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

Age	Commit message (Collapse)	Author
2021-10-15	Update issue with data/info flow	Frederick Muriuki Muriithi
	* Document the flow of data/information through the system to the point where we get the partial correlations results. This should help with future tracing of the implementation details, and in extracting the implementation details to help with the migration of the feature to GN3/GN2
2021-10-15	Add some tags	Frederick Muriuki Muriithi
	* Tag issue as a "migration" issue (that might be the wrong tag), and also tag it as "in progress"
2021-10-15	Partial Correlations: Add notes on exploration results	Frederick Muriuki Muriithi
	* Add some notes on the properties of the existing Partial Correlations feature as it exists in GN1
2021-10-15	Partial Correlations: New issue	Frederick Muriuki Muriithi
	* Create a new issue to track the migration of the partial correlations feature from GN1 to GN3/GN2
2021-10-15	Mark all tasks for the issue as done	Frederick Muriuki Muriithi

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.
2021-09-20	Add tags section	Frederick Muriuki Muriithi
	* Add a tags section to track things like "assigned to" etc.
2021-09-15	Remove kanban symlinks and add tag	Pjotr Prins

2021-09-09	Update issue with progress	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
2021-08-31	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
2021-08-26	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.
2021-08-20	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.
2021-08-12	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.
2021-07-22	Move editing-data file	Pjotr Prins

2021-07-21	Fix links(gemtext)	BonfaceKilz

2021-07-21	Add some docs on how to edit data(probeset/ traits) from gn2	BonfaceKilz

2021-07-19	Note the intertwining of computation and display	Muriithi Frederick Muriuki

2021-07-19	Fix gemini lists	Muriithi Frederick Muriuki

2021-07-19	Respond to initial topic notes	Muriithi Frederick Muriuki
	- Respond to issue note, and link produced images
2021-07-18	Add GN1 clustering	Pjotr Prins