gn-gemtext - GeneNetwork gemtext knowledge base and issue tracker (mirror right now)

Age	Commit message (Collapse)	Author
2021-10-01	Pjotr notes	Pjotr Prins

2021-10-01	New Issue: Non-Clustered and Flippable Heatmaps	Frederick Muriuki Muriithi
	* Add new "issue" to track the migration of heatmaps without the dendrograms and also allow the flipping of the heatmap from horizontal to vertical orientations and vice-versa.
2021-10-01	Adds guix container topic to notebooks	jgart

2021-10-01	Add jupyter cli options link to our notes on jupyter	jgart

2021-09-29	backups	Pjotr Prins

2021-09-24	Add tasks	Pjotr Prins

2021-09-24	Reinstate backups to epysode	Pjotr Prins

2021-09-22	Add binderlite static assets issue to issues directory	jgart

2021-09-20	Add tags section	Frederick Muriuki Muriithi
	* Add a tags section to track things like "assigned to" etc.
2021-09-20	More details regarding error context	jgart

2021-09-20	Add error regarding static assets after forwarding binderlite with nginx	jgart

2021-09-20	Adds nginx question regarding $rest arg	jgart
	https://git.genenetwork.org/jgart/binderlite/src/branch/master/nginx.conf#L36
2021-09-20	Add binderlite port map that I'm currently using	jgart

2021-09-20	Adds feature request idea for GeneNetwork CLI	jgart
	closes https://github.com/genenetwork/genenetwork3/issues/39
2021-09-17	Added issue on BNW not responding.	Pjotr Prins

2021-09-16	Add topic for authentication work	BonfaceKilz

2021-09-15	tasks	Pjotr Prins

2021-09-15	Remove kanban symlinks and add tag	Pjotr Prins

2021-09-13	Adds --ad-hoc to guix environment command	jgart
	Python dependencies are not available unless I use --ad-hoc or -m
2021-09-10	Comments on Jupyter	Pjotr Prins

2021-09-10	kill-jupyter permissions on penguin2	jgart
	I want to run the following on penguin2: ps aux \| grep jupyter \| awk '{ print $2 }' \| xargs kill -9
2021-09-09	Add current user-stories for binderlite	jgart
	* Next Steps Optimizations * Uniquely identify last built notebook * Shutdown notebook and save to memory * Shutdown kernels gracefully *** guix-kernel (AKA guix-jupyter) runs by default in a container
2021-09-09	Update issue with progress	Muriithi Frederick Muriuki

2021-09-09	Merge branch 'main' of github.com:genenetwork/gn-gemtext-threads	Muriithi Frederick Muriuki

2021-09-09	Update status of implementation efforts	Muriithi Frederick Muriuki
	* topics/gn1-migration-to-gn2/clustering.gmi: update status * topics/gn1-migration-to-gn2/sample_clustering_heatmap.png: add missing sample heatmap image
2021-09-08	Add extra topic on adding delete button for datasets	BonfaceKilz

2021-09-01	Jupyter	Pjotr Prins

2021-08-31	Add websocketd as a possible alternative to xtermjs	jgart
	Turn any program that uses STDIN/STDOUT into a WebSocket server. Like inetd, but for WebSockets.
2021-08-31	virtuoso: remove password to avoid confusion	Pjotr Prins

2021-08-31	pluto service and working on fallbacks	Pjotr Prins

2021-08-31	Update with progress	Muriithi Frederick Muriuki
	* Update issue with progress on genotype files
2021-08-30	Update with progress and notes	Muriithi Frederick Muriuki
	* Update issue with notes on traits file and strains in genotype file * Add notes on required TODOs
2021-08-30	Update issue with progress and notes	Muriithi Frederick Muriuki
	* Add notes on progress * Add notes on the genotype files, that is still not quite clear, to help with tracing the flow of information
2021-08-27	Instructions for virtuoso	Pjotr Prins

2021-08-26	Merge branch 'main' of github.com:genenetwork/gn-gemtext-threads	Muriithi Frederick Muriuki

2021-08-26	Update issue with findings on rust-qtlreaper	Muriithi Frederick Muriuki
	* The usage of ~rust-qtlreaper~ in GN2 is not quite clear. This commit details the findings of the search for the usage of ~rust-qtlreaper~ in GN2 and the attempts to replicate in GN3.
2021-08-22	Adds TODO item (unit tests)	jgart

2021-08-22	Adds TODO item	jgart

2021-08-22	Add current TODOs	jgart

2021-08-22	Adds basic working demo	jgart

2021-08-20	Update with progress	Muriithi Frederick Muriuki
	* Note use of QTLReaper * Update with notes on newly migrated portions of code
2021-08-20	Update issue with write-up on heatmap image generation	Muriithi Frederick Muriuki
	* Work through the migrated code, and the old GN1 code and write-up a flow of the data, to assist in figuring out the differences in the data. The write-up helped realise that the code migrated so far only helps with the "distance" lines, and there is still need to figure out, and compute or lay out the data needed for the actual heatmap generation.
2021-08-20	Update issue with notes for 2021-08-17	Muriithi Frederick Muriuki
	* Update issue with some progress report.
2021-08-16	Moved gemma issues	Pjotr Prins

2021-08-16	issue	Pjotr Prins

2021-08-14	Fixing gemma issue gh#210	Pjotr Prins

2021-08-13	Added file on LMMs	Pjotr Prins

2021-08-12	Add notes on differing colour scales	Muriithi Frederick Muriuki
	* The heatmaps in genenetwork1 have differing colour scales that the user can select, leading to a more complex implementation. This commit details some of the issues with the colour scales, and the possible places to look into to help with the implementation.
2021-08-12	Mention python-pooch in guix.	jgart
	https://issues.guix.gnu.org/47022 https://guix.gnu.org/packages/python-pooch-1.3.0/
2021-08-11	Update issue with notes on proof-of-concept explorations	Muriithi Frederick Muriuki
	* In the migration over from genenetwork1 to genenetwork3, there is a change in the libraries used, and even in the layout of the code. This necessitates the exploration of some features of the available libraries to get the work done as appropriate. In this commit, there is some detail of the exploratory results, complete with a code snippet to give an idea of what is possible, and what is still pending exploration.