/labop-check - danbryce opened this pull request over 3 years ago

Todot

github.com/Bioprotocols/labop-check - danbryce opened this pull request over 3 years ago

Cicd

github.com/Bioprotocols/labop-check - danbryce opened this pull request over 3 years ago

Create python-app.yml

github.com/Bioprotocols/labop-check - danbryce opened this pull request over 3 years ago

Rebase jack

github.com/Bioprotocols/labop-check - danbryce opened this pull request over 3 years ago

Replace poor ontology IRIs.

github.com/Bioprotocols/container-ontology - rpgoldman opened this pull request over 3 years ago

Add better temporary "parking" IRIs for the ontology

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 3 years ago

Add jupyter notebook showing use of the ontology from Python

github.com/Bioprotocols/container-ontology - rpgoldman opened this issue over 3 years ago