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path: root/topics/gn1-migration-to-gn2
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2021-12-22Update with results of profiling the codeFrederick Muriuki Muriithi
* After profiling the code, we document our results and ideas on future changes that would assist in optimising the code.
2021-10-19Updates to partial correlations issueFrederick Muriuki Muriithi
2021-10-15Update issue with data/info flowFrederick 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
2021-10-15Add some tagsFrederick Muriuki Muriithi
* Tag issue as a "migration" issue (that might be the wrong tag), and also tag it as "in progress"
2021-10-15Partial Correlations: Add notes on exploration resultsFrederick Muriuki Muriithi
* Add some notes on the properties of the existing Partial Correlations feature as it exists in GN1
2021-10-15Partial Correlations: New issueFrederick Muriuki Muriithi
* Create a new issue to track the migration of the partial correlations feature from GN1 to GN3/GN2
2021-10-15Mark all tasks for the issue as doneFrederick Muriuki Muriithi
2021-10-01New Issue: Non-Clustered and Flippable HeatmapsFrederick 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.
2021-09-20Add tags sectionFrederick Muriuki Muriithi
* Add a tags section to track things like "assigned to" etc.
2021-09-15Remove kanban symlinks and add tagPjotr Prins
2021-09-09Update issue with progressMuriithi Frederick Muriuki
2021-09-09Update status of implementation effortsMuriithi 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
2021-08-31Update with progressMuriithi Frederick Muriuki
* Update issue with progress on genotype files
2021-08-30Update with progress and notesMuriithi Frederick Muriuki
* Update issue with notes on traits file and strains in genotype file * Add notes on required TODOs
2021-08-30Update issue with progress and notesMuriithi 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
2021-08-26Update issue with findings on rust-qtlreaperMuriithi 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.
2021-08-20Update with progressMuriithi Frederick Muriuki
* Note use of QTLReaper * Update with notes on newly migrated portions of code
2021-08-20Update issue with write-up on heatmap image generationMuriithi 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.
2021-08-20Update issue with notes for 2021-08-17Muriithi Frederick Muriuki
* Update issue with some progress report.
2021-08-12Add notes on differing colour scalesMuriithi 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.
2021-08-12Mention python-pooch in guix.jgart
https://issues.guix.gnu.org/47022 https://guix.gnu.org/packages/python-pooch-1.3.0/
2021-08-11Update issue with notes on proof-of-concept explorationsMuriithi 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.
2021-07-22Move editing-data filePjotr Prins
2021-07-21Fix links(gemtext)BonfaceKilz
2021-07-21Add some docs on how to edit data(probeset/ traits) from gn2BonfaceKilz
2021-07-19Note the intertwining of computation and displayMuriithi Frederick Muriuki
2021-07-19Fix gemini listsMuriithi Frederick Muriuki
2021-07-19Respond to initial topic notesMuriithi Frederick Muriuki
- Respond to issue note, and link produced images
2021-07-18Add GN1 clusteringPjotr Prins
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