From b5113dc72a27d2c20432e46c80f8110eb25dbc45 Mon Sep 17 00:00:00 2001
From: GregFa
Date: Tue, 27 Jun 2023 20:58:07 -0500
Subject: added new issues: bulklmm, Pluto notebooks, geno file HSNIH Palmer

---
 issues/add-bulklmm-feature.gmi                | 14 +++++++++++++
 issues/add-pluto-notebooks.gmi                | 23 ++++++++++++++++++++
 issues/fix-genotype-filename-HSNIH-Palmer.gmi | 30 +++++++++++++++++++++++++++
 3 files changed, 67 insertions(+)
 create mode 100644 issues/add-bulklmm-feature.gmi
 create mode 100644 issues/add-pluto-notebooks.gmi
 create mode 100644 issues/fix-genotype-filename-HSNIH-Palmer.gmi

diff --git a/issues/add-bulklmm-feature.gmi b/issues/add-bulklmm-feature.gmi
new file mode 100644
index 0000000..8fdd784
--- /dev/null
+++ b/issues/add-bulklmm-feature.gmi
@@ -0,0 +1,14 @@
+## BulkLMM integration
+
+## Tags
+
+* assigned: pjotrp
+* type: feature
+* priority: high
+
+## Description
+
+Integrate BulkLMM in GeneNetwork. The first step is to test the command line interface to BulkLMM in GeneNetwork using the BulkLMMSysimage. 
+The BulkLMMSysimage files provides instructions for generating the BulkLMM.jl sysimage,along with the code for the command-line functions.
+
+=> https://github.com/senresearch/BulkLMMSysimage	BulkLMMSysimage files
\ No newline at end of file
diff --git a/issues/add-pluto-notebooks.gmi b/issues/add-pluto-notebooks.gmi
new file mode 100644
index 0000000..7c4c649
--- /dev/null
+++ b/issues/add-pluto-notebooks.gmi
@@ -0,0 +1,23 @@
+## Add Pluto Notebooks
+
+## Tags
+
+* assigned: pjotrp
+* type: feature
+* priority: high
+
+## Description
+
+Host Pluto Notebooks in GeneNetwork. As a proof of concept, we host:
+
+=> https://notebooks.one/	notebooks.one
+
+We used the package PlutoSliderServer.jl:
+
+=> https://github.com/JuliaPluto/PlutoSliderServer.jl	PlutoSliderServer.jl
+
+See also our deployment repo for notebooks.one:
+
+=> https://github.com/GregFa/visuals/tree/testing
+
+Considering its capabilities, PlutoSliderServer.jl could potentially serve as a viable solution for hosting Pluto Notebooks on GeneNetwork.
diff --git a/issues/fix-genotype-filename-HSNIH-Palmer.gmi b/issues/fix-genotype-filename-HSNIH-Palmer.gmi
new file mode 100644
index 0000000..246b230
--- /dev/null
+++ b/issues/fix-genotype-filename-HSNIH-Palmer.gmi
@@ -0,0 +1,30 @@
+## Fix genotype filename HSNIH-Palmer
+
+## Tags
+
+* assigned: pjotrp
+* type: bug fix
+* priority: high
+
+## Description
+
+
+When using the Rest API to get the groups for "rat", it mentions the group HSNIH-Palmer.
+But the REST API to obtain the geno file(http://gn2.genenetwork.org/api/v_pre1/gentotypes/HSNIH-Palmer.geno) failed.
+The file of HSNIF-Palmer has actually a different name from what is expected; we have to use "HSNIH-Palmer_true" instead.
+On GeneNetwork website, the following query does not return results from the search.
+
+Dataset try to access: HSNIH-Palmer
+
+Issues with genotyped data:
+Used this query:
+
+Species: Rat
+
+Group: NIH Heterogeneous Stock (Palmer)
+
+Type: DNA Markers and SNPs
+
+Dataset: HSNIH-Palmer Genotypes
+
+Get Any: *
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