diff options
Diffstat (limited to 'topics/meetings/jnduli_bmunyoki.gmi')
| -rw-r--r-- | topics/meetings/jnduli_bmunyoki.gmi | 56 |
1 files changed, 38 insertions, 18 deletions
diff --git a/topics/meetings/jnduli_bmunyoki.gmi b/topics/meetings/jnduli_bmunyoki.gmi index 55086c1..c4832c6 100644 --- a/topics/meetings/jnduli_bmunyoki.gmi +++ b/topics/meetings/jnduli_bmunyoki.gmi @@ -1,17 +1,37 @@ # Meeting Notes -# 2024-10-04 -* @priscilla @bonfacem Setting up GN3. @priscilla try out API endpoints that don't require auth. +## 2024-10-11 +* @priscilla @flisso: Try out API endpoints that don't require auth. * @jnduli Harden hook system for gn-auth. * @jnduli Remove gn-auth code from GN3. -* @jnduli Finish UI changes for RIF editing. -* @alex Work on R/Qtl. -* @alex @bonfacem Work on properly containerizing gn-guile. -* @bonfacem API/Display of NCBI Rif metadata. -* @bonfacem @alex RIF Indexing for RIF page in Xapian. -* @flisso Push data to production. Commence work on Arabidopsis data and HS Rats data. - -# 2024-09-27 +* @jnduli @bonfacem Finish up RIF Editing project. +* @jnduli @alexm Create issue on describing the monitoring system. +* @jnduli @alexm Create issue on prompt engineering in GN to improve what we already have. +* @alex Work on R/Qtl. NOTE: @jnduli/@bonfacem help out with this. +* @alex: Review @bmunyoki's work on RIF/Indexing. +* @flisso: Make sure we have C Elegans dataset and MIKK genotypes to production. +* @flisso: Make sure we have HS Rats in testing stage. +* @flisso: Make progress in learning back-end coding WRT GN. +* @shelbys: Modify existing Grant write-up for pangenomes. +* @shelbys: Finish getting all the R2R scores from the first study. +* @bonfacem RIF Indexing for RIF page in Xapian. +* @bonfacem Work on properly containerizing gn-guile. + +## 2024-10-04 +* IN PROGRESS: @priscilla @bonfacem Setting up GN3. @priscilla try out API endpoints that don't require auth. NOTE: @priscilla Able to set up guix as a package manager. Trouble with Guix set-up with GN3. @bonfacem good opportunity to improve docs in GN3. +* IN PROGRESS: @jnduli Harden hook system for gn-auth. +* IN PROGRESS: @jnduli Remove gn-auth code from GN3. +* DONE: @jnduli Finish UI changes for RIF editing. NOTE: Demo done in GN Learning team. +* IN PROGRESS: @alex Work on R/Qtl. NOTE: Met with Karl Brohman/PJ. Been reading the docs. Will track this issue in GN. +* NOT DONE: @alex @bonfacem Work on properly containerizing gn-guile. +* DONE: @bonfacem API/Display of NCBI Rif metadata. +* IN PROGRESS: @bonfacem @alex RIF Indexing for RIF page in Xapian. +* IN PROGRESS: @flisso Push data to production. Commence work on Arabidopsis data and HS Rats data. NOTE: C-Elegans pushed in process of being pushed to testing server, then later production. WIP with HS Rats data in collab with Palmer. +* DONE: @flisso: Learning how to use SQL WRT C Elegans data. +* IN PROGRESS: @shelbys Re-formatting grant to use pangenomes. Waiting for Garisson for feedback. +* DONE: @shelbys Got the R2R for the human generated questions. TODO: Run this for GPT 4.0 model. + +## 2024-09-27 * DONE: @jnduli @bonfacem @alex Look at base files refactor and merge work. * DONE: @priscilla continue to upload more papers. NOTE: Uploaded an extra 200 papers. @@ -26,7 +46,7 @@ * IN-PROGRESS: @flisso Continue work on uploading datasets: C Elegans and MIKK. NOTE: Managed to create data files that need to be upleaded to the testing gn2 stage server. * NOT DONE: @flisso @jnduli help @flisso with SQL. -# 2024-09-20 +## 2024-09-20 * NOT DONE: @priscilla @flisso @bmunyoki @jnduli set up GN ecosystem and review UI PRs * DONE: @priscilla continue to upload more papers. NOTE: Shared access to drive to @bmunyoki. We are at 800 papers. * DONE: @bmunyoki update tux02/01 with recent RIF modifications @@ -38,7 +58,7 @@ * NOT DONE: @bmunyoki NCBI Metadata - Modelling and Display. * DONE: @bmunyoki update tux02/01 with recent RIF modifications. NOTE: CD tests are broken and need to be fixed. -# 2024-09-13 +## 2024-09-13 * NOT DONE: @jnduli @bmunyoki fetch ncbi metadata and display them in GN2 * DONE: @jnduli @bmunyoki add auth layer to edit rifs functionality * DONE: @jnduli complete design doc for hooks system for gn-auth. NOTE: More experimentation with this. @@ -57,7 +77,7 @@ Nice to have: * @bmunyoki build system container for gn-guile and write documentation for creating containers -# 2024-09-06 +## 2024-09-06 * DONE: @bmunyoki Replicate GN1 WIKI+RIF in GN2. * DONE: @bmunyoki update server to include latest code changes @@ -78,9 +98,9 @@ Nice to have: * NOT DONE: @priscilla @flisso @bmunyoki @jnduli set up GN ecosystem and review UI PRs -# 2024-09-02 (Sync with @flisso+@bonfacem) +## 2024-09-02 (Sync with @flisso+@bonfacem) -## Case-Attributes +### Case-Attributes * @bmunyoki understood case attributes by reverse-engineering the relevant tables from GeneNetwork's database. @@ -96,7 +116,7 @@ SELECT * FROM CaseAttribute JOIN CaseAttributeXRef ON CaseAttribute.CaseAttribut * @bmunyoki. Most of the confusion around case-attributes is because of how we store case-attributes. We don't have unique identifiers for case-attributes. -# 2024-08-30 +## 2024-08-30 * IN PROGRESS: @bmunyoki Replicate GN1 WIKI+RIF in GN2. * DONE: @bmunyoki and @alex help Alex deploy gn-guile code on tux02, run this in a tmux session. @@ -112,11 +132,11 @@ SELECT * FROM CaseAttribute JOIN CaseAttributeXRef ON CaseAttribute.CaseAttribut * DONE: @flisso managed to upload <TODO> dataset to production -## nice to haves +### nice to haves * nice_to_have: @bmunyoki experiment and document updating gn-bioinformatics set up packages (to support rshiny) -# 2024-08-23 +## 2024-08-23 * @shelby re-ingest data and run RAGAs against the queries already in the system to perform comparison with new papers. * @shelby figure out Claude Sonnet stuff. * IN PROGRESS: @felix @fred push RQTL bundles to uploader, also includes metadata. |