Noctua
Interested: Seth (@kltm), Nakao (@nakao), and discussion with Kim (@jdkim)
Noctua: Collaborative editing of RDF instance graphs, and modeling biological processes
- https://github.com/geneontology/noctua
- http://noctua.berkeleybop.org
- http://create.monarchinitiative.org
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The Noctua (little owl) constellation
The purpose of this project is to create a bootstrap/orchestration system to quickly deploy the Noctua stack for new users with different user cases and ontology needs.
-
https://github.com/geneontology/noctua/issues/227 ; Closed
- AWS/ansible part: 99%; could use more debugging
- Successful migration to the new Ubuntu LTS 16.04
- Docker/ansible part 95%?; we decided not to finish pursuit of the Dockerfile deployment due to test machine constraints, but it seemed to be working last we checked
- These ansible playbooks will also provide future documentation for the project
- The playbooks themselves are currently being kept at https://github.com/geneontology/ansible-machine-bootstrap due to them being more generally applicable for the GO
- AWS/ansible part: 99%; could use more debugging
As part of this solution, we were also able to close a similar ticket for AmiGO (https://github.com/geneontology/amigo/issues/340), giving us an easy turnkey solution for a complete annotation creation and browsing system. Already being used to look at Pombe phenotype data (http://ec2-23-22-182-58.compute-1.amazonaws.com:9999/amigo/search/annotation, temporary).
The purpose of this project is to allow instances of Noctua to be used without unnecessary confusion by non-GO modelers.
-
https://github.com/geneontology/noctua/issues/305 ; Open, but 99%
- The code portion of this small project is done, adding an additional "open" context (in addition to "go" and "monarch") that removes a lot of the GO-specific sections
- Will be further refined on user feedback
- The default ontologies for this instance are still being decided
Added playground section looking at kick outs.
- https://github.com/geneontology/noctua/issues/316 ; Open, Noctua side likely ~90%
- After some discussion and trials of adding the JS client to Noctua, we abandoned it due to (likely) library intractable library interference in the client (boo jQuery and friends).
- Looking at previous work on Galaxy and AmiGO, it was proposed that a light-weight argument pass-through system could be easy to implement and beneficial to both projects
- The Noctua portion of this moved very quickly, riding on previous work done for Textpresso
-
https://github.com/geneontology/noctua/issues/283 ; Open, 75%?
- Continuing previous work with Textpresso, looking at intermediate solution to test process
What time is left will be spent on working on generalizing the remote annotation import functionality in Noctua (/tractorbeam). This will include refinements to the two above items, as well as implementing bulk remote model/annotation pushes from resource that we've talked to (e.g. Reactome, https://github.com/geneontology/noctua/issues/37).